From 7042dbe96294790ff90de9b224b31f93b69a30cb Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 11:51:35 +0200 Subject: [PATCH 001/262] yamls --- CONTRIBUTORS.yaml | 18 +++++++++++++++++- FUNDERS.yaml | 11 +++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 1abba40f5ba3f5..fc14b72f1c0906 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -131,6 +131,12 @@ alliecreason: almahmoud: name: Alex Mahmoud joined: 2019-06 + orcid: 0000-0001-7271-6655 + +amisev1971: + name: Anastas Mishev + joined: 2024-07 + orcid: 0000-0001-7271-6655 andreacabibbe: name: Andrea Cabibbe @@ -1181,6 +1187,11 @@ KlemensFroehlich: name: Klemens Fröhlich joined: 2021-08 +korvoj: + name: Vojdan Kjorveziroski + joined: 2024-07 + orcid: 0000-0003-0419-4300 + kostrykin: name: Leonid Kostrykin orcid: 0000-0003-1323-3762 @@ -1977,7 +1988,12 @@ sebastian-schaaf: sonalhenson: name: Sonal Henson joined: 2023-09 - + +sonjafiliposka: + name: Sonja Filiposka + joined: 2024-07 + orcid: 0000-0003-0034-2855 + Shians: name: Shian Su joined: 2019-02 diff --git a/FUNDERS.yaml b/FUNDERS.yaml index 236111cd1e622b..0d9632520c4690 100644 --- a/FUNDERS.yaml +++ b/FUNDERS.yaml @@ -290,6 +290,17 @@ sfb992: funder: true +skills4eosc: + name: Skills for European Open Science Cloud + short_name: "Skills4SEOSC" + joined: 2024-07 + funder: true + funding_id: "10040140" + funding_system: cordis + funder_name: Horizon Europe + url: https://www.skills4eosc.eu/ + github: https://github.com/FAIR-by-Design-Methodology + ukmrc: name: UK Medical Research Council url: https://mrc.ukri.org From 471f55651c49426c214076c36609d4e1dc58751d Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 11:54:27 +0200 Subject: [PATCH 002/262] fbd --- .../tutorials/fair-by-design/faqs/index.md | 3 + .../tutorials/fair-by-design/tutorial.bib | 11 +++ .../tutorials/fair-by-design/tutorial.md | 74 +++++++++++++++++++ 3 files changed, 88 insertions(+) create mode 100644 topics/contributing/tutorials/fair-by-design/faqs/index.md create mode 100644 topics/contributing/tutorials/fair-by-design/tutorial.bib create mode 100644 topics/contributing/tutorials/fair-by-design/tutorial.md diff --git a/topics/contributing/tutorials/fair-by-design/faqs/index.md b/topics/contributing/tutorials/fair-by-design/faqs/index.md new file mode 100644 index 00000000000000..9ce3fe4fce824b --- /dev/null +++ b/topics/contributing/tutorials/fair-by-design/faqs/index.md @@ -0,0 +1,3 @@ +--- +layout: faq-page +--- diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib new file mode 100644 index 00000000000000..8dacc622112ce7 --- /dev/null +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -0,0 +1,11 @@ +@article{wilkinson, + title={The FAIR Guiding Principles for scientific data management and stewardship}, + author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others}, + journal={Scientific data}, + doi = {10.1038/sdata.2016.18}, + volume={3}, + number={1}, + pages={1--9}, + year={2016}, + publisher={Nature Publishing Group} +} diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md new file mode 100644 index 00000000000000..6618d4ee8bae6e --- /dev/null +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -0,0 +1,74 @@ +--- +layout: tutorial_hands_on +title: FAIR-by-design +abbreviations: + FAIR: Findable, Accessible, Interoperable, Reusable +zenodo_link: https://zenodo.org/records/11548062 +questions: + - What do the FAIR principles stand for [Wilkinson et al. 2016](https://www.nature.com/articles/sdata201618)? + - How to develop FAIR learning materials? +objectives: + - Define FAIR learning objects + - Adapt and mix FAIR learning objects + - Identify licenses and attribute correspondingly + - Structure comprehensive learning materials + - Manage file formats and tools + - Define metadata using a schema + - Create and publish FAIR-by-Design learning materials + - Collaborate with other instructors + - Assess FAIR-ness of existing learning objects +time_estimation: 60M +key_points: + - FAIR data are data which meet principles of findability, accessibility, interoperability, and reusability (FAIR). + - FAIR data are as open as possible, and as closed as necessary. + - The main objective of FAIR data is to increase data reuse by researchers. +tags: + - fair + - FAIR + - by + - design + - Learning + - objects +priority: 1 +contributions: + authorship: + - sonjafiliposka + - amisev1971 + - korvoj + funding: + - skills4eosc + +--- + + +Welcome to the FAIR-by-Design GTN course. + +Below are the main stages of the FAIR-by-Design Methodology that will help guide you on your journey of creating FAIR learning materials. + + +> +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} + +# Main stages + +## Stage 1 - Prepare + +## Stage 2 - Discover + +## Stage 3 - Design + +### Time to brainstorm + +### Structure is everything + +### How to develop the learning content + + +# Conclusion + From f2bb79c14b1ea1c661dc04dd02ee72ce1753bc5f Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 14:05:16 +0200 Subject: [PATCH 003/262] prepare --- .gitignore | 1 + .../tutorials/fair-by-design/tutorial.md | 40 ++++++++++++++++--- 2 files changed, 35 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 9b9fdbac27c2a9..0f30850810ebd1 100644 --- a/.gitignore +++ b/.gitignore @@ -25,3 +25,4 @@ plnmotmp*.json # Planemo output for workflow autoupdate tools.yml api/** +/.obsidian diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 6618d4ee8bae6e..68a30c7a0a9ff7 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -5,7 +5,6 @@ abbreviations: FAIR: Findable, Accessible, Interoperable, Reusable zenodo_link: https://zenodo.org/records/11548062 questions: - - What do the FAIR principles stand for [Wilkinson et al. 2016](https://www.nature.com/articles/sdata201618)? - How to develop FAIR learning materials? objectives: - Define FAIR learning objects @@ -23,12 +22,12 @@ key_points: - FAIR data are as open as possible, and as closed as necessary. - The main objective of FAIR data is to increase data reuse by researchers. tags: - - fair + - FAIR-by-Design Learning Materials + - FAIR Learning Objects - FAIR - - by - - design - - Learning - - objects + - Metadata + - Learning objectives + - Blooms taxonomy priority: 1 contributions: authorship: @@ -55,9 +54,38 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > {: .agenda} + # Main stages ## Stage 1 - Prepare +> Before anything else, preparation is the key to success! +{: .quote author="Alexander Graham Bell"} + +### First things first: What is FAIR? + + +> Findable +> The editable learning material has a unique and persistent identifier (PID) and is described with sufficiently detailed metadata. +{: .comment } + + +> Accessible +> +> The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. +> +{: .details} + + +> Interoperable +> The metadata describing the learning material follows a the RDA minimum metadata schema combined with agreed-upon controlled vocabularies. +> Formal, accessible, shared, and broadly applicable language(s) and format(s) are used to develop the material. +{: .tip} + + +> Reusable +>The learning material has a clear usage license (CC-BY-4.0 recommended) and accurate information on provenance. +{: .question} + ## Stage 2 - Discover From f6b8fb3a529f047aac4ff076349eeff044e7ff11 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 14:18:52 +0200 Subject: [PATCH 004/262] Update tutorial.md --- .../contributing/tutorials/fair-by-design/tutorial.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 68a30c7a0a9ff7..13842f95c50e4b 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -1,6 +1,6 @@ --- layout: tutorial_hands_on -title: FAIR-by-design +title: FAIR-by-design methodology abbreviations: FAIR: Findable, Accessible, Interoperable, Reusable zenodo_link: https://zenodo.org/records/11548062 @@ -22,8 +22,8 @@ key_points: - FAIR data are as open as possible, and as closed as necessary. - The main objective of FAIR data is to increase data reuse by researchers. tags: - - FAIR-by-Design Learning Materials - - FAIR Learning Objects + - 'FAIR-by-Design Learning Materials' + - "FAIR Learning Objects" - FAIR - Metadata - Learning objectives @@ -66,14 +66,14 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > Findable > The editable learning material has a unique and persistent identifier (PID) and is described with sufficiently detailed metadata. -{: .comment } +{: .comment title=""} > Accessible > > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. > -{: .details} +{: .details icon=""} > Interoperable From 096bf4c1153630a648386ea156362e8b1a52cb79 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 14:25:54 +0200 Subject: [PATCH 005/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 13842f95c50e4b..aee4b67b90c6a8 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -73,7 +73,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. > -{: .details icon=""} +{: .details icon='spoken'} > Interoperable @@ -84,7 +84,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > Reusable >The learning material has a clear usage license (CC-BY-4.0 recommended) and accurate information on provenance. -{: .question} +{: .question } ## Stage 2 - Discover From e26bbdbf178bf17577fd22e58eca4b01724d3d21 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 14:28:10 +0200 Subject: [PATCH 006/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index aee4b67b90c6a8..6799d456605776 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -73,7 +73,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. > -{: .details icon='spoken'} +{: .details } > Interoperable From 7d5e1928005acd0d09ea9b8f54f0d729c7ce2fe0 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 14:30:19 +0200 Subject: [PATCH 007/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 6799d456605776..0dca9d0677ed83 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -73,7 +73,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. > -{: .details } +{: .details lang="es"} > Interoperable From 3a09a0c7a970476c87e9937612b2d3e967a402f4 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 14:33:29 +0200 Subject: [PATCH 008/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 0dca9d0677ed83..1fa1c9682f62b0 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -73,7 +73,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. > -{: .details lang="es"} +{: .details lang='es'} > Interoperable From 25ae7387ddab670d15f883a5ed670f0171a95a24 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 15:03:43 +0200 Subject: [PATCH 009/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 1fa1c9682f62b0..d372a111fb3598 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -66,14 +66,14 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > Findable > The editable learning material has a unique and persistent identifier (PID) and is described with sufficiently detailed metadata. -{: .comment title=""} +{: .comment} > Accessible > > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. > -{: .details lang='es'} +{: .details icon email} > Interoperable From e230746da4b72de7f495af4246c5e2578a4dd238 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 15:16:41 +0200 Subject: [PATCH 010/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index d372a111fb3598..a82d631ddd6819 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -64,22 +64,22 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### First things first: What is FAIR? -> Findable +> Findable > The editable learning material has a unique and persistent identifier (PID) and is described with sufficiently detailed metadata. -{: .comment} +{: .question} -> Accessible +> Accessible > > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. > -{: .details icon email} +{: .question} -> Interoperable +> Interoperable > The metadata describing the learning material follows a the RDA minimum metadata schema combined with agreed-upon controlled vocabularies. > Formal, accessible, shared, and broadly applicable language(s) and format(s) are used to develop the material. -{: .tip} +{: .question} > Reusable From 1f0090cc362b84eec336794c86a8c4abe1e63b69 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 15:41:22 +0200 Subject: [PATCH 011/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index a82d631ddd6819..52d950a4ded8c2 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -86,6 +86,37 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide >The learning material has a clear usage license (CC-BY-4.0 recommended) and accurate information on provenance. {: .question } +### Adopt a metadata schema + The RDA Minimal Metadata Set for Learning Resources + + +> {% include _includes/cyoa-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" %} +> + + +
+- **Title** = The human readable name of the resource +- **Abstract / Description** = A brief synopsis about or description of the learning resource +- **Author(s)** = Name of entity(ies) authoring the resource +- **Primary Language** = Language in which the resource was originally published or made available +- **Keyword(s)** = Keywords or tags used to describe the resource +- **Version Date** = Version date for the most recently published or broadcast resource +
+ +
+- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. +- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle +- **License** = A license document that applies to this content, typically indicated by URL +- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) +
+ +
+- **Target Group (Audience)** = Principal users(s) for which the resource was designed +- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource +- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource +- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced +
+ ## Stage 2 - Discover From c4b61e7ed02a5d7b42a8b153ecdd8f22f49a84bc Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 15:52:03 +0200 Subject: [PATCH 012/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 52d950a4ded8c2..c65e42f20b254e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -89,9 +89,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources - -> {% include _includes/cyoa-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" %} -> +{% include _includes/cyoa-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" %}
From bf5d982729e70960ecea75d1d2bdee8d82992ef3 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:00:21 +0200 Subject: [PATCH 013/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 50 +++++++++---------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index c65e42f20b254e..78939e57180bc4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -89,31 +89,31 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources -{% include _includes/cyoa-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" %} - - -
-- **Title** = The human readable name of the resource -- **Abstract / Description** = A brief synopsis about or description of the learning resource -- **Author(s)** = Name of entity(ies) authoring the resource -- **Primary Language** = Language in which the resource was originally published or made available -- **Keyword(s)** = Keywords or tags used to describe the resource -- **Version Date** = Version date for the most recently published or broadcast resource -
- -
-- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. -- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle -- **License** = A license document that applies to this content, typically indicated by URL -- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) -
- -
-- **Target Group (Audience)** = Principal users(s) for which the resource was designed -- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource -- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource -- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced -
+{% include _includes/cyoa-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} + + +>
+>- **Title** = The human readable name of the resource +>- **Abstract / Description** = A brief synopsis about or description of the learning resource +>- **Author(s)** = Name of entity(ies) authoring the resource +>- **Primary Language** = Language in which the resource was originally published or made available +>- **Keyword(s)** = Keywords or tags used to describe the resource +>- **Version Date** = Version date for the most recently published or broadcast resource +>
+ +>
+>- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. +>- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle +>- **License** = A license document that applies to this content, typically indicated by URL +>- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) +>
+ +>
+>- **Target Group (Audience)** = Principal users(s) for which the resource was designed +>- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource +>- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource +>- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced +>
## Stage 2 - Discover From 82a18eca760c448de59b2a000595d9fd79b214cd Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:06:26 +0200 Subject: [PATCH 014/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 78939e57180bc4..d03a93445bc81e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -92,7 +92,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide {% include _includes/cyoa-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} ->
+>
>- **Title** = The human readable name of the resource >- **Abstract / Description** = A brief synopsis about or description of the learning resource >- **Author(s)** = Name of entity(ies) authoring the resource @@ -101,14 +101,14 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide >- **Version Date** = Version date for the most recently published or broadcast resource >
->
+>
>- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. >- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle >- **License** = A license document that applies to this content, typically indicated by URL >- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) >
->
+>
>- **Target Group (Audience)** = Principal users(s) for which the resource was designed >- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource >- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource From dac1df9aa9b1e5896df2057ea918ffa9227cc901 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:15:50 +0200 Subject: [PATCH 015/262] tab_choices --- _includes/tab-choices.html | 39 +++++++++++++++++++ .../tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 40 insertions(+), 1 deletion(-) create mode 100644 _includes/tab-choices.html diff --git a/_includes/tab-choices.html b/_includes/tab-choices.html new file mode 100644 index 00000000000000..1ebb6400939d54 --- /dev/null +++ b/_includes/tab-choices.html @@ -0,0 +1,39 @@ +
+
+ {% if include.text %} +

+ {{ include.text }} +

+ {% endif %} + {% if include.option1 %} + + + {% endif %} + {% if include.option2 %} + + + {% endif %} + {% if include.option3 %} + + + {% endif %} + {% if include.option4 %} + + + {% endif %} + + {% if include.default %} + + {% endif %} +
diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index d03a93445bc81e..0b5e6c77c5ed18 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -89,7 +89,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources -{% include _includes/cyoa-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} +{% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} >
From edf4c2b163aecd37da83346e576ce8fe1896ddd7 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:19:46 +0200 Subject: [PATCH 016/262] Update tab-choices.html --- _includes/tab-choices.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/tab-choices.html b/_includes/tab-choices.html index 1ebb6400939d54..56b2c57d91a2cc 100644 --- a/_includes/tab-choices.html +++ b/_includes/tab-choices.html @@ -1,5 +1,5 @@
-
+
{% if include.text %}

{{ include.text }} From 1215bcf66a770b974ec7ea8d51f8bdb021fd4ace Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:24:44 +0200 Subject: [PATCH 017/262] Update tab-choices.html --- _includes/tab-choices.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/tab-choices.html b/_includes/tab-choices.html index 56b2c57d91a2cc..7c7003867022a6 100644 --- a/_includes/tab-choices.html +++ b/_includes/tab-choices.html @@ -1,5 +1,5 @@

-
+
{% if include.text %}

{{ include.text }} From 787f2476fa8e0b788de916f8ac2fd96a35f54dd8 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:33:19 +0200 Subject: [PATCH 018/262] tabs and prepare --- _includes/tab-choices.html | 2 +- .../tutorials/fair-by-design/tutorial.md | 50 +++++++++---------- 2 files changed, 24 insertions(+), 28 deletions(-) diff --git a/_includes/tab-choices.html b/_includes/tab-choices.html index 7c7003867022a6..92d6516617e4d7 100644 --- a/_includes/tab-choices.html +++ b/_includes/tab-choices.html @@ -1,5 +1,5 @@

-
+
{% if include.text %}

{{ include.text }} diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 0b5e6c77c5ed18..77bbb92e103a62 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -89,33 +89,29 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources -{% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} - - ->

->- **Title** = The human readable name of the resource ->- **Abstract / Description** = A brief synopsis about or description of the learning resource ->- **Author(s)** = Name of entity(ies) authoring the resource ->- **Primary Language** = Language in which the resource was originally published or made available ->- **Keyword(s)** = Keywords or tags used to describe the resource ->- **Version Date** = Version date for the most recently published or broadcast resource ->
- ->
->- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. ->- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle ->- **License** = A license document that applies to this content, typically indicated by URL ->- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) ->
- ->
->- **Target Group (Audience)** = Principal users(s) for which the resource was designed ->- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource ->- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource ->- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced ->
- - +> {% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} +>>
+>>- **Title** = The human readable name of the resource +>>- **Abstract / Description** = A brief synopsis about or description of the learning resource +>>- **Author(s)** = Name of entity(ies) authoring the resource +>>- **Primary Language** = Language in which the resource was originally published or made available +>>- **Keyword(s)** = Keywords or tags used to describe the resource +>>- **Version Date** = Version date for the most recently published or broadcast resource +>>
+>>
+>>- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. +>>- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle +>>- **License** = A license document that applies to this content, typically indicated by URL +>>- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) +>>
+>>
+>>- **Target Group (Audience)** = Principal users(s) for which the resource was designed +>>- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource +>>- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource +>>- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced +>>
+ +{: .hands_on} ## Stage 2 - Discover ## Stage 3 - Design From 0c3972a14d71b71c31abd4bd6787d69ff5f54e9e Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:36:16 +0200 Subject: [PATCH 019/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 1 + 1 file changed, 1 insertion(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 77bbb92e103a62..6c6c9aefe2016a 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -89,6 +89,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources +> Metadata field categories > {% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} >>
>>- **Title** = The human readable name of the resource From 8b1185ed593619a90ca85ab44235dc8e9ea41b88 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:39:34 +0200 Subject: [PATCH 020/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 41 ++++++++++--------- 1 file changed, 21 insertions(+), 20 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 6c6c9aefe2016a..b75ed7a6d424b2 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -91,28 +91,29 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > Metadata field categories > {% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} ->>
->>- **Title** = The human readable name of the resource ->>- **Abstract / Description** = A brief synopsis about or description of the learning resource ->>- **Author(s)** = Name of entity(ies) authoring the resource ->>- **Primary Language** = Language in which the resource was originally published or made available ->>- **Keyword(s)** = Keywords or tags used to describe the resource ->>- **Version Date** = Version date for the most recently published or broadcast resource ->>
->>
->>- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. ->>- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle ->>- **License** = A license document that applies to this content, typically indicated by URL ->>- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) ->>
->>
->>- **Target Group (Audience)** = Principal users(s) for which the resource was designed ->>- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource ->>- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource ->>- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced ->>
+>
+>- **Title** = The human readable name of the resource +>- **Abstract / Description** = A brief synopsis about or description of the learning resource +>- **Author(s)** = Name of entity(ies) authoring the resource +>- **Primary Language** = Language in which the resource was originally published or made available +>- **Keyword(s)** = Keywords or tags used to describe the resource +>- **Version Date** = Version date for the most recently published or broadcast resource +>
+>
+>- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. +>- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle +>- **License** = A license document that applies to this content, typically indicated by URL +>- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) +>
+>
+>- **Target Group (Audience)** = Principal users(s) for which the resource was designed +>- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource +>- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource +>- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced +>
{: .hands_on} + ## Stage 2 - Discover ## Stage 3 - Design From b1fe9bba550c217196f0673727505ed1ab218fb9 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:42:09 +0200 Subject: [PATCH 021/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b75ed7a6d424b2..7594296c780b69 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -89,7 +89,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources -> Metadata field categories +> Metadata field categories > {% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} >
>- **Title** = The human readable name of the resource @@ -112,7 +112,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide >- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced >
-{: .hands_on} +{: .question} ## Stage 2 - Discover From cc2ea008b472c5f858fba38df9d4de459a2d9533 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:45:07 +0200 Subject: [PATCH 022/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 7594296c780b69..eae652456bf31a 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -91,6 +91,8 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide > Metadata field categories > {% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} +{: .question} + >
>- **Title** = The human readable name of the resource >- **Abstract / Description** = A brief synopsis about or description of the learning resource @@ -112,7 +114,6 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide >- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced >
-{: .question} ## Stage 2 - Discover From f8f4e8f5371d99522de05e055ebe076fa33740d1 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:48:32 +0200 Subject: [PATCH 023/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index eae652456bf31a..addbdea7f793e0 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -89,9 +89,8 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources -> Metadata field categories -> {% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} -{: .question} + +{% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} >
>- **Title** = The human readable name of the resource From 318e1904facb444ea09d12d71b12d51ca52c6024 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 16:58:16 +0200 Subject: [PATCH 024/262] Update tab-choices.html --- _includes/tab-choices.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/tab-choices.html b/_includes/tab-choices.html index 92d6516617e4d7..a984bc65b2ef9b 100644 --- a/_includes/tab-choices.html +++ b/_includes/tab-choices.html @@ -1,5 +1,5 @@
-
+
{% if include.text %}

{{ include.text }} From ca273f784112e38f762d5c7ef77e4dd2decdfa98 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:25:57 +0200 Subject: [PATCH 025/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index addbdea7f793e0..889a01e29a93d3 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -113,6 +113,20 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide >- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced >

+ +More on the metadata here {% cite hoebelheinrich_2022_6769695 %} + + +More on FAIR learning objects definition + +Learn more about: + - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) + - [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) + - [FAIR learning objects](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-learning-objects) + +### Start Ideating... + + ## Stage 2 - Discover From 59a49d94e934083f3259ac3cac772e456f085eb0 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:26:58 +0200 Subject: [PATCH 026/262] Update tutorial.bib --- .../tutorials/fair-by-design/tutorial.bib | 36 +++++++++++++------ 1 file changed, 25 insertions(+), 11 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 8dacc622112ce7..9bfcc86728c360 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,11 +1,25 @@ -@article{wilkinson, - title={The FAIR Guiding Principles for scientific data management and stewardship}, - author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others}, - journal={Scientific data}, - doi = {10.1038/sdata.2016.18}, - volume={3}, - number={1}, - pages={1--9}, - year={2016}, - publisher={Nature Publishing Group} -} +@misc{hoebelheinrich_2022_6769695, + author = {Hoebelheinrich, Nancy J and + Biernacka, Katarzyna and + Brazas, Michelle and + Castro, Leyla Jael and + Fiore, Nicola and + Hellström, Margareta and + Lazzeri, Emma and + Leenarts, Ellen and + Martinez Lavanchy, Paula Maria and + Newbold, Elizabeth and + Nurnberger, Amy and + Plomp, Esther and + Vaira, Lucia and + van Gelder, Celia W G and + Whyte, Angus}, + title = {{Recommendations for a minimal metadata set to aid + harmonised discovery of learning resources}}, + month = jun, + year = 2022, + publisher = {Zenodo}, + version = {1.0}, + doi = {10.15497/RDA00073}, + url = {https://doi.org/10.15497/RDA00073} +} \ No newline at end of file From fd3406fd7c95e28ed0eba50faece2148bb7da8cb Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:30:59 +0200 Subject: [PATCH 027/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 889a01e29a93d3..2f3d4bd048a889 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -113,13 +113,9 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide >- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced >
- More on the metadata here {% cite hoebelheinrich_2022_6769695 %} - -More on FAIR learning objects definition - -Learn more about: +More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) - [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) - [FAIR learning objects](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-learning-objects) From 42b1120acbf78d0baa1dbc76d09eb62ab45de5ab Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:41:07 +0200 Subject: [PATCH 028/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 28 +++++++++++++++++++ .../tutorials/fair-by-design/tutorial.md | 2 ++ 2 files changed, 30 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 9bfcc86728c360..42cbb420e2dbe3 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,3 +1,31 @@ + + +@misc{contributing-fair-by-design, +author = "Sonja Filiposka and Anastas Mishev and Vojdan Kjorveziroski", + title = "FAIR-by-design methodology (Galaxy Training Materials)", + year = "", + month = "", + day = "" + url = "\url{http://localhost:4000/training-material/topics/contributing/tutorials/fair-by-design/tutorial.html}", + note = "[Online; accessed Wed Aug 07 2024]" +} + +@article{Hiltemann_2023, + doi = {10.1371/journal.pcbi.1010752}, + url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752}, + year = 2023, + month = {jan}, + publisher = {Public Library of Science ({PLoS})}, + volume = {19}, + number = {1}, + pages = {e1010752}, + author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and}, + editor = {Francis Ouellette}, + title = {Galaxy Training: A powerful framework for teaching!}, + journal = {PLoS Comput Biol} Computational Biology} +} + + @misc{hoebelheinrich_2022_6769695, author = {Hoebelheinrich, Nancy J and Biernacka, Katarzyna and diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 2f3d4bd048a889..25b11b9d9dc777 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,6 +115,8 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide More on the metadata here {% cite hoebelheinrich_2022_6769695 %} + + More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) - [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) From 0dfbe165771d1ef54cbb7ec432556d3b7ab52e78 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:45:47 +0200 Subject: [PATCH 029/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 16 ---------------- .../tutorials/fair-by-design/tutorial.md | 2 -- 2 files changed, 18 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 42cbb420e2dbe3..79122ace161647 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -9,22 +9,6 @@ @misc{contributing-fair-by-design url = "\url{http://localhost:4000/training-material/topics/contributing/tutorials/fair-by-design/tutorial.html}", note = "[Online; accessed Wed Aug 07 2024]" } - -@article{Hiltemann_2023, - doi = {10.1371/journal.pcbi.1010752}, - url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752}, - year = 2023, - month = {jan}, - publisher = {Public Library of Science ({PLoS})}, - volume = {19}, - number = {1}, - pages = {e1010752}, - author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and}, - editor = {Francis Ouellette}, - title = {Galaxy Training: A powerful framework for teaching!}, - journal = {PLoS Comput Biol} Computational Biology} -} - @misc{hoebelheinrich_2022_6769695, author = {Hoebelheinrich, Nancy J and diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 25b11b9d9dc777..2f3d4bd048a889 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,8 +115,6 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide More on the metadata here {% cite hoebelheinrich_2022_6769695 %} - - More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) - [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) From c037e00d48f550f6bd995e2ee29573e3bf90c87c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:47:45 +0200 Subject: [PATCH 030/262] Update tutorial.bib --- .../contributing/tutorials/fair-by-design/tutorial.bib | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 79122ace161647..d0eac4d46831f3 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -11,7 +11,7 @@ @misc{contributing-fair-by-design } @misc{hoebelheinrich_2022_6769695, - author = {Hoebelheinrich, Nancy J and + author = "Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and @@ -25,13 +25,11 @@ @misc{hoebelheinrich_2022_6769695 Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and - Whyte, Angus}, - title = {{Recommendations for a minimal metadata set to aid - harmonised discovery of learning resources}}, + Whyte, Angus"", + title = "Recommendations for a minimal metadata set to aid + harmonised discovery of learning resources"", month = jun, year = 2022, - publisher = {Zenodo}, - version = {1.0}, doi = {10.15497/RDA00073}, url = {https://doi.org/10.15497/RDA00073} } \ No newline at end of file From 017c5af46c440e83b21f73a299ba14c5420b8878 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:47:56 +0200 Subject: [PATCH 031/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 2f3d4bd048a889..25b11b9d9dc777 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,6 +115,8 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide More on the metadata here {% cite hoebelheinrich_2022_6769695 %} + + More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) - [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) From d199461408e1208b0a04b2eab702f072e5c22caa Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:50:29 +0200 Subject: [PATCH 032/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 17 +++-------------- .../tutorials/fair-by-design/tutorial.md | 2 -- 2 files changed, 3 insertions(+), 16 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index d0eac4d46831f3..ea6e303767566f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,15 +1,4 @@ - - -@misc{contributing-fair-by-design, -author = "Sonja Filiposka and Anastas Mishev and Vojdan Kjorveziroski", - title = "FAIR-by-design methodology (Galaxy Training Materials)", - year = "", - month = "", - day = "" - url = "\url{http://localhost:4000/training-material/topics/contributing/tutorials/fair-by-design/tutorial.html}", - note = "[Online; accessed Wed Aug 07 2024]" -} - + @misc{hoebelheinrich_2022_6769695, author = "Hoebelheinrich, Nancy J and Biernacka, Katarzyna and @@ -25,9 +14,9 @@ @misc{hoebelheinrich_2022_6769695 Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and - Whyte, Angus"", + Whyte, Angus", title = "Recommendations for a minimal metadata set to aid - harmonised discovery of learning resources"", + harmonised discovery of learning resources", month = jun, year = 2022, doi = {10.15497/RDA00073}, diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 25b11b9d9dc777..2f3d4bd048a889 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,8 +115,6 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide More on the metadata here {% cite hoebelheinrich_2022_6769695 %} - - More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) - [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) From 5313174953693773066ae5f1bbdd8a8caae3baf1 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 17:52:36 +0200 Subject: [PATCH 033/262] bib --- topics/contributing/tutorials/fair-by-design/tutorial.bib | 1 - topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index ea6e303767566f..8f2750db3cb420 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,4 +1,3 @@ - @misc{hoebelheinrich_2022_6769695, author = "Hoebelheinrich, Nancy J and Biernacka, Katarzyna and diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 2f3d4bd048a889..b103f1ed4080c5 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -113,7 +113,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide >- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced >
-More on the metadata here {% cite hoebelheinrich_2022_6769695 %} +>More on the metadata here {% cite nancy %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From 68a136dba8de0d35dc16f5961f339c9b915036db Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:00:15 +0200 Subject: [PATCH 034/262] bib --- topics/contributing/tutorials/fair-by-design/tutorial.bib | 2 +- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 8f2750db3cb420..ddfcbaf26f9775 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,4 +1,4 @@ -@misc{hoebelheinrich_2022_6769695, +@misc{nancy, author = "Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b103f1ed4080c5..86d913368dcc41 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -113,7 +113,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide >- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced >
->More on the metadata here {% cite nancy %} +More on the metadata here {% cite nancy %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From c00fa074660dea461b4e8440a34a369bc5ed09ff Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:01:40 +0200 Subject: [PATCH 035/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 40 +++++++++---------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 86d913368dcc41..86cfc270a0f0fa 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -92,26 +92,26 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide {% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} ->
->- **Title** = The human readable name of the resource ->- **Abstract / Description** = A brief synopsis about or description of the learning resource ->- **Author(s)** = Name of entity(ies) authoring the resource ->- **Primary Language** = Language in which the resource was originally published or made available ->- **Keyword(s)** = Keywords or tags used to describe the resource ->- **Version Date** = Version date for the most recently published or broadcast resource ->
->
->- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. ->- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle ->- **License** = A license document that applies to this content, typically indicated by URL ->- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) ->
->
->- **Target Group (Audience)** = Principal users(s) for which the resource was designed ->- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource ->- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource ->- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced ->
+
+- **Title** = The human readable name of the resource +- **Abstract / Description** = A brief synopsis about or description of the learning resource +- **Author(s)** = Name of entity(ies) authoring the resource +- **Primary Language** = Language in which the resource was originally published or made available +- **Keyword(s)** = Keywords or tags used to describe the resource +- **Version Date** = Version date for the most recently published or broadcast resource +
+
+- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. +- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle +- **License** = A license document that applies to this content, typically indicated by URL +- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) +
+
+- **Target Group (Audience)** = Principal users(s) for which the resource was designed +- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource +- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource +- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced +
More on the metadata here {% cite nancy %} From 06badfb556e4088f160e9c3990ac5e329c4f3e5e Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:04:02 +0200 Subject: [PATCH 036/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 40 ++++++++----------- .../tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 18 insertions(+), 24 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index ddfcbaf26f9775..a182ed2448db0c 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,23 +1,17 @@ -@misc{nancy, - author = "Hoebelheinrich, Nancy J and - Biernacka, Katarzyna and - Brazas, Michelle and - Castro, Leyla Jael and - Fiore, Nicola and - Hellström, Margareta and - Lazzeri, Emma and - Leenarts, Ellen and - Martinez Lavanchy, Paula Maria and - Newbold, Elizabeth and - Nurnberger, Amy and - Plomp, Esther and - Vaira, Lucia and - van Gelder, Celia W G and - Whyte, Angus", - title = "Recommendations for a minimal metadata set to aid - harmonised discovery of learning resources", - month = jun, - year = 2022, - doi = {10.15497/RDA00073}, - url = {https://doi.org/10.15497/RDA00073} -} \ No newline at end of file +@article{bebatut2018community, + title={Community-driven data analysis training for biology}, + author={Batut, B{\'e}r{\'e}nice and Hiltemann, Saskia and Bagnacani, Andrea and Baker, Dannon and Bhardwaj, Vivek and Blank, Clemens and Bretaudeau, Anthony and Brillet-Gu{\'e}guen, Loraine and {\v{C}}ech, Martin and Chilton, John and others}, + journal={Cell systems}, + volume={6}, + number={6}, + pages={752--758}, + year={2018}, + publisher={Elsevier}, + doi={10.1016/j.cels.2018.05.012} +} + +@misc{galaxy-training-materials, + url = {https://training.galaxyproject.org}, + note = {Accessed 2019-04-08}, + title = {Galaxy Training materials website} +} diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 86cfc270a0f0fa..fcf5578a636469 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -113,7 +113,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide - **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced
-More on the metadata here {% cite nancy %} +More on the metadata here {% cite bebatut2018community %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From 9cb0831ca7f7bb3089dc189dc52827b3a596750c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:06:46 +0200 Subject: [PATCH 037/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 42 +++++++++++-------- .../tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 26 insertions(+), 18 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index a182ed2448db0c..0bd16f273c584d 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,17 +1,25 @@ -@article{bebatut2018community, - title={Community-driven data analysis training for biology}, - author={Batut, B{\'e}r{\'e}nice and Hiltemann, Saskia and Bagnacani, Andrea and Baker, Dannon and Bhardwaj, Vivek and Blank, Clemens and Bretaudeau, Anthony and Brillet-Gu{\'e}guen, Loraine and {\v{C}}ech, Martin and Chilton, John and others}, - journal={Cell systems}, - volume={6}, - number={6}, - pages={752--758}, - year={2018}, - publisher={Elsevier}, - doi={10.1016/j.cels.2018.05.012} -} - -@misc{galaxy-training-materials, - url = {https://training.galaxyproject.org}, - note = {Accessed 2019-04-08}, - title = {Galaxy Training materials website} -} +@article{hoebelheinrich_2022_6769695, + author = {Hoebelheinrich, Nancy J and + Biernacka, Katarzyna and + Brazas, Michelle and + Castro, Leyla Jael and + Fiore, Nicola and + Hellström, Margareta and + Lazzeri, Emma and + Leenarts, Ellen and + Martinez Lavanchy, Paula Maria and + Newbold, Elizabeth and + Nurnberger, Amy and + Plomp, Esther and + Vaira, Lucia and + van Gelder, Celia W G and + Whyte, Angus}, + title = {{Recommendations for a minimal metadata set to aid + harmonised discovery of learning resources}}, + month = jun, + year = 2022, + publisher = {Zenodo}, + version = {1.0}, + doi = {10.15497/RDA00073}, + url = {https://doi.org/10.15497/RDA00073} +} \ No newline at end of file diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index fcf5578a636469..1b925dab5adebb 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -113,7 +113,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide - **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced
-More on the metadata here {% cite bebatut2018community %} +More on the metadata here {% cite hoebelheinrich_2022_6769695 %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From d71a2986e5ec73e21890f11f45f598652f2d9672 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:09:21 +0200 Subject: [PATCH 038/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 18 +++++++++--------- .../tutorials/fair-by-design/tutorial.md | 2 ++ 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 0bd16f273c584d..5315ef10e20fe6 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,5 +1,7 @@ @article{hoebelheinrich_2022_6769695, - author = {Hoebelheinrich, Nancy J and + title = {Recommendations for a minimal metadata set to aid + harmonised discovery of learning resources}, + author = {Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and @@ -14,12 +16,10 @@ @article{hoebelheinrich_2022_6769695 Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, - title = {{Recommendations for a minimal metadata set to aid - harmonised discovery of learning resources}}, - month = jun, - year = 2022, - publisher = {Zenodo}, - version = {1.0}, - doi = {10.15497/RDA00073}, - url = {https://doi.org/10.15497/RDA00073} + month = jun, + year = 2022, + publisher = {Zenodo}, + version = {1.0}, + doi = {10.15497/RDA00073}, + url = {https://doi.org/10.15497/RDA00073} } \ No newline at end of file diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 1b925dab5adebb..edb43c6d69129b 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -113,6 +113,8 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide - **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced
+ + More on the metadata here {% cite hoebelheinrich_2022_6769695 %} More on FAIR learning objects definition: From f6ccbdc50e6d45ce5736a52328ea794a29c3a86d Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:17:28 +0200 Subject: [PATCH 039/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 30 ++++--------------- .../tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 7 insertions(+), 25 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 5315ef10e20fe6..831fac4debf4ef 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,25 +1,7 @@ -@article{hoebelheinrich_2022_6769695, - title = {Recommendations for a minimal metadata set to aid - harmonised discovery of learning resources}, - author = {Hoebelheinrich, Nancy J and - Biernacka, Katarzyna and - Brazas, Michelle and - Castro, Leyla Jael and - Fiore, Nicola and - Hellström, Margareta and - Lazzeri, Emma and - Leenarts, Ellen and - Martinez Lavanchy, Paula Maria and - Newbold, Elizabeth and - Nurnberger, Amy and - Plomp, Esther and - Vaira, Lucia and - van Gelder, Celia W G and - Whyte, Angus}, - month = jun, - year = 2022, - publisher = {Zenodo}, - version = {1.0}, - doi = {10.15497/RDA00073}, - url = {https://doi.org/10.15497/RDA00073} +@article{hoebelheinrich_2022, + title = {Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, + author = {Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, + month = {jun}, + year = {2022}, + doi = {10.15497/RDA00073} } \ No newline at end of file diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index edb43c6d69129b..294f62fc058df9 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,7 +115,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide -More on the metadata here {% cite hoebelheinrich_2022_6769695 %} +More on the metadata here {% cite hoebelheinrich_2022 %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From dabd91b43b94cb009fa4078af8675a7168d6ba89 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:21:40 +0200 Subject: [PATCH 040/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 15 ++++++++++++++- .../tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 831fac4debf4ef..440f1cd6ed06be 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -4,4 +4,17 @@ @article{hoebelheinrich_2022 month = {jun}, year = {2022}, doi = {10.15497/RDA00073} -} \ No newline at end of file +} + + +@article{bebatut2018community, + title={Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, + author={Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, + journal={Cell systems}, + volume={6}, + number={6}, + pages={752--758}, + year={2022}, + publisher={Zenodo}, + doi={10.15497/RDA00073} +} diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 294f62fc058df9..18004f5aaf1123 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,7 +115,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide -More on the metadata here {% cite hoebelheinrich_2022 %} +More on the metadata here {% cite bebatut2018community %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From f7fc8bf523fc410ac8dda0e58f4b8a8b2480acbd Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:24:34 +0200 Subject: [PATCH 041/262] bib --- topics/contributing/tutorials/fair-by-design/tutorial.bib | 4 ++-- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 440f1cd6ed06be..a9dcd886473bfd 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,4 +1,4 @@ -@article{hoebelheinrich_2022, +@article{xxxx, title = {Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, author = {Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, month = {jun}, @@ -7,7 +7,7 @@ @article{hoebelheinrich_2022 } -@article{bebatut2018community, +@article{hoebelheinrich_2022, title={Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, author={Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, journal={Cell systems}, diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 18004f5aaf1123..294f62fc058df9 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,7 +115,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide -More on the metadata here {% cite bebatut2018community %} +More on the metadata here {% cite hoebelheinrich_2022 %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From 7d43438a9332ff631e90ea43a93619138205cca1 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:26:25 +0200 Subject: [PATCH 042/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 294f62fc058df9..04fb667a10f1ca 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,7 +115,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide -More on the metadata here {% cite hoebelheinrich_2022 %} +More on the metadata here {% cite xxxx %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From e890058f6fdb4da7234a5c99765cc72ff9c5565d Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:28:06 +0200 Subject: [PATCH 043/262] bib --- topics/contributing/tutorials/fair-by-design/tutorial.bib | 4 ++-- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index a9dcd886473bfd..440f1cd6ed06be 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,4 +1,4 @@ -@article{xxxx, +@article{hoebelheinrich_2022, title = {Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, author = {Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, month = {jun}, @@ -7,7 +7,7 @@ @article{xxxx } -@article{hoebelheinrich_2022, +@article{bebatut2018community, title={Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, author={Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, journal={Cell systems}, diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 04fb667a10f1ca..18004f5aaf1123 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,7 +115,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide -More on the metadata here {% cite xxxx %} +More on the metadata here {% cite bebatut2018community %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From 056ef96285e30beefe8302e15d5996c2d600ed19 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:30:22 +0200 Subject: [PATCH 044/262] bib --- topics/contributing/tutorials/fair-by-design/tutorial.bib | 2 +- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 440f1cd6ed06be..da2bdbefb48ab0 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -7,7 +7,7 @@ @article{hoebelheinrich_2022 } -@article{bebatut2018community, +@article{bebatut2018community1, title={Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, author={Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, journal={Cell systems}, diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 18004f5aaf1123..0f13e0aae215c1 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,7 +115,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide -More on the metadata here {% cite bebatut2018community %} +More on the metadata here {% cite bebatut2018community1 %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From ea37440a0a9434d3a03b49af8a2b2f7f256487de Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:33:51 +0200 Subject: [PATCH 045/262] bib --- topics/contributing/tutorials/fair-by-design/tutorial.bib | 2 +- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index da2bdbefb48ab0..72cfc77373da34 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -7,7 +7,7 @@ @article{hoebelheinrich_2022 } -@article{bebatut2018community1, +@article{bebatut2018community2, title={Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, author={Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, journal={Cell systems}, diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 0f13e0aae215c1..1b447d8a1250e3 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,7 +115,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide -More on the metadata here {% cite bebatut2018community1 %} +More on the metadata here {% cite bebatut2018community2 %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From 749e778fa8eef2acf60d1abca0b3d3ceb3ceca6c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:40:13 +0200 Subject: [PATCH 046/262] bib --- .../tutorials/fair-by-design/tutorial.bib | 13 +------------ .../tutorials/fair-by-design/tutorial.md | 2 +- 2 files changed, 2 insertions(+), 13 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 72cfc77373da34..1be16d219c0901 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -1,19 +1,8 @@ -@article{hoebelheinrich_2022, - title = {Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, - author = {Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, - month = {jun}, - year = {2022}, - doi = {10.15497/RDA00073} -} -@article{bebatut2018community2, +@article{hoebelheinrich_2022, title={Recommendations for a minimal metadata set to aid harmonised discovery of learning resources}, author={Hoebelheinrich, Nancy J and Biernacka, Katarzyna and Brazas, Michelle and Castro, Leyla Jael and Fiore, Nicola and Hellström, Margareta and Lazzeri, Emma and Leenarts, Ellen and Martinez Lavanchy, Paula Maria and Newbold, Elizabeth and Nurnberger, Amy and Plomp, Esther and Vaira, Lucia and van Gelder, Celia W G and Whyte, Angus}, - journal={Cell systems}, - volume={6}, - number={6}, - pages={752--758}, year={2022}, publisher={Zenodo}, doi={10.15497/RDA00073} diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 1b447d8a1250e3..294f62fc058df9 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -115,7 +115,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide -More on the metadata here {% cite bebatut2018community2 %} +More on the metadata here {% cite hoebelheinrich_2022 %} More on FAIR learning objects definition: - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) From f8b3ea4b90e8e7ede908003ed6bdefcf2cba15cd Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:45:57 +0200 Subject: [PATCH 047/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 294f62fc058df9..3020ecbea8709a 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -124,6 +124,43 @@ More on FAIR learning objects definition: ### Start Ideating... +
+
+ +
+ +
Think backward
+
+
Step 1
+

What are your desired effects, i.e. learning outcomes...

+
+
+
+ +
+
+
Think backward
+
+
Step 2
+

How are you going to assess their achievement....

+
+
+
+ +
+
+
Think backward
+
+
Step 3
+

How should you structure the material to reach them...

+
+
+
+ +
+ +More on backward learning: + [Steps of the backward learning process](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#backward-instructional-design-process) ## Stage 2 - Discover From c258cb5cf0af815f54041970b14043fe482beccd Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 18:52:46 +0200 Subject: [PATCH 048/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 3020ecbea8709a..4548685b1f1104 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -163,6 +163,55 @@ More on backward learning: [Steps of the backward learning process](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#backward-instructional-design-process) +
+ +- :material-flag-checkered:{ .lg .middle } __Purpose__ + + --- + + When and how the learning materials can be used and for what purposes? + +- :material-target-account:{ .lg .middle } __Target Audience__ + + --- + + Is there anything specific that needs to be taken into account, such as cultural context? + +- :material-history:{ .lg .middle } __Prerequisites__ + + --- + + What does the target audience need to know or understand before starting the learning process? + + +- :material-target-account:{ .lg .middle } __Scope__ + + --- + + Is it going to be a single learning unit, or a group such as a course? + +- :material-bullseye-arrow:{ .lg .middle } __Learning Objectives__ + + --- + + What competences will be gained after successful completing of the learning process? + + ??? info "Be SMART" + + Objectives should be specific, ​measurable, ​attainable, ​relevant and ​time-bound​. + + ??? hint "Use Blooms Taxonomy" + + Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. + + [:octicons-arrow-right-24: See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) + +
+ + +Start an in-depth training on the Prepare stage.... +FAIR-by-Design Methodology: Prepare stage.... + ## Stage 2 - Discover ## Stage 3 - Design From 60a77dda35cf4a5b6755f5445b2ec2f620e8db68 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 19:10:08 +0200 Subject: [PATCH 049/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 60 +++++++------------ 1 file changed, 22 insertions(+), 38 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 4548685b1f1104..42f869937e9c93 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -163,51 +163,35 @@ More on backward learning: [Steps of the backward learning process](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#backward-instructional-design-process) -
- -- :material-flag-checkered:{ .lg .middle } __Purpose__ - - --- - - When and how the learning materials can be used and for what purposes? - -- :material-target-account:{ .lg .middle } __Target Audience__ - - --- - - Is there anything specific that needs to be taken into account, such as cultural context? - -- :material-history:{ .lg .middle } __Prerequisites__ - - --- - - What does the target audience need to know or understand before starting the learning process? - - -- :material-target-account:{ .lg .middle } __Scope__ - - --- - - Is it going to be a single learning unit, or a group such as a course? - -- :material-bullseye-arrow:{ .lg .middle } __Learning Objectives__ - - --- +> Purpose +> When and how the learning materials can be used and for what purposes? +{: .question } - What competences will be gained after successful completing of the learning process? +> Target Audience +> Is there anything specific that needs to be taken into account, such as cultural context? +{: .question } - ??? info "Be SMART" +> Prerequisites +> What does the target audience need to know or understand before starting the learning process? +{: .question } - Objectives should be specific, ​measurable, ​attainable, ​relevant and ​time-bound​. +> Scope +> Is it going to be a single learning unit, or a group such as a course? +{: .question } - ??? hint "Use Blooms Taxonomy" - - Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. +> Learning Objectives +> What competences will be gained after successful completing of the learning process? - [:octicons-arrow-right-24: See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) +>>Be SMART +>>Objectives should be specific, ​measurable, ​attainable, ​relevant and ​time-bound​. +>{: .tip} -
+>>Use Blooms Taxonomy +>>Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. +>{: .tip} +>[See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) +{: .question } Start an in-depth training on the Prepare stage.... FAIR-by-Design Methodology: Prepare stage.... From 073c807f27978eadfc92cef4f299ebf7e29ed34e Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 19:13:10 +0200 Subject: [PATCH 050/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 42f869937e9c93..7a018e4e584b6a 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -181,16 +181,15 @@ More on backward learning: > Learning Objectives > What competences will be gained after successful completing of the learning process? - ->>Be SMART ->>Objectives should be specific, ​measurable, ​attainable, ​relevant and ​time-bound​. ->{: .tip} - ->>Use Blooms Taxonomy ->>Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. ->{: .tip} ->[See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) - +> +> >Be SMART +> >Objectives should be specific, ​measurable, ​attainable, ​relevant and ​time-bound​. +> {: .tip} +> +> >Use Blooms Taxonomy +> >Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. +> {: .tip} +> [See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) {: .question } Start an in-depth training on the Prepare stage.... From 770ad832bf88c66695ca5f78cbd942332ad0aa6a Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 19:21:04 +0200 Subject: [PATCH 051/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 7a018e4e584b6a..07824be6166a82 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -188,8 +188,8 @@ More on backward learning: > > >Use Blooms Taxonomy > >Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. +> >[See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) > {: .tip} -> [See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) {: .question } Start an in-depth training on the Prepare stage.... From 93079569cc60613e4d422783b5dd2f63453b4ef7 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Wed, 7 Aug 2024 19:22:52 +0200 Subject: [PATCH 052/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 1 + 1 file changed, 1 insertion(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 07824be6166a82..6ba0b4d7e3e990 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -188,6 +188,7 @@ More on backward learning: > > >Use Blooms Taxonomy > >Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. +> > > >[See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) > {: .tip} {: .question } From 58dc42034b2b94bcf9e2baf80eeadee963efef06 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 09:57:55 +0200 Subject: [PATCH 053/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 6ba0b4d7e3e990..b1aedfcf4e30ca 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -197,6 +197,29 @@ More on backward learning: FAIR-by-Design Methodology: Prepare stage.... ## Stage 2 - Discover +> Greater even than the greatest discovery is to keep open the way to future discovery. +{: .quote author="John Jacob Abel"} +### Get inspired +Reusable materials can be found anywhere. These are just some examples: +> OER_ +> [DOAB](https://directory.doabooks.org/) +> [MERLOT](https://www.merlot.org/merlot/index.htm) +> [OASIS](https://oasis.geneseo.edu/index.php) +> [OER Commons](https://www.oercommons.org/) +> [OERTX CORA](https://www.projectcora.org/) +> [GALILEO](https://oer.galileo.usg.edu/) +> [FORRT](https://forrt.org/) +{: .code-in} + +### Potential for reuse +> Danger "Respect the licenses, to be respected! +> Materials with non-permissible licenses can be used for inspiration only. Materials with permissible licenses should be reused based on the license rules. +{: .warning} + +### Don't forget the multimedia search +Different learners have different learning modalities (read/write, auditory, visual, kinesthetic). You should use all types of multimedia in your learning materials. +Start an in-depth training on the Discover stage.... +FAIR-by-Design Methodology: Discover stage.... ## Stage 3 - Design From b645c4af681d3714eee127b5a2df515a36531ded Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:04:05 +0200 Subject: [PATCH 054/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 43 +++++++++++++++++-- 1 file changed, 39 insertions(+), 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b1aedfcf4e30ca..a6371934852b05 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -201,7 +201,7 @@ More on backward learning: {: .quote author="John Jacob Abel"} ### Get inspired Reusable materials can be found anywhere. These are just some examples: -> OER_ +> OER > [DOAB](https://directory.doabooks.org/) > [MERLOT](https://www.merlot.org/merlot/index.htm) > [OASIS](https://oasis.geneseo.edu/index.php) @@ -211,8 +211,20 @@ Reusable materials can be found anywhere. These are just some examples: > [FORRT](https://forrt.org/) {: .code-in} +> EOSC +> [EOSC Training catalogue on the EOSC Marketplace](https://search.marketplace.eosc-portal.eu/search/training?q=*) +> +> Most EOSC projects have their own training catalogues and/or platforms... +{: .code-in} + +> General +> [Creative Commons Search](https://search.creativecommons.org/) - content provided under a CC license +> [Zenodo](https://zenodo.org/) - a multi-disciplinary open repository +> [OSF](https://osf.io/) - a free, open research platform +{: .code-in} + ### Potential for reuse -> Danger "Respect the licenses, to be respected! +> Respect the licenses, to be respected! > Materials with non-permissible licenses can be used for inspiration only. Materials with permissible licenses should be reused based on the license rules. {: .warning} @@ -222,13 +234,36 @@ Different learners have different learning modalities (read/write, auditory, vis FAIR-by-Design Methodology: Discover stage.... ## Stage 3 - Design - +> Design is intelligence made visible. +{: .quote author="Alina Wheeler"} ### Time to brainstorm ### Structure is everything ### How to develop the learning content +### Stage 4 - Produce + + +### Stage 5 - Publish + +### Stage 6 - Verify + +### Stage 7 - Continuous Improvement +> To improve is to change; to be perfect is to change often +{: .quote author="Winston Churchill"} + +#### {% icon galaxy-download } Gather +Gather feedback from all available internal & external sources. + +Potential sources: +- Feedback form  +- QA recommendations  +- self-reflection after training  +- Survey  +- Direct mail contact  +- Other means of communication + -# Conclusion +# About From f11b8e25181b89527980e6919cbd72afe93463e2 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:06:41 +0200 Subject: [PATCH 055/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index a6371934852b05..22e825b5f09764 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -253,7 +253,7 @@ Different learners have different learning modalities (read/write, auditory, vis > To improve is to change; to be perfect is to change often {: .quote author="Winston Churchill"} -#### {% icon galaxy-download } Gather +#### {% icon galaxy-download %} Gather Gather feedback from all available internal & external sources. Potential sources: From ed60fdf243ad17609c0e3753e2e2950558d0fce3 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:11:50 +0200 Subject: [PATCH 056/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 22e825b5f09764..4339713becdc11 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -264,6 +264,25 @@ Potential sources: - Direct mail contact  - Other means of communication +
+
+ +
+ +
+
{% icon galaxy-download %} Gather
+

Potential sources: +- Feedback form  +- QA recommendations  +- self-reflection after training  +- Survey  +- Direct mail contact  +- Other means of communication +

+
+
+
+
# About From bafa3f54d0fb4848677792df103cb04890b83bf0 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:15:22 +0200 Subject: [PATCH 057/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 4339713becdc11..1fe37f6e4b69b9 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -271,14 +271,15 @@ Potential sources:
{% icon galaxy-download %} Gather
-

Potential sources: -- Feedback form  -- QA recommendations  -- self-reflection after training  -- Survey  -- Direct mail contact  -- Other means of communication -

+

Potential sources:

+
    +
  • Feedback form 
    • +
  • QA recommendations 
    • +
  • self-reflection after training
    •   +
  • Survey 
    • +
  • Direct mail contact 
    • +
  • Other means of communication
    • +
From 4165c6562e0155383a9c670de5cd3cc4f8d80e42 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:24:06 +0200 Subject: [PATCH 058/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 43 ++++++++++++++++++- 1 file changed, 41 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 1fe37f6e4b69b9..19b382193e7a54 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -276,14 +276,53 @@ Potential sources:
  • Feedback form 
  • QA recommendations 
  • self-reflection after training
    •   -
  • Survey 
    • -
  • Direct mail contact 
    • +
  • Survey 
    • +
  • Direct mail contact 
  • Other means of communication
    • + +
    + +
    + +
    +
    {% icon galaxy-barchart %} Analyse
    +

    Analyse the gathered information in a structured way.
    + Create a list of potential improvements with impact level (high, moderate, low). +

    +
    +
    +
    + +
    + +
    + +
    +
    {% icon galaxy-wf-edit %} Improve
    +

    Select items from the list that will be part of a new version.
    Choose items that make sense to be in the same new release

    +
    +
    +
    + +
    + +
    + +
    +
    {% icongalaxy-history-refresh %} Repeat
    +

    Start a new cycle of the FAIR-by-Design methodology that will implement the selected items.
    After the Verify stage, you will reenter continuous improvement with newly gathered information....

    +
    +
    +
    +​Start an in-depth training on the Continuous Improvement stage.... + +FAIR-by-Design Methodology: Continuous Improvement stage.... + # About From 82d0efa7a7587d23c8ada19a93755c2570605f61 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:25:03 +0200 Subject: [PATCH 059/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 19b382193e7a54..c4ecbbb792036a 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -313,7 +313,7 @@ Potential sources:
    -
    {% icongalaxy-history-refresh %} Repeat
    +
    {% icon galaxy-history-refresh %} Repeat

    Start a new cycle of the FAIR-by-Design methodology that will implement the selected items.
    After the Verify stage, you will reenter continuous improvement with newly gathered information....

    From 43005b8351c159f3584a3355b1e25a65f4d6dd6c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:27:46 +0200 Subject: [PATCH 060/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index c4ecbbb792036a..4e82a1ec885293 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -296,7 +296,8 @@ Potential sources: - + +
    From 1cdf88666022dc17d554487305e8c2d2f19d4170 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:43:51 +0200 Subject: [PATCH 061/262] tabs --- _includes/tab-choices.html | 8 ++-- .../tutorials/fair-by-design/tutorial.md | 37 ++++++++++++++++--- 2 files changed, 37 insertions(+), 8 deletions(-) diff --git a/_includes/tab-choices.html b/_includes/tab-choices.html index a984bc65b2ef9b..099fc36052627b 100644 --- a/_includes/tab-choices.html +++ b/_includes/tab-choices.html @@ -1,10 +1,12 @@
    -
    +
    + {% if include.icon %} + {{% icon include.icon %}} + {% endif %} {% if include.text %} -

    {{ include.text }} -

    {% endif %} +
    {% if include.option1 %} diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 4e82a1ec885293..4016f3ebb687ee 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -90,7 +90,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide The RDA Minimal Metadata Set for Learning Resources -{% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" %} +{% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" icon="notebook" %}
    - **Title** = The human readable name of the resource @@ -242,14 +242,41 @@ Different learners have different learning modalities (read/write, auditory, vis ### How to develop the learning content -### Stage 4 - Produce +## Stage 4 - Produce -### Stage 5 - Publish +## Stage 5 - Publish -### Stage 6 - Verify +## Stage 6 - Verify +> You will find it a very good practice always to verify your references, sir! +{: .quote author="Martin Routh"} +### External QA +> A fresh set of eyes +> Have someone who has not participated in the development of the learning materials review the final work. This will guarantee a review free of cognitive bias. +{: .tip} -### Stage 7 - Continuous Improvement +> Don't forget to QA the LMS +> The reviewer should play the role of a new learner in the LMS and check everything from the learner perspective. +{: .tip} + +> Go through the QA checklists +> In Skills4EOSC T2.4 has developed a number of QA checklists that you and your external reviewer need to go through so that you can ensure high-quality learning materials. +{: .tip} + +### FAIR or not FAIR, that is the question... + + +### Feedback QA + +> Regularly gather feedback from learners and instructors +> Ensure that you actively and regularly gather feedback from both perspectives: the learners and the instructors. +{: .comment} + +Start an in-depth training on the Verify stage.... + +FAIR-by-Design Methodology: Verify stage.... + +## Stage 7 - Continuous Improvement > To improve is to change; to be perfect is to change often {: .quote author="Winston Churchill"} From b58f6c9d9abf90d72ad233aa025669a0b8fff3af Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 11:59:00 +0200 Subject: [PATCH 062/262] verify --- _includes/tab-choices.html | 8 +++++--- .../tutorials/fair-by-design/tutorial.md | 19 ++++++++++++++++++- 2 files changed, 23 insertions(+), 4 deletions(-) diff --git a/_includes/tab-choices.html b/_includes/tab-choices.html index 099fc36052627b..ea4d96d00d6667 100644 --- a/_includes/tab-choices.html +++ b/_includes/tab-choices.html @@ -1,12 +1,14 @@
    - {% if include.icon %} - {{% icon include.icon %}} + {% if include.title %} + {{ include.title }} {% endif %} +
    {% if include.text %} +

    {{ include.text }} +

    {% endif %} -
    {% if include.option1 %} diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 4016f3ebb687ee..efd970247f3157 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -90,7 +90,7 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide The RDA Minimal Metadata Set for Learning Resources -{% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" text="Metadata fields categories" icon="notebook" %} +{% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" title="Metadata fields categories" %}
    - **Title** = The human readable name of the resource @@ -265,6 +265,23 @@ Different learners have different learning modalities (read/write, auditory, vis ### FAIR or not FAIR, that is the question... +{% include _includes/tab-choices.html option1="Essential requirements" option2="Optional requirements" default="Essential requirements" title="Measure FAIRness" text="Use the FAIR-by-Design methodology QA checklist to check if you have followed the most important aspects of the methodology and managed to produce FAIR learning materials. +
    +The questions marked as essential achieve bare minimum FAIRness." %} + +
    +- **Findable** = Is the complete learning resource (including instructors info) registered or indexed in at least one searchable repository? Is it in a FAIR repository?
    Is metadata for the resource provided in both human- and machine-readable format (e.g JSON, XMLor YAML? +- **Accessible** = Has an accessibility checker tool been utilised to improve the accessibility of all learning resource files (PDF, HTML, video, etc.)?
    Are access rules (authentication & authorisation) implemented for the learning resource? +- **Interoperable** = Is the RDA minimal (or domain specific) metadata schema used for the learning material description?
    Is the resource available in open file formats which are tool agnostic and compatible with a wide variety of existing software? +- **Resuable** = Is there clear attribution for all reused resources with compatible licenses?
    Has the learning resource been made available for use by defining a permissable license or policy information that allows derivations? +
    +
    +- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. +- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle +- **License** = A license document that applies to this content, typically indicated by URL +- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) +
    + ### Feedback QA From c5d99385f5cf23a77b4614569052eb21d48bba1b Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 12:04:46 +0200 Subject: [PATCH 063/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index efd970247f3157..14af4bdb5c101c 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -265,7 +265,7 @@ Different learners have different learning modalities (read/write, auditory, vis ### FAIR or not FAIR, that is the question... -{% include _includes/tab-choices.html option1="Essential requirements" option2="Optional requirements" default="Essential requirements" title="Measure FAIRness" text="Use the FAIR-by-Design methodology QA checklist to check if you have followed the most important aspects of the methodology and managed to produce FAIR learning materials. +{% include _includes/tab-choices.html option1="Essential requirements" option2="Optional requirements" default="Essential requirements" title="Measure FAIRness" disambiguation="second" text="Use the FAIR-by-Design methodology QA checklist to check if you have followed the most important aspects of the methodology and managed to produce FAIR learning materials.
    The questions marked as essential achieve bare minimum FAIRness." %} From 7536b824519178dd126e014bbb40a3760cad4d57 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 12:08:55 +0200 Subject: [PATCH 064/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 30 ++++++++++++++----- 1 file changed, 22 insertions(+), 8 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 14af4bdb5c101c..c3cd8baebfedc4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -270,16 +270,30 @@ Different learners have different learning modalities (read/write, auditory, vis The questions marked as essential achieve bare minimum FAIRness." %}
    -- **Findable** = Is the complete learning resource (including instructors info) registered or indexed in at least one searchable repository? Is it in a FAIR repository?
    Is metadata for the resource provided in both human- and machine-readable format (e.g JSON, XMLor YAML? -- **Accessible** = Has an accessibility checker tool been utilised to improve the accessibility of all learning resource files (PDF, HTML, video, etc.)?
    Are access rules (authentication & authorisation) implemented for the learning resource? -- **Interoperable** = Is the RDA minimal (or domain specific) metadata schema used for the learning material description?
    Is the resource available in open file formats which are tool agnostic and compatible with a wide variety of existing software? -- **Resuable** = Is there clear attribution for all reused resources with compatible licenses?
    Has the learning resource been made available for use by defining a permissable license or policy information that allows derivations? +- **Findable** = Is the complete learning resource (including instructors info) registered or indexed in at least one searchable repository? Is it in a FAIR repository? Is metadata for the resource provided in both human- and machine-readable format (e.g JSON, XMLor YAML? +- **Accessible** = Has an accessibility checker tool been utilised to improve the accessibility of all learning resource files (PDF, HTML, video, etc.)? Are access rules (authentication & authorisation) implemented for the learning resource? +- **Interoperable** = Is the RDA minimal (or domain specific) metadata schema used for the learning material description?
    Is the resource available in open file formats which are tool agnostic and compatible with a wide variety of existing software? +- **Resuable** = Is there clear attribution for all reused resources with compatible licenses? Has the learning resource been made available for use by defining a permissable license or policy information that allows derivations?
    -- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. -- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle -- **License** = A license document that applies to this content, typically indicated by URL -- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) +- Did you follow the stages of the backward instructional design process while developing the learning resource? +-  Are controlled vocabularies (CVs) used for describing the resource characteristics aligned with the chosen metadata schema? +-  Does the learning resource represent a complete learning object defined around minimum one learning objective? +-  Does the resource incorporate an instructor kit that aids in facilitating the process of others reusing learning material by offering helpful how-to guides? + -  facilitator guide + -  activities description + -  assessment activities and strategy to assess + -  general learning content or instructor notes + -  lesson unit plan + -  syllabus +-  Have you employed a versioning system to track and control changes in your materials? +-  Are the resource access rules (how to access, e.g. registration procedure) explicitly communicated to learners? +-  Is the learning resource searchable in at least one relevant catalogue?  + -  Is it FAIR (can be searched based on metadata)? +-  Does the course include the possibility to provide feedback or comments from users and-or trainers/designers?  + -  If so, do you regularly gather and analyse that feedback? +-  Does the resource adopt an open community approach regarding its quality and reachability? +-  Has the learning resource been checked by a third party regarding its learning experience quality?
    From 02dda4bf627cc4cadfe5435fbfe444090324eaca Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 12:28:48 +0200 Subject: [PATCH 065/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index c3cd8baebfedc4..bd98032cd70ca1 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -246,6 +246,23 @@ Different learners have different learning modalities (read/write, auditory, vis ## Stage 5 - Publish +> Publishing is the art of working on a creative idea and turning it into a masterpiece​! +{: .quote author="Unknown"} + +>Publishing closed FAIR materials +> Having FAIR learning materials does not always mean that the materials are open to everyone and there are no costs or access rules attached. In this case the bundle that is going to be published in an open repository such as Zenodo should contain the following: +> 1. Syllabus - that contains all metadata that describe the materials and metadata should always be open +> 2. Accompanying files - optional - augment the description of the materials and describe the details when it comes to accessing and using the materials from a trainer perspective +> Another alternative is to publish the materials in a closed repository where the corresponding access rules can be implemented. +{: .warning} + +### Final preparations +>Time to create the accompanying files +>These are files that are provided in the root of your learning materials and describe the content and define the rules of reuse. +{: .tip} + + +### Store in a repository ## Stage 6 - Verify > You will find it a very good practice always to verify your references, sir! @@ -296,7 +313,6 @@ The questions marked as essential achieve bare minimum FAIRness." %} -  Has the learning resource been checked by a third party regarding its learning experience quality?
    - ### Feedback QA > Regularly gather feedback from learners and instructors From 9dfefa20ed38870d7fc19c60c67e007edb42ce17 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 12:51:17 +0200 Subject: [PATCH 066/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index bd98032cd70ca1..7128ec8eff26c4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -261,6 +261,82 @@ Different learners have different learning modalities (read/write, auditory, vis >These are files that are provided in the root of your learning materials and describe the content and define the rules of reuse. {: .tip} +
    +
    + +
    + +
    +
    {% icon text-document %} LICENSE
    +

    + Plaintext file that defines the license of your learning materials. Just copy paste it from the official CC website. CC-BY-4.0 is the recommended license. +
    + [{% icon point-right %} CC license](https://creativecommons.org/licenses/by/4.0/legalcode.txt) +

    +
    +
    +
    +
    + +
    + +
    +
    {% icon sticky-note %} README
    +

    + A README is a text file that introduces and explains the contents of your learning materials. It usually describes the context and defines how the materials may be reused or co-created. It is usually written in a plain text format. +
    + [{% icon point-right %} Make a README](https://www.makeareadme.com/) + Plaintext file that defines the license of your learning materials. Just copy paste it from the official CC website. CC-BY-4.0 is the recommended license. +

    +
    +
    +
    +
    + +
    + +
    +
    {% icon references %} CITATION.cff
    +

    + Citation files are plain text files with human- and machine-readable citation information that tells others how to cite or attribute your work. +
    + [{% icon point-right %} Create a citation file](https://citation-file-format.github.io/) +

    +
    +
    +
    +
    + +
    +
    + +
    + +
    +
    {% icon license %} CODE_OF_CONDUCT
    +

    + A code of conduct defines the rules for how to engage in a co-creation community. It is based on a premise of an inclusive environment that respects all contributions. +
    + [{% icon point-right %} Code of conduct template](https://github.com/probot/template/blob/master/CODE_OF_CONDUCT.md) +

    +
    +
    +
    +
    + +
    + +
    +
    {% icon comment %} RELEASE NOTES
    +

    + A release note is a report published alongside new or updated version of your learning materials that details the changes in the new version. +
    + [{% icon point-right %} Creating Release Notes](https://slite.com/templates/release-notes) +

    +
    +
    +
    +
    ### Store in a repository From 504c5117fcf30dad23d97f0a05fefdf17825e391 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 13:01:14 +0200 Subject: [PATCH 067/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 7128ec8eff26c4..c03d05b1b1e53e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -331,8 +331,8 @@ Different learners have different learning modalities (read/write, auditory, vis

    A release note is a report published alongside new or updated version of your learning materials that details the changes in the new version.
    - [{% icon point-right %} Creating Release Notes](https://slite.com/templates/release-notes) -

    +[{% icon point-right %} Creating Release Notes](https://slite.com/templates/release-notes) +

    From 0a68b0662ff607f40e67c3bd7f7643469ae4e21d Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 13:04:01 +0200 Subject: [PATCH 068/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index c03d05b1b1e53e..a60da59d749103 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -286,7 +286,6 @@ Different learners have different learning modalities (read/write, auditory, vis A README is a text file that introduces and explains the contents of your learning materials. It usually describes the context and defines how the materials may be reused or co-created. It is usually written in a plain text format.
    [{% icon point-right %} Make a README](https://www.makeareadme.com/) - Plaintext file that defines the license of your learning materials. Just copy paste it from the official CC website. CC-BY-4.0 is the recommended license.

    @@ -331,7 +330,9 @@ Different learners have different learning modalities (read/write, auditory, vis

    A release note is a report published alongside new or updated version of your learning materials that details the changes in the new version.
    -[{% icon point-right %} Creating Release Notes](https://slite.com/templates/release-notes) + + [{% icon point-right %} Creating Release Notes](https://slite.com/templates/release-notes) +

    From bbd4d517f8e68e06f3961e2b7ccede381b995edc Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 13:06:27 +0200 Subject: [PATCH 069/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index a60da59d749103..62ad0dac89f90d 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -330,9 +330,7 @@ Different learners have different learning modalities (read/write, auditory, vis

    A release note is a report published alongside new or updated version of your learning materials that details the changes in the new version.
    - [{% icon point-right %} Creating Release Notes](https://slite.com/templates/release-notes) -

    From 80fe5dbcb0d7897622b32ecf78ea17e1ebc7060d Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 13:10:49 +0200 Subject: [PATCH 070/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 62ad0dac89f90d..60351bef1cd49a 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -271,7 +271,8 @@ Different learners have different learning modalities (read/write, auditory, vis

    Plaintext file that defines the license of your learning materials. Just copy paste it from the official CC website. CC-BY-4.0 is the recommended license.
    - [{% icon point-right %} CC license](https://creativecommons.org/licenses/by/4.0/legalcode.txt) + {% icon point-right %} CC license +

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    A README is a text file that introduces and explains the contents of your learning materials. It usually describes the context and defines how the materials may be reused or co-created. It is usually written in a plain text format.
    - [{% icon point-right %} Make a README](https://www.makeareadme.com/) + + {% icon point-right %} Make a README +

    @@ -300,7 +302,9 @@ Different learners have different learning modalities (read/write, auditory, vis

    Citation files are plain text files with human- and machine-readable citation information that tells others how to cite or attribute your work.
    - [{% icon point-right %} Create a citation file](https://citation-file-format.github.io/) + + {% icon point-right %} Create a citation file +

    @@ -317,7 +321,9 @@ Different learners have different learning modalities (read/write, auditory, vis

    A code of conduct defines the rules for how to engage in a co-creation community. It is based on a premise of an inclusive environment that respects all contributions.
    - [{% icon point-right %} Code of conduct template](https://github.com/probot/template/blob/master/CODE_OF_CONDUCT.md) + + {% icon point-right %} Code of conduct template +

    @@ -331,7 +337,9 @@ Different learners have different learning modalities (read/write, auditory, vis

    A release note is a report published alongside new or updated version of your learning materials that details the changes in the new version.
    - [{% icon point-right %} Creating Release Notes](https://slite.com/templates/release-notes) + + {% icon point-right %} Creating Release Notes +

    @@ -339,6 +347,8 @@ Different learners have different learning modalities (read/write, auditory, vis ### Store in a repository +![Zenodo logo](../images/Zenodo_logo.png "Example of an image with a caption") + ## Stage 6 - Verify > You will find it a very good practice always to verify your references, sir! From aed4d9555cc781f582a5597f4b03d370b38386f9 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 13:32:31 +0200 Subject: [PATCH 072/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index d740bdc5f6916f..bb4c78b180ece2 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -349,6 +349,8 @@ Different learners have different learning modalities (read/write, auditory, vis ### Store in a repository ![Zenodo logo](../images/Zenodo_logo.png "Example of an image with a caption") +![Zenodot logo](../images/Zenodo_logo.png "Logo ") + ## Stage 6 - Verify > You will find it a very good practice always to verify your references, sir! 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a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index bb4c78b180ece2..c5ea92870c2e5d 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -347,9 +347,9 @@ Different learners have different learning modalities (read/write, auditory, vis ### Store in a repository -![Zenodo logo](../images/Zenodo_logo.png "Example of an image with a caption") +![Zenodo logo](../../images/Zenodo_logo.png "Example of an image with a caption") -![Zenodot logo](../images/Zenodo_logo.png "Logo ") +![Zenodo logo](../../images/Zenodo_logo.png "Logo ") ## Stage 6 - Verify From a8d4bccc98c1f038fbe389d32a9b5cc2bfdf16db Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 13:43:15 +0200 Subject: [PATCH 075/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index c5ea92870c2e5d..3532bf3836cb68 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -347,9 +347,11 @@ Different learners have different learning modalities (read/write, auditory, vis ### Store in a repository -![Zenodo logo](../../images/Zenodo_logo.png "Example of an image with a caption") -![Zenodo logo](../../images/Zenodo_logo.png "Logo ") +![Zenodo logo](../../images/Zenodo_logo.png) + +Zenodo logo by a Twitter user from Wikimedia licensed under the Creative Commons Attribution-Share Alike 4.0 International license + ## Stage 6 - Verify From 01007c90dca95c7b8c4cd88fa3804d404701adbb Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 13:43:52 +0200 Subject: [PATCH 076/262] Delete Zenodo_logo.png --- .../fair-by-design/images/Zenodo_logo.png | Bin 9531 -> 0 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3532bf3836cb68..96fc72234d8493 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -350,8 +350,15 @@ Different learners have different learning modalities (read/write, auditory, vis ![Zenodo logo](../../images/Zenodo_logo.png) +
    Zenodo logo by a Twitter user from Wikimedia licensed under the Creative Commons Attribution-Share Alike 4.0 International license     +#### To Zenodo +Deposit your editable learning materials set to make available to other designers and instructors. +1. Create an archive of all the files in your logical hierarchical structure. +2. Create a new Zenodo record with the archive. +3. 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zM!j&@8W3LRKX2`-&u!#m?f2`1O(#UZbVEv>nqYm$)6UTcJ=r&+@$m?wb1;^IjFif= z?chNrojZoUgU8#c+l3AHpuWhpZTqK;|D4R{N+Ji=E~E5u-nFBVh(K*hF6G!OT|^<-0#o0D zj-~8NSxx&ldeI+(ljS&xEft;r*n8O<|8SaAko;X?|ZWNIq!u9cg;S7vb*VoC_+I zGb1XaMUl@?=5QY9@{5b}){5qb)aRb(*oH?4v11H)hMa{gHiL%0oJ)JNz3 z_`4j)u@@0<7GWSysPQ*dB*qh;*uSjygZx!a#BhWl()p5;eo?qtKMIH*b(d{t>(y5f z$KlwSFWz+zB^^xNO;D=d^4MM>zGD8F=AK-Mk4AX=1EqD9(Q~yjceNI>bhds204@$L z9##%+R&EY0P97mHK_O0lW)2P^4h}VLOq%~i-~h6+{o?h16Hq!fzWufW0P->_(iKu> G!T$qP@yxaW literal 0 HcmV?d00001 diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 96fc72234d8493..380e3d5e262fc9 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -358,8 +358,43 @@ Deposit your editable learning materials set to make available to other designer 1. Create an archive of all the files in your logical hierarchical structure. 2. Create a new Zenodo record with the archive. 3. Provide a rich metadata description and link to any related resources. + How to deposit in Zenodo +>Automated publishing to Zenodo +>If you are working on GitHub using the provided templates repository then the "publish to Zenodo" step is fully automated for you. Just follow the [guide to publishing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%205%20%E2%80%93%20Publish/17-Zenodo%20Publishing/17-Zenodo%20Publishing/). +{: .tip} + +>To training catalogue +>You are at the point when you should also consider making a record in a relevant training catalogue such as the EOSC training catalogue. +{: .tip} + +### Provide to learners + +![Moodle logo](../../images/Moodle_logo.svg.png) + +
    +Moodle logo by Moodle.org from Wikipedia licensed under the GNU General Public License.     + +#### To LMS +Generate the final versions from your editable content and add it to a course on the Skills4EOSC Learning Platform to make it available for learners. + +0. Provide the course metadata. + +1. Add the learning content in general non-editable file formats. + +2. Add assessments such as quizzes or assignments. + +3. Setup feedback gathering. + +4. Define recognition mechanism such as open digital badges for successful completion. + +Managing a Moodle course + + +​​Start an in-depth training on the Publish stage.... + +FAIR-by-Design Methodology: Publish stage.... ## Stage 6 - Verify > You will find it a very good practice always to verify your references, sir! From f71cb852c2853edc5a8256959cb85857ba96a4df Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 14:03:10 +0200 Subject: [PATCH 079/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 380e3d5e262fc9..fb12b9ba402eaa 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -371,7 +371,7 @@ Deposit your editable learning materials set to make available to other designer ### Provide to learners -![Moodle logo](../../images/Moodle_logo.svg.png) +![Moodle logo](../../images/Moodle-logo.svg.png)
    Moodle logo by Moodle.org from Wikipedia licensed under the GNU General Public License.     From 4fa4abfed0fd985eed70f80786bd4198e57f646b Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 18:17:48 +0200 Subject: [PATCH 080/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 54 ++++++++++++++++++- 1 file changed, 53 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index fb12b9ba402eaa..ba84b4575ed931 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -243,8 +243,60 @@ Different learners have different learning modalities (read/write, auditory, vis ### How to develop the learning content ## Stage 4 - Produce +> To contrive is nothing! To construct is something! To produce is everything! +{: .quote author="Edward Rickenbacker​"} +### Choose Tools & Formats +### Plan to reuse existing material? + +### Accessibility + +### Internal QA + +
    +
    + +
    + +
    +
    {% icon congratulations %} QA Self-assessment
    +

    + to check if everything is as it should be. +

    +
    +
    +
    +
    + +
    + +
    +
    {% icon pref-list %} Quantitative
    +

    + are all required elements produced +

    +
    +
    +
    +
    + +
    + +
    +
    {% icon solution %} Qualitative
    +

    + do all learning units provide materials to reach the learning objectives with different modalities. +

    +
    +
    +
    +
    + + +​Start an in-depth training on the Produce stage.... + +FAIR-by-Design Methodology: Produce stage.... ## Stage 5 - Publish > Publishing is the art of working on a creative idea and turning it into a masterpiece​! {: .quote author="Unknown"} @@ -374,7 +426,7 @@ Deposit your editable learning materials set to make available to other designer ![Moodle logo](../../images/Moodle-logo.svg.png)
    -Moodle logo by Moodle.org from Wikipedia licensed under the GNU General Public License.     +Moodle logo by Moodle.org from Wikipedia licensed under the GNU General Public License #### To LMS Generate the final versions from your editable content and add it to a course on the Skills4EOSC Learning Platform to make it available for learners. 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H;|Ko(#bk$4 literal 0 HcmV?d00001 diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index ba84b4575ed931..86dbe3fa20f9c8 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -251,6 +251,25 @@ Different learners have different learning modalities (read/write, auditory, vis ### Plan to reuse existing material? ### Accessibility +> +>The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. +{: .tip} + +![Universal access logo](../../images/universal-access-6602642_640.png) + +
    +J S from Pixabay +     + +#### Standards +There are several standards that govern the rules on level of accessibility. 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H;|Ko(#bk$4 From 56aa5a30f20fdead2b7fc5e15e84861987ef2613 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 18:39:05 +0200 Subject: [PATCH 083/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 86dbe3fa20f9c8..5d439faac7c607 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -271,6 +271,24 @@ PDF document accessibility is measured with a separate technical specification < Learn more +{% include _includes/tab-choices.html option1="Slides" option2=""Web content" option3=""PDF document" default="Slides" title="Use accessibility evaluation tools!" disambiguation="third" text="Accessibility evaluation tools are not perfect. Even if they say that all is ok, it does not mean that your content is truly accessible. But they are a very good starting point." %} + +
    +Use the integrated accessibility checker in Power Point: + 1. Open an existing presentation in PowerPoint and review the content. + 2. Select the Review tab. + 3. Select Check Accessibility. + 4. An Accessibility Checker pane will appear on the right with 'Inspection Results' displayed. +
    +
    +- Choose from the [Web Accessibility Evaluation Tools List](https://www.w3.org/WAI/test-evaluate/tools/list/) developed by W3C. +
    +
    +- Check accessibility in Adobe Acrobat Pro. +- Open the PDF and then from the All tools menu on the left, select View more and then select Prepare for accessibility. +
    + + ### Internal QA
    From 0f2a3e588831eafd9105cc7108af4a2ddaf9f375 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 18:40:44 +0200 Subject: [PATCH 084/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 5d439faac7c607..27f38c25798945 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -271,7 +271,7 @@ PDF document accessibility is measured with a separate technical specification < Learn more -{% include _includes/tab-choices.html option1="Slides" option2=""Web content" option3=""PDF document" default="Slides" title="Use accessibility evaluation tools!" disambiguation="third" text="Accessibility evaluation tools are not perfect. Even if they say that all is ok, it does not mean that your content is truly accessible. But they are a very good starting point." %} +{% include _includes/tab-choices.html option1="Slides" option2="Web content" option3="PDF document" default="Slides" title="Use accessibility evaluation tools!" disambiguation="third" text="Accessibility evaluation tools are not perfect. Even if they say that all is ok, it does not mean that your content is truly accessible. But they are a very good starting point." %}
    Use the integrated accessibility checker in Power Point: From e4246fcb1bd212acbfa4f3f38d0426448d1cb650 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 18:43:38 +0200 Subject: [PATCH 085/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 27f38c25798945..a096e91d750df6 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -275,17 +275,18 @@ PDF document accessibility is measured with a separate technical specification <
    Use the integrated accessibility checker in Power Point: - 1. Open an existing presentation in PowerPoint and review the content. - 2. Select the Review tab. - 3. Select Check Accessibility. - 4. An Accessibility Checker pane will appear on the right with 'Inspection Results' displayed. +1. Open an existing presentation in PowerPoint and review the content. +2. Select the Review tab. +3. Select Check Accessibility. +4. An Accessibility Checker pane will appear on the right with 'Inspection Results' displayed.
    -- Choose from the [Web Accessibility Evaluation Tools List](https://www.w3.org/WAI/test-evaluate/tools/list/) developed by W3C. +Choose from the [Web Accessibility Evaluation Tools List](https://www.w3.org/WAI/test-evaluate/tools/list/) developed by W3C.
    -- Check accessibility in Adobe Acrobat Pro. -- Open the PDF and then from the All tools menu on the left, select View more and then select Prepare for accessibility. +Check accessibility in Adobe Acrobat Pro. + +Open the PDF and then from the All tools menu on the left, select View more and then select Prepare for accessibility.
    From f3cedf413de56d0754fd9655b5eaeb965457af7e Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 18:53:45 +0200 Subject: [PATCH 086/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index a096e91d750df6..b4082fb08d0fcf 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -250,6 +250,21 @@ Different learners have different learning modalities (read/write, auditory, vis ### Plan to reuse existing material? +{% include _includes/tab-choices.html option1="I want to reuse it as a whole" option2="I want to reuse a small part of it" option3="Learn more about IPR" default="I want to reuse it as a whole" title="Check the license" disambiguation="fourth" text="The existing material is available under a CC license, but it is different than the one you plan to use for your materials..." %} + +
    +You can't use something that is licensed with ND (no derivatives). In this case you must follow the rules on combining and adapting CC material. [Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material) +
    +
    +No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. If the work is licensed with ND, do not modify it while reusing. +
    +
    +[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) +
    + +[{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) + + ### Accessibility > >The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. From 23bbbda20f406a5a39d3da7e75175a474a13c8f0 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 18:59:41 +0200 Subject: [PATCH 087/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b4082fb08d0fcf..30c32ac64c7aa8 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -259,7 +259,7 @@ You can't use something that is licensed with ND (no derivatives). In this case No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. If the work is licensed with ND, do not modify it while reusing.
    -[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) + [How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr)
    [{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) From 2dcbd52080b5390d6bfec83157a458fbbd900542 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 19:01:57 +0200 Subject: [PATCH 088/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 30c32ac64c7aa8..5aeb84887f983c 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -258,8 +258,8 @@ You can't use something that is licensed with ND (no derivatives). In this case
    No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. If the work is licensed with ND, do not modify it while reusing.
    -
    - [How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) +
    +[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr)
    [{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) From 4d93124d5f32dd8f2138f2ef728c75d7ec6c967c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 19:14:25 +0200 Subject: [PATCH 089/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 5aeb84887f983c..d8d732ff74d300 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -265,6 +265,42 @@ No problem, you can reuse any existing CC licensed material in your learning mat [{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) +{% include _includes/tab-choices.html option1="Use the authors recommended attribution" option2="Use TASL" option3="Examples" option4="Learn more" default="Use the authors recommended attribution" title="Attribute" disambiguation="fifth" text="All CC licenses require that you attribute the author, and this rule is recommended even if the license is public domain CC-0. +If the work you are reusing has a copyright notice ("© some text") you need to reproduce it while you credit the work. +You should also be able to remove attribution upon request." %} + +
    +If the original author has provided a cite-as information, use it to attribute the work. +
    +
    +Provide the Title, Author, Source and License of the work that you are reusing. +Source is the URL to the original work. +If there is a URL to the author personal pages, provide it together with the name. +Provide the name of the license and a URL to the license. +
    +
    +> Examples are taken from [Best Practices for Creative Commons attributions - how to attribute works you reuse under a Creative Commons license](https://www.newmediarights.org/guide/how_to/creative_commons/best_practices_creative_commons_attributions) submitted by [New Media Rights](https://www.newmediarights.org/) available under a [CC BY-NC 3.0 US DEED](https://creativecommons.org/licenses/by-nc/3.0/us/) +> - Webpage/Blog - Title (with link to original work), author (or username) (with link to author's website), and license (with link). +> [Undercover Vampire Policeman](https://chriszabriskie.bandcamp.com/album/undercover-vampire-policeman) by [Chris Zabriskie](https://chriszabriskie.bandcamp.com/), available under a [Creative Commons Attribution 4.0 License](http://creativecommons.org/licenses/by/4.0/) +> - Book – Title, author, license written somewhere near the title and author if it’s a hard copy or if it’s an online book you should include a link to the licensed terms. +> [From Dust to Digital: Ten Years of the Endangered Archives Programme](https://books.google.com/books?id=ImO3BgAAQBAJ&pg=PR4&dq=creative+commons+4.0&hl=en&sa=X&ved=0CEoQ6AEwCGoVChMIspCXhPPxxgIVSF0eCh27NA5X#v=onepage&q=creative%20commons%204.0&f=false) by Maja Kominko under a Creative Commons Attribution Non-commercial Non-Derivative 4.0 International license (CC BY-NC-ND 4.0) + +> - Online Video - Title, author, license written into credits at end of video. Ideally make the text clickable to the original work. Put links to the original work and the license terms in the information section for the particular work (i.e. on the right in YouTube). +> [http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s](http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s) +> - Podcast/Audio - Title, author, license read at the end of the entire work. +> [“Je Suis Rick Springfield”](http://www.jonathancoulton.com/wiki/Je_Suis_Rick_Springfield) from the album [Artificial Heart](http://www.jonathancoulton.com/wiki/Artificial_Heart_(album)), by Jonathan Coulton, used under a [Creative Commons Attribution-Noncommercial 3.0 Unported License](http://creativecommons.org/licenses/by-nc/3.0/) + +>- Photo/Drawing/Illustration – Title, author, license (with link online) or in close proximity to the tangible work (either in the border or directly on the work, if applicable). +> “[Comcast protest](http://www.flickr.com/photos/ari/8503459/in/set-214952/)” by Flikr user [Steve Rhodes](http://www.flickr.com/photos/ari/) used under [Creative Commons Attribution 2.0 license](http://creativecommons.org/licenses/by/2.0/deed.en) +
    +
    +[{% icon point-right %} Attribution and Citing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#attribution-and-citing) +
    + +[{% icon point-right %} How to handle attribution?](https://courses.lumenlearning.com/suny-oerguide/chapter/how-to-handle-attribution/) + + + ### Accessibility > >The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. From 04c6d699295b562925b6a02fa470daab95edabe6 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 19:16:13 +0200 Subject: [PATCH 090/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index d8d732ff74d300..0aa3551102b72b 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -266,7 +266,7 @@ No problem, you can reuse any existing CC licensed material in your learning mat {% include _includes/tab-choices.html option1="Use the authors recommended attribution" option2="Use TASL" option3="Examples" option4="Learn more" default="Use the authors recommended attribution" title="Attribute" disambiguation="fifth" text="All CC licenses require that you attribute the author, and this rule is recommended even if the license is public domain CC-0. -If the work you are reusing has a copyright notice ("© some text") you need to reproduce it while you credit the work. +If the work you are reusing has a copyright notice ('© some text') you need to reproduce it while you credit the work. You should also be able to remove attribution upon request." %}
    From 4b4dc73317b504efdbaa5881bf68c99e2f1c3a1b Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 19:18:43 +0200 Subject: [PATCH 091/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 0aa3551102b72b..64099d336f134e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -281,9 +281,9 @@ Provide the name of the license and a URL to the license.
    > Examples are taken from [Best Practices for Creative Commons attributions - how to attribute works you reuse under a Creative Commons license](https://www.newmediarights.org/guide/how_to/creative_commons/best_practices_creative_commons_attributions) submitted by [New Media Rights](https://www.newmediarights.org/) available under a [CC BY-NC 3.0 US DEED](https://creativecommons.org/licenses/by-nc/3.0/us/) > - Webpage/Blog - Title (with link to original work), author (or username) (with link to author's website), and license (with link). -> [Undercover Vampire Policeman](https://chriszabriskie.bandcamp.com/album/undercover-vampire-policeman) by [Chris Zabriskie](https://chriszabriskie.bandcamp.com/), available under a [Creative Commons Attribution 4.0 License](http://creativecommons.org/licenses/by/4.0/) +> - [Undercover Vampire Policeman](https://chriszabriskie.bandcamp.com/album/undercover-vampire-policeman) by [Chris Zabriskie](https://chriszabriskie.bandcamp.com/), available under a [Creative Commons Attribution 4.0 License](http://creativecommons.org/licenses/by/4.0/) > - Book – Title, author, license written somewhere near the title and author if it’s a hard copy or if it’s an online book you should include a link to the licensed terms. -> [From Dust to Digital: Ten Years of the Endangered Archives Programme](https://books.google.com/books?id=ImO3BgAAQBAJ&pg=PR4&dq=creative+commons+4.0&hl=en&sa=X&ved=0CEoQ6AEwCGoVChMIspCXhPPxxgIVSF0eCh27NA5X#v=onepage&q=creative%20commons%204.0&f=false) by Maja Kominko under a Creative Commons Attribution Non-commercial Non-Derivative 4.0 International license (CC BY-NC-ND 4.0) +> - [From Dust to Digital: Ten Years of the Endangered Archives Programme](https://books.google.com/books?id=ImO3BgAAQBAJ&pg=PR4&dq=creative+commons+4.0&hl=en&sa=X&ved=0CEoQ6AEwCGoVChMIspCXhPPxxgIVSF0eCh27NA5X#v=onepage&q=creative%20commons%204.0&f=false) by Maja Kominko under a Creative Commons Attribution Non-commercial Non-Derivative 4.0 International license (CC BY-NC-ND 4.0) > - Online Video - Title, author, license written into credits at end of video. Ideally make the text clickable to the original work. Put links to the original work and the license terms in the information section for the particular work (i.e. on the right in YouTube). > [http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s](http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s) From ebc282154e44e18e9dc60ff7f7a4e7696715ad14 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 19:20:37 +0200 Subject: [PATCH 092/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 64099d336f134e..e3b03dd57e548e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -286,12 +286,12 @@ Provide the name of the license and a URL to the license. > - [From Dust to Digital: Ten Years of the Endangered Archives Programme](https://books.google.com/books?id=ImO3BgAAQBAJ&pg=PR4&dq=creative+commons+4.0&hl=en&sa=X&ved=0CEoQ6AEwCGoVChMIspCXhPPxxgIVSF0eCh27NA5X#v=onepage&q=creative%20commons%204.0&f=false) by Maja Kominko under a Creative Commons Attribution Non-commercial Non-Derivative 4.0 International license (CC BY-NC-ND 4.0) > - Online Video - Title, author, license written into credits at end of video. Ideally make the text clickable to the original work. Put links to the original work and the license terms in the information section for the particular work (i.e. on the right in YouTube). -> [http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s](http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s) +> - [http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s](http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s) > - Podcast/Audio - Title, author, license read at the end of the entire work. -> [“Je Suis Rick Springfield”](http://www.jonathancoulton.com/wiki/Je_Suis_Rick_Springfield) from the album [Artificial Heart](http://www.jonathancoulton.com/wiki/Artificial_Heart_(album)), by Jonathan Coulton, used under a [Creative Commons Attribution-Noncommercial 3.0 Unported License](http://creativecommons.org/licenses/by-nc/3.0/) +> -[“Je Suis Rick Springfield”](http://www.jonathancoulton.com/wiki/Je_Suis_Rick_Springfield) from the album [Artificial Heart](http://www.jonathancoulton.com/wiki/Artificial_Heart_(album)), by Jonathan Coulton, used under a [Creative Commons Attribution-Noncommercial 3.0 Unported License](http://creativecommons.org/licenses/by-nc/3.0/) >- Photo/Drawing/Illustration – Title, author, license (with link online) or in close proximity to the tangible work (either in the border or directly on the work, if applicable). -> “[Comcast protest](http://www.flickr.com/photos/ari/8503459/in/set-214952/)” by Flikr user [Steve Rhodes](http://www.flickr.com/photos/ari/) used under [Creative Commons Attribution 2.0 license](http://creativecommons.org/licenses/by/2.0/deed.en) +> -[Comcast protest](http://www.flickr.com/photos/ari/8503459/in/set-214952/)” by Flikr user [Steve Rhodes](http://www.flickr.com/photos/ari/) used under [Creative Commons Attribution 2.0 license](http://creativecommons.org/licenses/by/2.0/deed.en)
    [{% icon point-right %} Attribution and Citing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#attribution-and-citing) From 5dd753a5ba33964877eb2cc0f29ea6a4aebaa24c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 19:28:42 +0200 Subject: [PATCH 093/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 28 +++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index e3b03dd57e548e..3b6a107364a811 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -247,6 +247,30 @@ Different learners have different learning modalities (read/write, auditory, vis {: .quote author="Edward Rickenbacker​"} ### Choose Tools & Formats +> Collaborative environment for team work +> Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. Two examples are workplace or GitHub (find out more here). Replicate the folder tree in the environment and start using the provided templates to generate the content. +{: .tip} + +> Granular versioning for easy rollback +> Versioning helps you maintain control over your changes. If the collaborative environment does not provide versioning and history retention then keep a history of the files by adopting a naming convention such as combining the file name with an increasing version number. +{: .tip} + +> Open file formats to foster reuse +> For other people to reuse your materials they should be made available using open file formats (docx, pptx, pdf, md, html, etc.). If you use close file formats then you MUST clearly state the tools that have been used for development in your README file. +{: .tip} + +> Multimodal content to reach all audience +> Don't forget to include different types of multimedia to provide support for different learning modalities: read/write, auditory, visual, kinesthetic. +{: .tip} + +> Two file sets: editable + final +> Always work with and keep a history of your editable files. These are what matters for you and other instructors. The second set of final files should be obtained from the editable when needed (before distributing them to the learners). The final files should be kept on the learning platform only. In this way you don't need to worry about keeping the versions in sync. +{: .tip} + +> Don't forget to support co-creation +> Truly FAIR learning materials should enable co-creation with external parties. If you don't use a collaborative environment that supports this from the start (such as GitHub), then think how are you going to enable this in the future and how are you going to deal with versioning then. +{: .tip} + ### Plan to reuse existing material? @@ -288,10 +312,10 @@ Provide the name of the license and a URL to the license. > - Online Video - Title, author, license written into credits at end of video. Ideally make the text clickable to the original work. Put links to the original work and the license terms in the information section for the particular work (i.e. on the right in YouTube). > - [http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s](http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s) > - Podcast/Audio - Title, author, license read at the end of the entire work. -> -[“Je Suis Rick Springfield”](http://www.jonathancoulton.com/wiki/Je_Suis_Rick_Springfield) from the album [Artificial Heart](http://www.jonathancoulton.com/wiki/Artificial_Heart_(album)), by Jonathan Coulton, used under a [Creative Commons Attribution-Noncommercial 3.0 Unported License](http://creativecommons.org/licenses/by-nc/3.0/) +> - [“Je Suis Rick Springfield”](http://www.jonathancoulton.com/wiki/Je_Suis_Rick_Springfield) from the album [Artificial Heart](http://www.jonathancoulton.com/wiki/Artificial_Heart_(album)), by Jonathan Coulton, used under a [Creative Commons Attribution-Noncommercial 3.0 Unported License](http://creativecommons.org/licenses/by-nc/3.0/) >- Photo/Drawing/Illustration – Title, author, license (with link online) or in close proximity to the tangible work (either in the border or directly on the work, if applicable). -> -[Comcast protest](http://www.flickr.com/photos/ari/8503459/in/set-214952/)” by Flikr user [Steve Rhodes](http://www.flickr.com/photos/ari/) used under [Creative Commons Attribution 2.0 license](http://creativecommons.org/licenses/by/2.0/deed.en) +> - [Comcast protest](http://www.flickr.com/photos/ari/8503459/in/set-214952/)” by Flikr user [Steve Rhodes](http://www.flickr.com/photos/ari/) used under [Creative Commons Attribution 2.0 license](http://creativecommons.org/licenses/by/2.0/deed.en)
    [{% icon point-right %} Attribution and Citing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#attribution-and-citing) From 6d58c94b25b3b9a8f910c1820ffdb5fe9ecb22ca Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 19:33:21 +0200 Subject: [PATCH 094/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 3b6a107364a811..f00d06947a6077 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -276,7 +276,7 @@ Different learners have different learning modalities (read/write, auditory, vis {% include _includes/tab-choices.html option1="I want to reuse it as a whole" option2="I want to reuse a small part of it" option3="Learn more about IPR" default="I want to reuse it as a whole" title="Check the license" disambiguation="fourth" text="The existing material is available under a CC license, but it is different than the one you plan to use for your materials..." %} -
    +
    You can't use something that is licensed with ND (no derivatives). In this case you must follow the rules on combining and adapting CC material. [Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material)
    From a3b736e3cf312561667c0f4bc35e69c09aba40f0 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 19:37:04 +0200 Subject: [PATCH 095/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index f00d06947a6077..45e263ced302e9 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -276,7 +276,7 @@ Different learners have different learning modalities (read/write, auditory, vis {% include _includes/tab-choices.html option1="I want to reuse it as a whole" option2="I want to reuse a small part of it" option3="Learn more about IPR" default="I want to reuse it as a whole" title="Check the license" disambiguation="fourth" text="The existing material is available under a CC license, but it is different than the one you plan to use for your materials..." %} -
    +
    You can't use something that is licensed with ND (no derivatives). In this case you must follow the rules on combining and adapting CC material. [Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material)
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b/topics/contributing/tutorials/fair-by-design/tutorial.md index 45e263ced302e9..e41120546f0f98 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -237,9 +237,36 @@ Different learners have different learning modalities (read/write, auditory, vis > Design is intelligence made visible. {: .quote author="Alina Wheeler"} ### Time to brainstorm +![Brain image](../../images/brain-3829057_640.jpg) + +
    +Gerd Altmann from Pixabay +     +#### Concept map +Build a concept map of your learning materials aligning with the MVS profiles. + +The aligned MVS profile can help you cristalize the learning objectives using MVS taxonomy. + +Each MVS profile defines a list of technical and soft skills required for the profile. Think on how to incorporate both aspects in your learning materials. + +Go to MVS profiles catalogue ### Structure is everything +> +>{%icon galaxy-gear %}Create an intuitive logical organisation of all learning materials. +{: .comment} + +> +>The goal is for other people to easily reuse a single item (plan, activity, unit, assessment, ...). +{: .comment} + +> +>Use a hierarchical structure to combine learning units into larger compositions. +{: .comment} + + + ### How to develop the learning content ## Stage 4 - Produce @@ -276,7 +303,7 @@ Different learners have different learning modalities (read/write, auditory, vis {% include _includes/tab-choices.html option1="I want to reuse it as a whole" option2="I want to reuse a small part of it" option3="Learn more about IPR" default="I want to reuse it as a whole" title="Check the license" disambiguation="fourth" text="The existing material is available under a CC license, but it is different than the one you plan to use for your materials..." %} -
    +
    You can't use something that is licensed with ND (no derivatives). In this case you must follow the rules on combining and adapting CC material. [Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material)
    From 63cbc158e943275d11aee0c6feeab25d93d5874e Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 23:14:59 +0200 Subject: [PATCH 097/262] Update tutorial.md --- .../contributing/tutorials/fair-by-design/tutorial.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index e41120546f0f98..e968f1663261bf 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -254,18 +254,23 @@ Each MVS profile defines a list of technical and soft skills required for the pr ### Structure is everything > ->{%icon galaxy-gear %}Create an intuitive logical organisation of all learning materials. +>{%icon galaxy-gear %} Create an intuitive logical organisation of all learning materials. {: .comment} > ->The goal is for other people to easily reuse a single item (plan, activity, unit, assessment, ...). +>{%icon trophy %} The goal is for other people to easily reuse a single item (plan, activity, unit, assessment, ...). {: .comment} > ->Use a hierarchical structure to combine learning units into larger compositions. +>{%icon galaxy-dataset-map %} Use a hierarchical structure to combine learning units into larger compositions. {: .comment} +>How to organise the files +> The diagram shows how to organise all files in folders and subfolders. Click on the links to discover and use pre-prepared templates. +{: .warning} + + ### How to develop the learning content From bbba2398c0fcd83503df18aa3214e3ef26137621 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 23:18:04 +0200 Subject: [PATCH 098/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index e968f1663261bf..70b5563744cc77 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -266,9 +266,9 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .comment} ->How to organise the files +>How to organise the files > The diagram shows how to organise all files in folders and subfolders. Click on the links to discover and use pre-prepared templates. -{: .warning} +{: .hands-on} From f061742e0817e48b733bc1da20f029ed4faec317 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 23:27:20 +0200 Subject: [PATCH 099/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 70b5563744cc77..0e4e2a19539d6f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -271,9 +271,33 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .hands-on} +>Syllabus is ready +> You should by now have the first draft of your syllabus. It contains all the fields from the RDA min metadata set plus the high level topics covered by the learning material. +{: .comment} + +>Available feedback form +> The feedback form template is ready to be used as is. All you need to do is change the name of the training. It should be shared with training participants after the training, to gather quantitative and qualitative feedback. +{: .tip} + +>Available facilitation guide kit +> The facilitation guide should help prepare for the actual training. If you don't want to develop your own, use something that is already available such as the [TRIPLE project TRAINING TOOLKIT](https://project.gotriple.eu/project-deliverables/triple-training-toolkit/). +{: .tip} + +>Don't worry, we got you covered with templates +> All templates are readily available for use in the specialised [templates repository](https://github.com/FAIR-by-Design-Methodology/templates). See the detailed training on how to use it step by step. +{: .tip} + +> +> Need to be detailed enough so that anyone can reuse the slides properly. Don't put them in the slide deck. This is what the learning content file is for. +{: .question} ### How to develop the learning content + + +Start an in-depth training on the Design stage.... + +FAIR-by-Design Methodology: Design stage.... ## Stage 4 - Produce > To contrive is nothing! To construct is something! To produce is everything! {: .quote author="Edward Rickenbacker​"} From 74ed865397ff8d29d982ec60291f573e031d88dc Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 23:44:32 +0200 Subject: [PATCH 100/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 103 +++++++++++++++++- 1 file changed, 102 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 0e4e2a19539d6f..97e0e797ad1a87 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -287,12 +287,113 @@ Each MVS profile defines a list of technical and soft skills required for the pr > All templates are readily available for use in the specialised [templates repository](https://github.com/FAIR-by-Design-Methodology/templates). See the detailed training on how to use it step by step. {: .tip} -> +>What about instructor notes? > Need to be detailed enough so that anyone can reuse the slides properly. Don't put them in the slide deck. This is what the learning content file is for. {: .question} ### How to develop the learning content +Use the Hunter Model + +
    +
    +
    +
    +
    {% icon congratulations %} 1. Set Learning Objectives
    +

    + ... what is the goal +

    +
    +
    +
    +
    +
    +
    +
    {% icon pref-list %} 2. Identify Needs
    +

    + ... how to get there +

    +
    +
    +
    +
    +
    +
    +
    {% icon solution %} 3. Plan
    +

    + ... share the agenda +

    +
    +
    +
    +
    + +
    +
    +
    +
    +
    {% icon congratulations %} 4. Hook
    +

    + ... why is the content important +

    +
    +
    +
    +
    +
    +
    +
    {% icon pref-list %} 5. Instruct
    +

    + ... watch how I do it +

    +
    +
    +
    +
    +
    +
    +
    {% icon solution %} 6. Practise
    +

    + ... you help me do it, I'll watch you do it +

    +
    +
    +
    +
    + +
    +
    +
    +
    +
    {% icon congratulations %} 7. Wrap-Up
    +

    + ... foster retention and reinforcement +

    +
    +
    +
    +
    +
    +
    +
    {% icon pref-list %} 8. Evaluate
    +

    + ... monitor progress +

    +
    +
    +
    +
    +
    +
    +
    {% icon solution %} 9. Reflect
    +

    + .. how did it go? +

    +
    +
    +
    +
    + Start an in-depth training on the Design stage.... From 661e43146c75a7c2972d66fd5bb9125ed409df01 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 8 Aug 2024 23:52:37 +0200 Subject: [PATCH 101/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 97e0e797ad1a87..b0fae12203987c 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -299,7 +299,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon congratulations %} 1. Set Learning Objectives
    +
    {% icon curriculum %} 1. Set Learning Objectives

    ... what is the goal

    @@ -309,7 +309,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon pref-list %} 2. Identify Needs
    +
    {% icon pref-identities %} 2. Identify Needs

    ... how to get there

    @@ -319,7 +319,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon solution %} 3. Plan
    +
    {% icon galaxy-panelview %} 3. Plan

    ... share the agenda

    @@ -332,7 +332,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon congratulations %} 4. Hook
    +
    {% icon version %} 4. Hook

    ... why is the content important

    @@ -342,7 +342,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon pref-list %} 5. Instruct
    +
    {% icon galaxy-wf-edit %} 5. Instruct

    ... watch how I do it

    @@ -352,7 +352,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon solution %} 6. Practise
    +
    {% icon galaxy-rulebuilder-history %} 6. Practise

    ... you help me do it, I'll watch you do it

    @@ -365,7 +365,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon congratulations %} 7. Wrap-Up
    +
    {% icon galaxy-barchart %} 7. Wrap-Up

    ... foster retention and reinforcement

    @@ -375,7 +375,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon pref-list %} 8. Evaluate
    +
    {% icon license %} 8. Evaluate

    ... monitor progress

    @@ -385,7 +385,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -
    {% icon solution %} 9. Reflect
    +
    {% icon galaxy-history-answer %} 9. Reflect

    .. how did it go?

    From 7adab9cd0794366fa5dc154bb6063439339d6bd0 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 09:48:00 +0200 Subject: [PATCH 102/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b0fae12203987c..b27db7d68f1c99 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -270,6 +270,19 @@ Each MVS profile defines a list of technical and soft skills required for the pr > The diagram shows how to organise all files in folders and subfolders. Click on the links to discover and use pre-prepared templates. {: .hands-on} +``` +├── README +├── CITATION.cff +├── LICENCE +├── resources +├───├── attachments +│ ├── Learning Unit1 +├───├───├── attachments +│ │ ├── assesment +│ │ ├── activities +│ ├── Learning Unit2 + +``` >Syllabus is ready > You should by now have the first draft of your syllabus. It contains all the fields from the RDA min metadata set plus the high level topics covered by the learning material. From ff7f623bbfa795dc1749d95689db53c68a216123 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 10:07:30 +0200 Subject: [PATCH 103/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b27db7d68f1c99..24a716b2f39056 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -64,9 +64,9 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### First things first: What is FAIR? -> Findable +> Findable > The editable learning material has a unique and persistent identifier (PID) and is described with sufficiently detailed metadata. -{: .question} +{: .answer} > Accessible From c473ad8dc84b4ae497481787b380216421a59be2 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 10:10:23 +0200 Subject: [PATCH 104/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 24a716b2f39056..ef4ac3b9c85f6e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -64,15 +64,13 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### First things first: What is FAIR? -> Findable +> Findable > The editable learning material has a unique and persistent identifier (PID) and is described with sufficiently detailed metadata. -{: .answer} +{: .solution} > Accessible -> > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. -> {: .question} From 393233f98011c8233ec8ad939df4281a56abe90d Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 10:16:27 +0200 Subject: [PATCH 105/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 22 ++++++++++--------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index ef4ac3b9c85f6e..084e33efcd496b 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -69,20 +69,20 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide {: .solution} -> Accessible +> Accessible > The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. -{: .question} +{: .solution} -> Interoperable +> Interoperable > The metadata describing the learning material follows a the RDA minimum metadata schema combined with agreed-upon controlled vocabularies. > Formal, accessible, shared, and broadly applicable language(s) and format(s) are used to develop the material. -{: .question} +{: .solution} -> Reusable +> Reusable >The learning material has a clear usage license (CC-BY-4.0 recommended) and accurate information on provenance. -{: .question } +{: .solution } ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources @@ -115,10 +115,12 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide More on the metadata here {% cite hoebelheinrich_2022 %} -More on FAIR learning objects definition: - - [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) - - [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) - - [FAIR learning objects](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-learning-objects) + +>More on FAIR learning objects definition: +>- [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) + >- [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) + >- [FAIR learning objects](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-learning-objects) +{: .tip} ### Start Ideating... From 8efb1ece0811109718623ee5b1f60ed2f13b1e99 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 10:23:55 +0200 Subject: [PATCH 106/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 084e33efcd496b..cee6bff8d68f5f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -158,10 +158,11 @@ More on the metadata here {% cite hoebelheinrich_2022 %}
    +>More on backward learning: +> - [Steps of the backward learning process](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#backward-instructional-design-process) +{: .tip } -More on backward learning: - [Steps of the backward learning process](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#backward-instructional-design-process) - +### Define. > Purpose > When and how the learning materials can be used and for what purposes? @@ -188,9 +189,9 @@ More on backward learning: > > >Use Blooms Taxonomy > >Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. -> > -> >[See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) > {: .tip} +> +> [See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) {: .question } Start an in-depth training on the Prepare stage.... @@ -219,7 +220,9 @@ Reusable materials can be found anywhere. These are just some examples: > General > [Creative Commons Search](https://search.creativecommons.org/) - content provided under a CC license +> > [Zenodo](https://zenodo.org/) - a multi-disciplinary open repository +> > [OSF](https://osf.io/) - a free, open research platform {: .code-in} From 9854c76aab36f18792ee614778738650c2eadc66 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 10:54:28 +0200 Subject: [PATCH 107/262] remove images --- topics/contributing/images/Moodle-logo.svg.png | Bin 7631 -> 0 bytes topics/contributing/images/Zenodo_logo.png | Bin 9531 -> 0 bytes 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 topics/contributing/images/Moodle-logo.svg.png delete mode 100644 topics/contributing/images/Zenodo_logo.png diff --git a/topics/contributing/images/Moodle-logo.svg.png b/topics/contributing/images/Moodle-logo.svg.png deleted file mode 100644 index 11e0411507e3445dffa6ffd883f6de47c9d6ef01..0000000000000000000000000000000000000000 GIT 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amisev1971 Date: Fri, 9 Aug 2024 10:54:35 +0200 Subject: [PATCH 108/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 90 +++++-------------- 1 file changed, 24 insertions(+), 66 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index cee6bff8d68f5f..ad74673835e33f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -87,31 +87,28 @@ Below are the main stages of the FAIR-by-Design Methodology that will help guide ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources - -{% include _includes/tab-choices.html option1="Descriptive info fields" option2="Access info fields" option3="Educational info fields" default="Descriptive info fields" title="Metadata fields categories" %} - -
    -- **Title** = The human readable name of the resource -- **Abstract / Description** = A brief synopsis about or description of the learning resource -- **Author(s)** = Name of entity(ies) authoring the resource -- **Primary Language** = Language in which the resource was originally published or made available -- **Keyword(s)** = Keywords or tags used to describe the resource -- **Version Date** = Version date for the most recently published or broadcast resource -
    -
    -- **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. -- **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle -- **License** = A license document that applies to this content, typically indicated by URL -- **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) -
    -
    -- **Target Group (Audience)** = Principal users(s) for which the resource was designed -- **Learning Resource Type** = The predominant type or kind that characterizes the learning resource -- **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource -- **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced -
    - - +> Descriptive info metadata fields +> - **Title** = The human readable name of the resource +> - **Abstract / Description** = A brief synopsis about or description of the learning resource +> - **Author(s)** = Name of entity(ies) authoring the resource +> - **Primary Language** = Language in which the resource was originally published or made available +> - **Keyword(s)** = Keywords or tags used to describe the resource +> - **Version Date** = Version date for the most recently published or broadcast resource +{: .details} + +> Access info metadata fields +> - **URL to Resource** = URL that resolves to the learning resource or to a "landing page" for the resource that contains important contextual information including the direct resolvable link to the resource, if applicable. +> - **Resource URL Type** = Designation of the identifier scheme used for the resource URL, e.g., DOI, ARK, Handle +> - **License** = A license document that applies to this content, typically indicated by URL +> - **Access Cost** = Choice stating whether or not there is a fee for use of the resource (yes, no, maybe) +{: .details} + +> Educational info metadata fields +> - **Target Group (Audience)** = Principal users(s) for which the resource was designed +> - **Learning Resource Type** = The predominant type or kind that characterizes the learning resource +> - **Learning Outcome** = Descriptions of what knowledge, skills or abilities a learner should acquire on completion of the resource +> - **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced +{: .details} More on the metadata here {% cite hoebelheinrich_2022 %} @@ -261,7 +258,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .comment} > ->{%icon trophy %} The goal is for other people to easily reuse a single item (plan, activity, unit, assessment, ...). +>{%icon tool-versions %} The goal is for other people to easily reuse a single item (plan, activity, unit, assessment, ...). {: .comment} > @@ -686,20 +683,7 @@ Open the PDF and then from the All tools menu on the left, select View more and ### Store in a repository -![Zenodo logo](../../images/Zenodo_logo.png) - -
    -Zenodo logo by a Twitter user from Wikimedia licensed under the Creative Commons Attribution-Share Alike 4.0 International license -     -#### To Zenodo -Deposit your editable learning materials set to make available to other designers and instructors. -1. Create an archive of all the files in your logical hierarchical structure. -2. Create a new Zenodo record with the archive. -3. Provide a rich metadata description and link to any related resources. - -How to deposit in Zenodo - ->Automated publishing to Zenodo +>Automated publishing >If you are working on GitHub using the provided templates repository then the "publish to Zenodo" step is fully automated for you. Just follow the [guide to publishing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%205%20%E2%80%93%20Publish/17-Zenodo%20Publishing/17-Zenodo%20Publishing/). {: .tip} @@ -707,28 +691,6 @@ Deposit your editable learning materials set to make available to other designer >You are at the point when you should also consider making a record in a relevant training catalogue such as the EOSC training catalogue. {: .tip} -### Provide to learners - -![Moodle logo](../../images/Moodle-logo.svg.png) - -
    -Moodle logo by Moodle.org from Wikipedia licensed under the GNU General Public License -     -#### To LMS -Generate the final versions from your editable content and add it to a course on the Skills4EOSC Learning Platform to make it available for learners. - -0. Provide the course metadata. - -1. Add the learning content in general non-editable file formats. - -2. Add assessments such as quizzes or assignments. - -3. Setup feedback gathering. - -4. Define recognition mechanism such as open digital badges for successful completion. - -Managing a Moodle course - ​​Start an in-depth training on the Publish stage.... @@ -742,10 +704,6 @@ Generate the final versions from your editable content and add it to a course on > Have someone who has not participated in the development of the learning materials review the final work. This will guarantee a review free of cognitive bias. {: .tip} -> Don't forget to QA the LMS -> The reviewer should play the role of a new learner in the LMS and check everything from the learner perspective. -{: .tip} - > Go through the QA checklists > In Skills4EOSC T2.4 has developed a number of QA checklists that you and your external reviewer need to go through so that you can ensure high-quality learning materials. {: .tip} From eb37fc04585634f630af43a79b89831c3d2be644 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 11:39:41 +0200 Subject: [PATCH 109/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 65 +++++++++++-------- 1 file changed, 37 insertions(+), 28 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index ad74673835e33f..7e7bec4db4fba9 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -444,52 +444,61 @@ Each MVS profile defines a list of technical and soft skills required for the pr ### Plan to reuse existing material? -{% include _includes/tab-choices.html option1="I want to reuse it as a whole" option2="I want to reuse a small part of it" option3="Learn more about IPR" default="I want to reuse it as a whole" title="Check the license" disambiguation="fourth" text="The existing material is available under a CC license, but it is different than the one you plan to use for your materials..." %} +#### Check the license -
    -You can't use something that is licensed with ND (no derivatives). In this case you must follow the rules on combining and adapting CC material. [Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material) -
    -
    -No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. If the work is licensed with ND, do not modify it while reusing. -
    -
    -[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) -
    +The existing materials is available under a CC license, but it is different than the one you plan to use for your materials... + +>I want to reuse it as a whole +>You can't use something that is licensed with ND (no derivatives). In this case you must follow the rules on combining and adapting CC material. +>[Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material) +{: .details} + +>I want to reuse a small part of it +> No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. If the work is licensed with ND, do not modify it while reusing. +{: .details} + +>Learn more about IPR +>[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) +{: .details} [{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) -{% include _includes/tab-choices.html option1="Use the authors recommended attribution" option2="Use TASL" option3="Examples" option4="Learn more" default="Use the authors recommended attribution" title="Attribute" disambiguation="fifth" text="All CC licenses require that you attribute the author, and this rule is recommended even if the license is public domain CC-0. +#### Attribute + +All CC licenses require that you attribute the author, and this rule is recommended even if the license is public domain CC-0. If the work you are reusing has a copyright notice ('© some text') you need to reproduce it while you credit the work. -You should also be able to remove attribution upon request." %} +You should also be able to remove attribution upon request. -
    -If the original author has provided a cite-as information, use it to attribute the work. -
    -
    -Provide the Title, Author, Source and License of the work that you are reusing. -Source is the URL to the original work. -If there is a URL to the author personal pages, provide it together with the name. -Provide the name of the license and a URL to the license. -
    -
    +> Use the authors recommended attribution +> If the original author has provided a cite-as information, use it to attribute the work. +{: .details} + +> Use TASL +> Provide the Title, Author, Source and License of the work that you are reusing. +> +>- Source is the URL to the original work. +>- If there is a URL to the author personal pages, provide it together with the name. +>- Provide the name of the license and a URL to the license. +{: .details} + +> Examples > Examples are taken from [Best Practices for Creative Commons attributions - how to attribute works you reuse under a Creative Commons license](https://www.newmediarights.org/guide/how_to/creative_commons/best_practices_creative_commons_attributions) submitted by [New Media Rights](https://www.newmediarights.org/) available under a [CC BY-NC 3.0 US DEED](https://creativecommons.org/licenses/by-nc/3.0/us/) > - Webpage/Blog - Title (with link to original work), author (or username) (with link to author's website), and license (with link). > - [Undercover Vampire Policeman](https://chriszabriskie.bandcamp.com/album/undercover-vampire-policeman) by [Chris Zabriskie](https://chriszabriskie.bandcamp.com/), available under a [Creative Commons Attribution 4.0 License](http://creativecommons.org/licenses/by/4.0/) > - Book – Title, author, license written somewhere near the title and author if it’s a hard copy or if it’s an online book you should include a link to the licensed terms. > - [From Dust to Digital: Ten Years of the Endangered Archives Programme](https://books.google.com/books?id=ImO3BgAAQBAJ&pg=PR4&dq=creative+commons+4.0&hl=en&sa=X&ved=0CEoQ6AEwCGoVChMIspCXhPPxxgIVSF0eCh27NA5X#v=onepage&q=creative%20commons%204.0&f=false) by Maja Kominko under a Creative Commons Attribution Non-commercial Non-Derivative 4.0 International license (CC BY-NC-ND 4.0) - > - Online Video - Title, author, license written into credits at end of video. Ideally make the text clickable to the original work. Put links to the original work and the license terms in the information section for the particular work (i.e. on the right in YouTube). > - [http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s](http://www.youtube.com/watch?v=fDbbdeIXO0w#t=3m0s) > - Podcast/Audio - Title, author, license read at the end of the entire work. > - [“Je Suis Rick Springfield”](http://www.jonathancoulton.com/wiki/Je_Suis_Rick_Springfield) from the album [Artificial Heart](http://www.jonathancoulton.com/wiki/Artificial_Heart_(album)), by Jonathan Coulton, used under a [Creative Commons Attribution-Noncommercial 3.0 Unported License](http://creativecommons.org/licenses/by-nc/3.0/) - >- Photo/Drawing/Illustration – Title, author, license (with link online) or in close proximity to the tangible work (either in the border or directly on the work, if applicable). > - [Comcast protest](http://www.flickr.com/photos/ari/8503459/in/set-214952/)” by Flikr user [Steve Rhodes](http://www.flickr.com/photos/ari/) used under [Creative Commons Attribution 2.0 license](http://creativecommons.org/licenses/by/2.0/deed.en) -
    -
    -[{% icon point-right %} Attribution and Citing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#attribution-and-citing) -
    +{: .details} + +> Learn more +> [{% icon point-right %} Attribution and Citing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#attribution-and-citing) +{: .details} [{% icon point-right %} How to handle attribution?](https://courses.lumenlearning.com/suny-oerguide/chapter/how-to-handle-attribution/) From 3da4622e7e38863a3bbd13a85379938a1b5c0033 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 11:43:09 +0200 Subject: [PATCH 110/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 36 ++++++++++--------- 1 file changed, 20 insertions(+), 16 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 7e7bec4db4fba9..332b550085c960 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -525,23 +525,27 @@ PDF document accessibility is measured with a separate technical specification < Learn more -{% include _includes/tab-choices.html option1="Slides" option2="Web content" option3="PDF document" default="Slides" title="Use accessibility evaluation tools!" disambiguation="third" text="Accessibility evaluation tools are not perfect. Even if they say that all is ok, it does not mean that your content is truly accessible. But they are a very good starting point." %} - -
    -Use the integrated accessibility checker in Power Point: -1. Open an existing presentation in PowerPoint and review the content. -2. Select the Review tab. -3. Select Check Accessibility. -4. An Accessibility Checker pane will appear on the right with 'Inspection Results' displayed. -
    -
    -Choose from the [Web Accessibility Evaluation Tools List](https://www.w3.org/WAI/test-evaluate/tools/list/) developed by W3C. -
    -
    -Check accessibility in Adobe Acrobat Pro. +#### Use accessibility evaluation tools! -Open the PDF and then from the All tools menu on the left, select View more and then select Prepare for accessibility. -
    +Accessibility evaluation tools are not perfect. Even if they say that all is ok, it does not mean that your content is truly accessible. But they are a very good starting point. + +> Slides +> Use the integrated accessibility checker in Power Point: +> 1. Open an existing presentation in PowerPoint and review the content. +> 2. Select the Review tab. +> 3. Select Check Accessibility. +> 4. An Accessibility Checker pane will appear on the right with 'Inspection Results' displayed. +{: .details} + +> Web content +> Choose from the [Web Accessibility Evaluation Tools List](https://www.w3.org/WAI/test-evaluate/tools/list/) developed by W3C. +{: .details} + +> PDF document +> Check accessibility in Adobe Acrobat Pro. +> +> Open the PDF and then from the All tools menu on the left, select View more and then select Prepare for accessibility. +{: .details} ### Internal QA From 2328c8d174f402acb2c41790346178b8aa8c2f59 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 11:50:59 +0200 Subject: [PATCH 111/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 131 +++++++----------- 1 file changed, 48 insertions(+), 83 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 332b550085c960..5a959355c7f6eb 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -723,36 +723,39 @@ Accessibility evaluation tools are not perfect. Even if they say that all is ok, ### FAIR or not FAIR, that is the question... -{% include _includes/tab-choices.html option1="Essential requirements" option2="Optional requirements" default="Essential requirements" title="Measure FAIRness" disambiguation="second" text="Use the FAIR-by-Design methodology QA checklist to check if you have followed the most important aspects of the methodology and managed to produce FAIR learning materials. -
    -The questions marked as essential achieve bare minimum FAIRness." %} +#### Measure FAIRness -
    -- **Findable** = Is the complete learning resource (including instructors info) registered or indexed in at least one searchable repository? Is it in a FAIR repository? Is metadata for the resource provided in both human- and machine-readable format (e.g JSON, XMLor YAML? -- **Accessible** = Has an accessibility checker tool been utilised to improve the accessibility of all learning resource files (PDF, HTML, video, etc.)? Are access rules (authentication & authorisation) implemented for the learning resource? -- **Interoperable** = Is the RDA minimal (or domain specific) metadata schema used for the learning material description?
    Is the resource available in open file formats which are tool agnostic and compatible with a wide variety of existing software? -- **Resuable** = Is there clear attribution for all reused resources with compatible licenses? Has the learning resource been made available for use by defining a permissable license or policy information that allows derivations? -
    -
    -- Did you follow the stages of the backward instructional design process while developing the learning resource? --  Are controlled vocabularies (CVs) used for describing the resource characteristics aligned with the chosen metadata schema? --  Does the learning resource represent a complete learning object defined around minimum one learning objective? --  Does the resource incorporate an instructor kit that aids in facilitating the process of others reusing learning material by offering helpful how-to guides? - -  facilitator guide - -  activities description - -  assessment activities and strategy to assess - -  general learning content or instructor notes - -  lesson unit plan - -  syllabus --  Have you employed a versioning system to track and control changes in your materials? --  Are the resource access rules (how to access, e.g. registration procedure) explicitly communicated to learners? --  Is the learning resource searchable in at least one relevant catalogue?  - -  Is it FAIR (can be searched based on metadata)? --  Does the course include the possibility to provide feedback or comments from users and-or trainers/designers?  - -  If so, do you regularly gather and analyse that feedback? --  Does the resource adopt an open community approach regarding its quality and reachability? --  Has the learning resource been checked by a third party regarding its learning experience quality? -
    +Use the FAIR-by-Design methodology QA checklist to check if you have followed the most important aspects of the methodology and managed to produce FAIR learning materials. + +The questions marked as essential achieve bare minimum FAIRness. + +>Essential requirements +> - **Findable** = Is the complete learning resource (including instructors info) registered or indexed in at least one searchable repository? Is it in a FAIR repository? Is metadata for the resource provided in both human- and machine-readable format (e.g JSON, XMLor YAML? +> - **Accessible** = Has an accessibility checker tool been utilised to improve the accessibility of all learning resource files (PDF, HTML, video, etc.)? Are access rules (authentication & authorisation) implemented for the learning resource? +> - **Interoperable** = Is the RDA minimal (or domain specific) metadata schema used for the learning material description? Is the resource available in open file formats which are tool agnostic and compatible with a wide variety of existing software? +> - **Reusable** = Is there clear attribution for all reused resources with compatible licenses? Has the learning resource been made available for use by defining a permissable license or policy information that allows derivations? +{: .details} + +>Optional requirements +> - Did you follow the stages of the backward instructional design process while developing the learning resource? +> -  Are controlled vocabularies (CVs) used for describing the resource characteristics aligned with the chosen metadata schema? +> -  Does the learning resource represent a complete learning object defined around minimum one learning objective? +> -  Does the resource incorporate an instructor kit that aids in facilitating the process of others reusing learning material by offering helpful how-to guides? +> -  facilitator guide +> -  activities description +> -  assessment activities and strategy to assess +> -  general learning content or instructor notes +> -  lesson unit plan +> -  syllabus +> -  Have you employed a versioning system to track and control changes in your materials? +> -  Are the resource access rules (how to access, e.g. registration procedure) explicitly communicated to learners? +> -  Is the learning resource searchable in at least one relevant catalogue?  +> -  Is it FAIR (can be searched based on metadata)? +> -  Does the course include the possibility to provide feedback or comments from users and-or trainers/designers?  +> -  If so, do you regularly gather and analyse that feedback? +> -  Does the resource adopt an open community approach regarding its quality and reachability? +> -  Has the learning resource been checked by a third party regarding its learning experience quality? +{: .details} ### Feedback QA @@ -769,6 +772,7 @@ The questions marked as essential achieve bare minimum FAIRness." %} {: .quote author="Winston Churchill"} #### {% icon galaxy-download %} Gather + Gather feedback from all available internal & external sources. Potential sources: @@ -779,62 +783,23 @@ Potential sources: - Direct mail contact  - Other means of communication -
    -
    - -
    - -
    -
    {% icon galaxy-download %} Gather
    -

    Potential sources:

    -
      -
    • Feedback form 
      • -
    • QA recommendations 
      • -
    • self-reflection after training
      •   -
    • Survey 
      • -
    • Direct mail contact 
      • -
    • Other means of communication
      • -
    -
    -
    -
    +#### {% icon galaxy-barchart %} Analyse -
    - -
    - -
    -
    {% icon galaxy-barchart %} Analyse
    -

    Analyse the gathered information in a structured way.
    - Create a list of potential improvements with impact level (high, moderate, low). -

    -
    -
    -
    -
    -
    -
    - -
    - -
    -
    {% icon galaxy-wf-edit %} Improve
    -

    Select items from the list that will be part of a new version.
    Choose items that make sense to be in the same new release

    -
    -
    -
    +Analyse the gathered information in a structured way. -
    - -
    - -
    -
    {% icon galaxy-history-refresh %} Repeat
    -

    Start a new cycle of the FAIR-by-Design methodology that will implement the selected items.
    After the Verify stage, you will reenter continuous improvement with newly gathered information....

    -
    -
    -
    -
    +Create a list of potential improvements with impact level (high, moderate, low). + +#### {% icon galaxy-wf-edit %} Improve + +Select items from the list that will be part of a new version. + +Choose items that make sense to be in the same new release. + +#### {% icon galaxy-history-refresh %} Repeat + +Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. + +After the Verify stage, you will reenter continuous improvement with newly gathered information.... ​Start an in-depth training on the Continuous Improvement stage.... From d4418efeeb34f634063af3c88b9742a9295a6909 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 11:54:56 +0200 Subject: [PATCH 112/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 32 ++++++------------- 1 file changed, 10 insertions(+), 22 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 5a959355c7f6eb..8da0d08aa63c49 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -191,8 +191,7 @@ More on the metadata here {% cite hoebelheinrich_2022 %} > [See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) {: .question } -Start an in-depth training on the Prepare stage.... -FAIR-by-Design Methodology: Prepare stage.... +Go to FAIR-by-Design Methodology: Prepare stage.... ## Stage 2 - Discover > Greater even than the greatest discovery is to keep open the way to future discovery. @@ -229,9 +228,10 @@ Reusable materials can be found anywhere. These are just some examples: {: .warning} ### Don't forget the multimedia search + Different learners have different learning modalities (read/write, auditory, visual, kinesthetic). You should use all types of multimedia in your learning materials. -Start an in-depth training on the Discover stage.... -FAIR-by-Design Methodology: Discover stage.... + +Go to FAIR-by-Design Methodology: Discover stage.... ## Stage 3 - Design > Design is intelligence made visible. @@ -407,12 +407,10 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    +Go to FAIR-by-Design Methodology: Design stage.... - -Start an in-depth training on the Design stage.... - -FAIR-by-Design Methodology: Design stage.... ## Stage 4 - Produce + > To contrive is nothing! To construct is something! To produce is everything! {: .quote author="Edward Rickenbacker​"} @@ -589,10 +587,7 @@ Accessibility evaluation tools are not perfect. Even if they say that all is ok,
    - -​Start an in-depth training on the Produce stage.... - -FAIR-by-Design Methodology: Produce stage.... +Go to FAIR-by-Design Methodology: Produce stage.... ## Stage 5 - Publish > Publishing is the art of working on a creative idea and turning it into a masterpiece​! {: .quote author="Unknown"} @@ -704,10 +699,7 @@ Accessibility evaluation tools are not perfect. Even if they say that all is ok, >You are at the point when you should also consider making a record in a relevant training catalogue such as the EOSC training catalogue. {: .tip} - -​​Start an in-depth training on the Publish stage.... - -FAIR-by-Design Methodology: Publish stage.... +Go to FAIR-by-Design Methodology: Publish stage.... ## Stage 6 - Verify > You will find it a very good practice always to verify your references, sir! @@ -763,9 +755,7 @@ The questions marked as essential achieve bare minimum FAIRness. > Ensure that you actively and regularly gather feedback from both perspectives: the learners and the instructors. {: .comment} -Start an in-depth training on the Verify stage.... - -FAIR-by-Design Methodology: Verify stage.... +Go to FAIR-by-Design Methodology: Verify stage.... ## Stage 7 - Continuous Improvement > To improve is to change; to be perfect is to change often @@ -801,9 +791,7 @@ Start a new cycle of the FAIR-by-Design methodology that will implement the sele After the Verify stage, you will reenter continuous improvement with newly gathered information.... -​Start an in-depth training on the Continuous Improvement stage.... - -FAIR-by-Design Methodology: Continuous Improvement stage.... +Go to FAIR-by-Design Methodology: Continuous Improvement stage.... # About From 5b6471f9b0bb104fedd70e5429509e229888639a Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:09:42 +0200 Subject: [PATCH 113/262] Delete tab-choices.html --- _includes/tab-choices.html | 43 -------------------------------------- 1 file changed, 43 deletions(-) delete mode 100644 _includes/tab-choices.html diff --git a/_includes/tab-choices.html b/_includes/tab-choices.html deleted file mode 100644 index ea4d96d00d6667..00000000000000 --- a/_includes/tab-choices.html +++ /dev/null @@ -1,43 +0,0 @@ -
    -
    - {% if include.title %} - {{ include.title }} - {% endif %} -
    - {% if include.text %} -

    - {{ include.text }} -

    - {% endif %} - {% if include.option1 %} - - - {% endif %} - {% if include.option2 %} - - - {% endif %} - {% if include.option3 %} - - - {% endif %} - {% if include.option4 %} - - - {% endif %} - - {% if include.default %} - - {% endif %} -
    From 2570259ea960a1207f55c45a4a10c828e0bb9833 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:09:48 +0200 Subject: [PATCH 114/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 44 ++++++++++++++----- 1 file changed, 34 insertions(+), 10 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 8da0d08aa63c49..0cb8fa7627bac7 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -40,19 +40,43 @@ contributions: --- -Welcome to the FAIR-by-Design GTN course. +Welcome to the FAIR-by-Design Methodology Microlearning GTN tutorial. Below are the main stages of the FAIR-by-Design Methodology that will help guide you on your journey of creating FAIR learning materials. - -> -> -> In this tutorial, we will cover: -> -> 1. TOC -> {:toc} -> -{: .agenda} +The FAIR-by-Design Methodology is defined into [a number of stages](#main-stages) that help you incorporate the FAIR principles into the backward learning instructional design process so that the final output are FAIR learning materials from both learners and instructors perspective: + +1. [Prepare](#stage-1---prepare) + - Do you understand FAIR and its implications + - Define purpose, learning objectives, target audience +2. Discover + - Find existing resources + - Identify potential for reuse +3. Design + - Define the syllabus and structure + - Identify granularity + - Define facilitation materials +4. Produce + - Develop content using common apps and file formats + - Define machine readable metadata + - Perform internal QA check +5. Publish + - Define license and other related info + - Release for instructors and learners + - Enable feedback gathering +6. Verify + - Final QA check + - Use gathered feedback for continuous improvement +7. Continuous Improvement + - Create a list of potential improvements + - Choose a set of improvements to be implemented + - Start a new release cycle + +Review each stage and the essential steps that it includes. + +If you have any questions at any stage on your journey do not hesitate to contact the FAIR-by-Design methodology team. + +May all your materials be FAIR! # Main stages From 5469d02e92d779d8a97fe1efcb9de2e05b3e1835 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:13:46 +0200 Subject: [PATCH 115/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 66 ++++++++++--------- 1 file changed, 35 insertions(+), 31 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 0cb8fa7627bac7..4362f3ba3a29c6 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -42,37 +42,41 @@ contributions: Welcome to the FAIR-by-Design Methodology Microlearning GTN tutorial. -Below are the main stages of the FAIR-by-Design Methodology that will help guide you on your journey of creating FAIR learning materials. - -The FAIR-by-Design Methodology is defined into [a number of stages](#main-stages) that help you incorporate the FAIR principles into the backward learning instructional design process so that the final output are FAIR learning materials from both learners and instructors perspective: - -1. [Prepare](#stage-1---prepare) - - Do you understand FAIR and its implications - - Define purpose, learning objectives, target audience -2. Discover - - Find existing resources - - Identify potential for reuse -3. Design - - Define the syllabus and structure - - Identify granularity - - Define facilitation materials -4. Produce - - Develop content using common apps and file formats - - Define machine readable metadata - - Perform internal QA check -5. Publish - - Define license and other related info - - Release for instructors and learners - - Enable feedback gathering -6. Verify - - Final QA check - - Use gathered feedback for continuous improvement -7. Continuous Improvement - - Create a list of potential improvements - - Choose a set of improvements to be implemented - - Start a new release cycle - -Review each stage and the essential steps that it includes. +> +> +>Below are the main stages of the FAIR-by-Design Methodology that will help guide you on your journey of creating FAIR learning materials. +> +>The FAIR-by-Design Methodology is defined into [a number of stages](#main-stages) that help you incorporate the FAIR principles into the backward learning instructional design process so that the final output are FAIR learning materials from both learners and instructors perspective: +> +>1. [Prepare](#stage-1---prepare) +> - Do you understand FAIR and its implications +> - Define purpose, learning objectives, target audience +>2. Discover +> - Find existing resources +> - Identify potential for reuse +>3. Design +> - Define the syllabus and structure +> - Identify granularity +> - Define facilitation materials +>4. Produce +> - Develop content using common apps and file formats +> - Define machine readable metadata +> - Perform internal QA check +>5. Publish +> - Define license and other related info +> - Release for instructors and learners +> - Enable feedback gathering +>6. Verify +> - Final QA check +> - Use gathered feedback for continuous improvement +>7. Continuous Improvement +> - Create a list of potential improvements +> - Choose a set of improvements to be implemented +> - Start a new release cycle +> +>Review each stage and the essential steps that it includes. +> +{: .agenda} If you have any questions at any stage on your journey do not hesitate to contact the FAIR-by-Design methodology team. From 0df978250cbe8c9d40229e093e70a885c3a9346b Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:17:06 +0200 Subject: [PATCH 116/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 4362f3ba3a29c6..59fe0ece03038f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -51,25 +51,25 @@ Welcome to the FAIR-by-Design Methodology Microlearning GTN tutorial. >1. [Prepare](#stage-1---prepare) > - Do you understand FAIR and its implications > - Define purpose, learning objectives, target audience ->2. Discover +>2. [Discover](#stage-2---discover) > - Find existing resources > - Identify potential for reuse ->3. Design +>3. [Design](#stage-3---design) > - Define the syllabus and structure > - Identify granularity > - Define facilitation materials ->4. Produce +>4. [Produce](#stage-4---produce) > - Develop content using common apps and file formats > - Define machine readable metadata > - Perform internal QA check ->5. Publish +>5. [Publish](#stage-5---publish) > - Define license and other related info > - Release for instructors and learners > - Enable feedback gathering ->6. Verify +>6. [Verify](#stage-6---verify) > - Final QA check > - Use gathered feedback for continuous improvement ->7. Continuous Improvement +>7. [Continuous Improvement](#stage-7---continuous-improvement) > - Create a list of potential improvements > - Choose a set of improvements to be implemented > - Start a new release cycle From e847338bd9fd56ab4388108e81489ea9a88a6d57 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:20:27 +0200 Subject: [PATCH 117/262] add fbd image --- topics/contributing/images/methodology.png | Bin 0 -> 59332 bytes .../tutorials/fair-by-design/tutorial.md | 2 ++ 2 files changed, 2 insertions(+) create mode 100644 topics/contributing/images/methodology.png diff --git a/topics/contributing/images/methodology.png b/topics/contributing/images/methodology.png new file mode 100644 index 0000000000000000000000000000000000000000..903dfdef5bbb15eafc2340378c6c91a115a26e20 GIT binary patch literal 59332 zcmeFZWpEtH5-uv%h?&{4n3tGc(`W-LvPNi1+XP zdl7dcI;y*(GP^RXDl;qV>xocOkV1mThX(@#Lz4a?t^x)IF$D$&o(zBh)o6WDjsO+l z&MH!(V815_k3bI|rdrZw^73G`pnCuq6gWN@^j}RtmmoO7fA1y1slg!st_Sf6vjl_s 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z9kSCaXNSBUmE*DBG=1p^A&ws$@IjsB9YE*pJP8Yw-#f#8gA+{q`(U$KUFsBWQKnjb_9$!iSt%D|Ir~r|#nW zttST&9|nz)h6eR2(ai=tsD4l;t5FHkdF6=Q(T*Pa>+t`a4bZh+ZD@fWR(7)3 zei{s$WN@5Q&mQux6qd;3SH5F;wIELQspKRg5B2|K+&jp&AkJV&gcaIS+CEm`l!~>A z`VY?ZrUE>Lxig*0xsjcIl^p0lukv}H`e^MKXFT=k_Q-sA|GMV%e|ccM1QR?@QObW^Gs3WRbBYae_+R`Esm4Vaj{g5E`G4_B?g_icBSA9d SI7MivOG!apzEaja^nU;nRvK^s literal 0 HcmV?d00001 diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 59fe0ece03038f..44e020bc41de6f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -46,6 +46,8 @@ Welcome to the FAIR-by-Design Methodology Microlearning GTN tutorial. > >Below are the main stages of the FAIR-by-Design Methodology that will help guide you on your journey of creating FAIR learning materials. > +>![FAIR-by-Design Methodology Stages](../../images/methodology.png) +> >The FAIR-by-Design Methodology is defined into [a number of stages](#main-stages) that help you incorporate the FAIR principles into the backward learning instructional design process so that the final output are FAIR learning materials from both learners and instructors perspective: > >1. [Prepare](#stage-1---prepare) From 719c25a1cbb47f10bb0ea67ee96c3d32f451f1d9 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:29:02 +0200 Subject: [PATCH 118/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 44e020bc41de6f..3174f775c55768 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -78,6 +78,8 @@ Welcome to the FAIR-by-Design Methodology Microlearning GTN tutorial. > >Review each stage and the essential steps that it includes. > +>Essential information about this microlearning unit can be found in the [About](#about) section. +> {: .agenda} If you have any questions at any stage on your journey do not hesitate to contact the FAIR-by-Design methodology team. @@ -825,3 +827,69 @@ After the Verify stage, you will reenter continuous improvement with newly gathe # About +## FAIR-by-Design Microlearning + +### Self-paced how to FAIR-by-Design guide + +### Original Location + +- online: [https://fair-by-design-methodology.github.io/microlearning/latest/](https://fair-by-design-methodology.github.io/microlearning/latest/) +- this tutorial is an adapted version of the original microlearning guide + +### Training Description + +Short how to guide that guides you through the stages of the FAIR-by-Design methodology without any specific choice on tools and formats. + +### Target audience + +All interested parties who need to develop learning materials for any type of project-related training. + +### Expertise Level / Skill Level: Beginner + +### Primary Language: English + +### Access Cost: No + +### Prerequisites + +No prior knowledge is required. + +### Learning Objectives + +- Structure FAIR learning materials +- Create and publish FAIR-by-Design learning materials +- Assess FAIR-ness of learning objects + +### Keywords + +FAIR, learning objects, methodology, practical implementation + +### Certification Information + +This training has no certification or any recognition mechanism included. + +### Author(s) + +- Sonja Filiposka, Dominique Green, Anastas Mishev, Vojdan Kjorveziroski, Andrea Corleto, Eleornora Napolitano, Gabriella Paolini, Sara di Giorgio, Joanna Janik, Luca Schirru, Arnaud Gingold, Christine Chardosek, Irakleitos Souyioultzoglou, Carolin Leister, Emma Lazzeri + + +### Contact information + +- For more information please contact the T2.3 FAIR-by-Design Methodology Task Leader Sonja Filiposka using [sonja.filiposka@finki.ukim.mk](mailto:sonja.filiposka@finki.ukim.mk). + +### License + +Creative Commons License
    This work is licensed under a Creative Commons Attribution 4.0 International License. + +### DOI + +[https://doi.org/10.5281/zenodo.11548062](https://doi.org/10.5281/zenodo.11548062) + +### Accessibility Mission + +Skills4EOSC is dedicated to ensuring that all produced learning materials are accessible to as many visitors as possible regardless of their ability or technology. We have an active commitment to increasing our learning materials accessibility. The main standards that we aim to comply with are WCAG v.2.1 Level AA criteria and PDF/UA (ISO 14289). + +#### Acknowledgement + +These learning materials have been developed by following the [FAIR-by-Design Methodology](https://zenodo.org/records/8305540). + From b9ef9c9b124a9151828b103d105f22d95ded2bb1 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:39:19 +0200 Subject: [PATCH 119/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 32 ++++++++----------- 1 file changed, 13 insertions(+), 19 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 3174f775c55768..2d3442c4caf4b4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -1,33 +1,26 @@ --- layout: tutorial_hands_on -title: FAIR-by-design methodology +title: FAIR-by-Design methodology abbreviations: FAIR: Findable, Accessible, Interoperable, Reusable zenodo_link: https://zenodo.org/records/11548062 questions: - How to develop FAIR learning materials? + - How to incorporate the FAIR principles in the instructional design process? objectives: - - Define FAIR learning objects - - Adapt and mix FAIR learning objects - - Identify licenses and attribute correspondingly - - Structure comprehensive learning materials - - Manage file formats and tools - - Define metadata using a schema + - Design FAIR learning materials + - Structure FAIR learning materials - Create and publish FAIR-by-Design learning materials - - Collaborate with other instructors - - Assess FAIR-ness of existing learning objects -time_estimation: 60M + - Assess FAIR-ness of learning objects +time_estimation: 20M key_points: - - FAIR data are data which meet principles of findability, accessibility, interoperability, and reusability (FAIR). - - FAIR data are as open as possible, and as closed as necessary. - - The main objective of FAIR data is to increase data reuse by researchers. + - The FAIR-by-Design Methodology ensures that the output of the instructional design process are FAIR learning materials. + - Each stage of the FAIR-by-Design Methodology incorporates specific parts of the FAIR principles. + - The ouput of the FAIR-by-Design Methodology are FAIR learning materials from both the perspective of instructors and of learners. tags: - 'FAIR-by-Design Learning Materials' - "FAIR Learning Objects" - - FAIR - - Metadata - - Learning objectives - - Blooms taxonomy + - FAIR-by-Design Methodology priority: 1 contributions: authorship: @@ -856,6 +849,7 @@ No prior knowledge is required. ### Learning Objectives +- Design FAIR learning materials - Structure FAIR learning materials - Create and publish FAIR-by-Design learning materials - Assess FAIR-ness of learning objects @@ -877,11 +871,11 @@ This training has no certification or any recognition mechanism included. - For more information please contact the T2.3 FAIR-by-Design Methodology Task Leader Sonja Filiposka using [sonja.filiposka@finki.ukim.mk](mailto:sonja.filiposka@finki.ukim.mk). -### License +### Original License Creative Commons License
    This work is licensed under a Creative Commons Attribution 4.0 International License. -### DOI +### Original microlearning unit DOI [https://doi.org/10.5281/zenodo.11548062](https://doi.org/10.5281/zenodo.11548062) From 95f79d77ac1726ce6e1354c01bae6cc80d531a39 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:57:32 +0200 Subject: [PATCH 120/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 2d3442c4caf4b4..783b7efebccf01 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -862,9 +862,9 @@ FAIR, learning objects, methodology, practical implementation This training has no certification or any recognition mechanism included. -### Author(s) +### Original Author(s) -- Sonja Filiposka, Dominique Green, Anastas Mishev, Vojdan Kjorveziroski, Andrea Corleto, Eleornora Napolitano, Gabriella Paolini, Sara di Giorgio, Joanna Janik, Luca Schirru, Arnaud Gingold, Christine Chardosek, Irakleitos Souyioultzoglou, Carolin Leister, Emma Lazzeri +- Sonja Filiposka, Dominique Green, Anastas Mishev, Vojdan Kjorveziroski, Andrea Corleto, Eleonora Napolitano, Gabriella Paolini, Sara di Giorgio, Joanna Janik, Luca Schirru, Arnaud Gingold, Christine Chardosek, Irakleitos Souyioultzoglou, Carolin Leister, Emma Lazzeri ### Contact information From 4bed2df41181e72e69e180a793e8ceaae44b3724 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 12:57:37 +0200 Subject: [PATCH 121/262] Update tutorial.bib --- .../tutorials/fair-by-design/tutorial.bib | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index 1be16d219c0901..f39a7080d69aa4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -7,3 +7,16 @@ @article{hoebelheinrich_2022 publisher={Zenodo}, doi={10.15497/RDA00073} } + +@misc{filiposka_2024_11548062, + author = {Filiposka, Sonja and + Mishev, Anastas and + Leister, Carolin}, + title = {FAIR-by-Design Microlearning}, + month = jun, + year = 2024, + publisher = {Zenodo}, + version = {1.0.0}, + doi = {10.5281/zenodo.11548062}, + url = {https://doi.org/10.5281/zenodo.11548062} +} \ No newline at end of file From 8fbfe156296bcbbde8ac44f876820d33c9bb34c4 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 9 Aug 2024 13:16:55 +0200 Subject: [PATCH 122/262] Create FAQ1.md --- .../contributing/tutorials/fair-by-design/faqs/FAQ1.md | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 topics/contributing/tutorials/fair-by-design/faqs/FAQ1.md diff --git a/topics/contributing/tutorials/fair-by-design/faqs/FAQ1.md b/topics/contributing/tutorials/fair-by-design/faqs/FAQ1.md new file mode 100644 index 00000000000000..87053abffb1a0c --- /dev/null +++ b/topics/contributing/tutorials/fair-by-design/faqs/FAQ1.md @@ -0,0 +1,10 @@ +--- +title: How does one convert RAW files to MGF peak lists within Galaxy? +box_type: tip +layout: faq +contributors: [millen2223] +redirect_from: + - /topics/proteomics/faqs/convert_to_MGF +--- + +Galaxy has implemented msconvert tool so that RAW files from Thermo instruments can be converted into MGF or mzML formats. From c537e6cf6810f13d7b1d7ff2f4da00b1f7fc619f Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 10:30:19 +0200 Subject: [PATCH 123/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 783b7efebccf01..74a49c82d90661 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -29,6 +29,15 @@ contributions: - korvoj funding: - skills4eosc +follow_up_training: + - type: external + title: Skill4EOSC FAIR-by-design Methodology Training of Trainers + link: "https://learning.skills4eosc.eu/course/view.php?id=19" +lang: "en" +level: "Introductory" +extra: + - target_audience: "Instructional designers" + --- From c9250e99b689122a19c4cb2bf7d8a6ccc4c5fae9 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 10:32:22 +0200 Subject: [PATCH 124/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 74a49c82d90661..884aad3f3f54a7 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -30,7 +30,7 @@ contributions: funding: - skills4eosc follow_up_training: - - type: external +- type: external title: Skill4EOSC FAIR-by-design Methodology Training of Trainers link: "https://learning.skills4eosc.eu/course/view.php?id=19" lang: "en" From 797e8a4c6ad8a883b2626a1db2715ff59206e9ac Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 10:33:29 +0200 Subject: [PATCH 125/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 884aad3f3f54a7..db32e4c80278a4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -30,7 +30,7 @@ contributions: funding: - skills4eosc follow_up_training: -- type: external +- type:external title: Skill4EOSC FAIR-by-design Methodology Training of Trainers link: "https://learning.skills4eosc.eu/course/view.php?id=19" lang: "en" From 1fbd2da875a29ff1fc91b9c1cbeeb9fd707983a6 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 10:36:07 +0200 Subject: [PATCH 126/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index db32e4c80278a4..ce431e0e18ba49 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -30,9 +30,10 @@ contributions: funding: - skills4eosc follow_up_training: -- type:external - title: Skill4EOSC FAIR-by-design Methodology Training of Trainers - link: "https://learning.skills4eosc.eu/course/view.php?id=19" + - type: internal + topic_name: genome-annotation + tutorials: + - repeatmasker lang: "en" level: "Introductory" extra: From f8dc420b1b0de5e93284c037a9b86ba8c17ec373 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 10:37:51 +0200 Subject: [PATCH 127/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index ce431e0e18ba49..1dcaaf0a0bbe01 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -30,10 +30,9 @@ contributions: funding: - skills4eosc follow_up_training: - - type: internal - topic_name: genome-annotation - tutorials: - - repeatmasker + - type: external + title: Skill4EOSC FAIR-by-design Methodology Training of Trainers + link: "https://learning.skills4eosc.eu/course/view.php?id=19" lang: "en" level: "Introductory" extra: From 9bdba256053b5953a22a60bcd78da803f89d5ce6 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 10:39:57 +0200 Subject: [PATCH 128/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 1dcaaf0a0bbe01..6d3270f0e86212 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -36,7 +36,7 @@ follow_up_training: lang: "en" level: "Introductory" extra: - - target_audience: "Instructional designers" + target_audience: "Instructional designers" --- From bebd32afc6b727c8493947f0c4ecee9a9e2a5665 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 10:41:07 +0200 Subject: [PATCH 129/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 6d3270f0e86212..23052f6b3e2986 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -35,10 +35,8 @@ follow_up_training: link: "https://learning.skills4eosc.eu/course/view.php?id=19" lang: "en" level: "Introductory" -extra: - target_audience: "Instructional designers" - - +extra: + target_audience: "Instructional designers" --- From 06618b2faf90434524f8998767763aff590cd029 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 10:50:10 +0200 Subject: [PATCH 130/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 23052f6b3e2986..870590905cf63c 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -36,7 +36,12 @@ follow_up_training: lang: "en" level: "Introductory" extra: + description: "Short how to guide that guides you through the stages of the FAIR-by-Design methodology without any specific choice on tools and formats." target_audience: "Instructional designers" + URL_resource_type: "Permanent URL" + learning_resource_type: "self-paced microlearning unit" + access_cost: "No" + attribution: "This microlearning unit is based on Filiposka, Sonja, Mishev, Anastas. (2024). FAIR-by-Design Microlearning (1.0.0). https://doi.org/10.5281/zenodo.11548062" --- From 7cdddcc5ab2a0ca16def7f27d17a049d7737d0a8 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 11:07:45 +0200 Subject: [PATCH 131/262] Update tutorial.bib --- .../tutorials/fair-by-design/tutorial.bib | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index f39a7080d69aa4..a13549fc193243 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -19,4 +19,33 @@ @misc{filiposka_2024_11548062 version = {1.0.0}, doi = {10.5281/zenodo.11548062}, url = {https://doi.org/10.5281/zenodo.11548062} +} + +@misc{filiposka_2023_8305540, + author = {Filiposka, Sonja and + Green, Dominique and + Mishev, Anastas and + Kjorveziroski, Vojdan and + Corleto, Andrea and + Napolitano, Eleonora and + Paolini, Gabriella and + Di Giorgio, Sara and + Janik, Johanna and + Schirru, Luca and + Gingold, Arnaud and + Hadrossek, Christine and + Souyioultzoglou, Irakleitos and + Leister, Carolin and + Pavone, Gina and + Sharma, Saba and + Mendez Rodriguez, Eva Maria and + Lazzeri, Emma}, + title = {{D2.2 Methodology for FAIR-by-Design Training + Materials}}, + month = aug, + year = 2023, + publisher = {Zenodo}, + version = {1.4}, + doi = {10.5281/zenodo.8305540}, + url = {https://doi.org/10.5281/zenodo.8305540} } \ No newline at end of file From 3e7bde1bda73419118e08b6a82857487bf427670 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 11:07:50 +0200 Subject: [PATCH 132/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 870590905cf63c..a63fe9e71cce4f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -45,15 +45,15 @@ extra: --- -Welcome to the FAIR-by-Design Methodology Microlearning GTN tutorial. +Welcome to the FAIR-by-Design Methodology Microlearning GTN adapted tutorial. > > ->Below are the main stages of the FAIR-by-Design Methodology that will help guide you on your journey of creating FAIR learning materials. +>Below are the main stages of the FAIR-by-Design Methodology {% cite filiposka_2023_8305540 %} that will help guide you on your journey of creating FAIR learning materials. > ->![FAIR-by-Design Methodology Stages](../../images/methodology.png) +>![Visual representation of the FAIR-by-Design Methodology flow with its separate stages](../../images/methodology.png) > ->The FAIR-by-Design Methodology is defined into [a number of stages](#main-stages) that help you incorporate the FAIR principles into the backward learning instructional design process so that the final output are FAIR learning materials from both learners and instructors perspective: +>The FAIR-by-Design Methodology is defined in [a number of stages](#main-stages) that help you incorporate the FAIR principles into the backward learning instructional design process so that the final output are FAIR learning materials from both learners and instructors perspective: > >1. [Prepare](#stage-1---prepare) > - Do you understand FAIR and its implications @@ -83,7 +83,7 @@ Welcome to the FAIR-by-Design Methodology Microlearning GTN tutorial. > >Review each stage and the essential steps that it includes. > ->Essential information about this microlearning unit can be found in the [About](#about) section. +>Essential information about the original microlearning unit that this adaptation is based on can be found in the [About](#about) section. > {: .agenda} @@ -121,6 +121,12 @@ May all your materials be FAIR! >The learning material has a clear usage license (CC-BY-4.0 recommended) and accurate information on provenance. {: .solution } +> More details on the FAIR principles ... +> [Follow the FAIR in a nutshell tutorial available on GTN]( {% link topics/fair/tutorials/fair-intro/tutorial.md %} ) +> +> [Follow the FAIR Galaxy Training Material tutorial available on GTN]( {% link topics/fair/tutorials/fair-gtn/tutorial.md %} ) +{: .details} + ### Adopt a metadata schema The RDA Minimal Metadata Set for Learning Resources From f6c6a533611d5803bf92e60f240648f1d2dda448 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 11:23:04 +0200 Subject: [PATCH 133/262] Update tutorial.bib --- topics/contributing/tutorials/fair-by-design/tutorial.bib | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index a13549fc193243..e02cee25b764cb 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -40,8 +40,8 @@ @misc{filiposka_2023_8305540 Sharma, Saba and Mendez Rodriguez, Eva Maria and Lazzeri, Emma}, - title = {{D2.2 Methodology for FAIR-by-Design Training - Materials}}, + title = {D2.2 Methodology for FAIR-by-Design Training + Materials}, month = aug, year = 2023, publisher = {Zenodo}, From 60e90c0218f2723752ee58acbfae5ead4b7a07c6 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 11:23:07 +0200 Subject: [PATCH 134/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 24 +++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index a63fe9e71cce4f..8e71fceb2bc1e8 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -128,7 +128,12 @@ May all your materials be FAIR! {: .details} ### Adopt a metadata schema - The RDA Minimal Metadata Set for Learning Resources + +If you are not using a discipline specific metadata schema, then, to ensure that your learning materials are appropriately described using a common approach, you should adopt the: + + Go to the RDA Minimal Metadata Set for Learning Resources description details + +The following are the fields described in the RDA Minimal Metadata Set divided into three categories: > Descriptive info metadata fields > - **Title** = The human readable name of the resource @@ -153,14 +158,25 @@ May all your materials be FAIR! > - **Expertise (Skill) Level** = Target skill level in the topic being taught; example values include beginner, intermediate, advanced {: .details} -More on the metadata here {% cite hoebelheinrich_2022 %} +More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} + +> Using metadata in GTN tutorials ... +> +>- When developing materials in GTN, this information should be included in the Tutorial.md file header metadata. +>- Most of the fields are already defined in the GTN Tutorial metadata schema. The ones that are missing can be added using the "extra" field. +> +> > More details on the GTN Metadata ... +> > [Follow the GTN Metadata tutorial]( {% link topics/fair/tutorials/contributing/tutorials/schemas/tutorial.md %} ) +> {: .details} +> +{: .tip} ->More on FAIR learning objects definition: +>Learn more about FAIR learning objects ... >- [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) >- [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) >- [FAIR learning objects](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-learning-objects) -{: .tip} +{: .details} ### Start Ideating... From e9c40a42e7f5900ed2c98a73b79e3c35be50aa81 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 11:32:20 +0200 Subject: [PATCH 135/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 8e71fceb2bc1e8..980b551de3d01c 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -160,13 +160,13 @@ The following are the fields described in the RDA Minimal Metadata Set divided i More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} -> Using metadata in GTN tutorials ... +> Using metadata in GTN tutorials > >- When developing materials in GTN, this information should be included in the Tutorial.md file header metadata. >- Most of the fields are already defined in the GTN Tutorial metadata schema. The ones that are missing can be added using the "extra" field. > > > More details on the GTN Metadata ... -> > [Follow the GTN Metadata tutorial]( {% link topics/fair/tutorials/contributing/tutorials/schemas/tutorial.md %} ) +> > [Follow the GTN Metadata tutorial]( {% link topics/contributing/tutorials/schemas/tutorial.md %} ) > {: .details} > {: .tip} @@ -198,7 +198,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %}
    Think backward
    Step 2
    -

    How are you going to assess their achievement....

    +

    How are you going to assess the learners achievement....

    @@ -208,17 +208,17 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %}
    Think backward
    Step 3
    -

    How should you structure the material to reach them...

    +

    How should you structure the material to provide effective learning experience...

    ->More on backward learning: +>Learn more about the backward learning process ... > - [Steps of the backward learning process](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#backward-instructional-design-process) {: .tip } -### Define. +### Define: > Purpose > When and how the learning materials can be used and for what purposes? @@ -247,10 +247,14 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > >Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. > {: .tip} > -> [See more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) +> [Read more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) {: .question } -Go to FAIR-by-Design Methodology: Prepare stage.... +> More details on ideating learning outcomes and related information ... +> [Follow the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md %} ) +{: .details} + +Go to the full description of FAIR-by-Design Methodology: Prepare stage.... ## Stage 2 - Discover > Greater even than the greatest discovery is to keep open the way to future discovery. From dc28907f2ad7432fe240960ba3a5559fb3faa703 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 11:46:44 +0200 Subject: [PATCH 136/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 980b551de3d01c..beffb7152a5574 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -3,6 +3,9 @@ layout: tutorial_hands_on title: FAIR-by-Design methodology abbreviations: FAIR: Findable, Accessible, Interoperable, Reusable + OER: Open Educational Repositories + EOSC: European Open Science Cloud + CC: Creative Commons zenodo_link: https://zenodo.org/records/11548062 questions: - How to develop FAIR learning materials? @@ -257,10 +260,18 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} Go to the full description of FAIR-by-Design Methodology: Prepare stage.... ## Stage 2 - Discover + > Greater even than the greatest discovery is to keep open the way to future discovery. {: .quote author="John Jacob Abel"} ### Get inspired + Reusable materials can be found anywhere. These are just some examples: + +> GTN +> [GTN learning resources](https://training.galaxyproject.org) +> [TeSS Catalogue by Elixir](https://tess.elixir-europe.com) +{: .code-in} + > OER > [DOAB](https://directory.doabooks.org/) > [MERLOT](https://www.merlot.org/merlot/index.htm) @@ -287,14 +298,15 @@ Reusable materials can be found anywhere. These are just some examples: ### Potential for reuse > Respect the licenses, to be respected! -> Materials with non-permissible licenses can be used for inspiration only. Materials with permissible licenses should be reused based on the license rules. +> - Materials with non-permissible licenses can be used for inspiration only. +> - Materials with permissible licenses should be reused based on the license rules. {: .warning} ### Don't forget the multimedia search -Different learners have different learning modalities (read/write, auditory, visual, kinesthetic). You should use all types of multimedia in your learning materials. +Different learners have different learning modalities (read/write, auditory, visual, kinesthetic). To elevate the learning experience you should use all types of multimedia in your learning materials. -Go to FAIR-by-Design Methodology: Discover stage.... +Go to the full description of FAIR-by-Design Methodology: Discover stage.... ## Stage 3 - Design > Design is intelligence made visible. 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zwKU}5iW}=YZVCty#IMfJB+%rev1gO^*L%Yra$^qzMZA-2=?0*2dC@&X%cri|)@_Kg zoMfTa?NBaS5sMU8c#UrO+o15vo=sfp`kF~rT=DJvU^>)HvlV#CxM7MgRnME$5ey12 z%eVT(!#NbI6Z%v|tOw+jCn?s>1L8znfGQK&9r5X=k5^Aykd$4mAcOOLfw zJglD$&{y0a+PIX|Uzi@V4KT0T)~u(Oszg+V1XXm;9-fJ`rJ1GjbJ)nOUrMd6QewYj z6k`_fY>p?GF1EwjZ6TOe<6+~3A{}|sxK!YvUF*za`z;%ItMpT>%Q!x4oa|JH1Ra1MTDXXDAhHrgAd*~3sk%O7~LW2FBpy7GrXS|~~o>^6} z^-JwxS6h_d!b!ZkeYYjT+x)U|q7-P+Gr@}gk$$d;rnvd6A?t8!>^!MuCt*7sMD@EpnZ z^G{$kV=HLJA=3F#o50NXukun}tp2JJK7sBHE$&NgLJgY`O=rl1{TiWevyAphO<@Mj zXAl$3kao|2^VAj059q5g{VgQK+5hG3eSw|p5v3q#G`ym_Y8Lmp)>8uM7x)^zG}z_r z^afUa%}Yyc5Z!VNiW3{I!Z(Z3#lCvaxdoeBs-B4IGtSdD&f{kj&X|BVVpvXd4hG`3 zq2SEkNlSZ9JzQHS>%l%#OgNS>XT7o;VN0t>=69SHRSV{BOMasLNm6Mc5%=SkC@4(W zCQl6vwz)WT+c^F?*x7f$$pLxb>6wzKP2USXuJS83-fNrL&MC8uc_HAO-wwm7R}HP0 zlA&@)HBcQ);OIUougQ)#9*-Nr^T5qL;njvqFrT|rE!mOBrn&l7;P>q*=2NBmZj|67 zWmB$CwVv9Ha_WyFCbh;Vx6WM7W83=mf0i)+)+vc|{~oS?|Frqve&oagM8y9CZgnY= From 3a68683495343c4f1288a02595ab9e570ce76d85 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 11:58:56 +0200 Subject: [PATCH 138/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 29 ++++++++++++------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index beffb7152a5574..25798751306ba0 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -6,6 +6,7 @@ abbreviations: OER: Open Educational Repositories EOSC: European Open Science Cloud CC: Creative Commons + MVS: Minimum Viable Skills zenodo_link: https://zenodo.org/records/11548062 questions: - How to develop FAIR learning materials? @@ -254,7 +255,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} {: .question } > More details on ideating learning outcomes and related information ... -> [Follow the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md %} ) +> [Read about defining intended Learning Outcomes in the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md#define-intended-learning-outcomes-los %} ) {: .details} Go to the full description of FAIR-by-Design Methodology: Prepare stage.... @@ -269,6 +270,7 @@ Reusable materials can be found anywhere. These are just some examples: > GTN > [GTN learning resources](https://training.galaxyproject.org) +> > [TeSS Catalogue by Elixir](https://tess.elixir-europe.com) {: .code-in} @@ -309,22 +311,27 @@ Different learners have different learning modalities (read/write, auditory, vis Go to the full description of FAIR-by-Design Methodology: Discover stage.... ## Stage 3 - Design + > Design is intelligence made visible. {: .quote author="Alina Wheeler"} -### Time to brainstorm -![Brain image](../../images/brain-3829057_640.jpg) - -
    -Gerd Altmann from Pixabay -     -#### Concept map -Build a concept map of your learning materials aligning with the MVS profiles. -The aligned MVS profile can help you cristalize the learning objectives using MVS taxonomy. +Now it's time to brainstorm... + +### Concept map + +1. Build a concept map of your learning materials. + +> More details on concept maps ... +> [Read about Concept Maps in the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md#concept-maps %} ) +{: .details} + +2. Make sure you align your concept map with the MVS profiles. + +The aligned MVS profile can help you crystalise the learning objectives using the MVS taxonomy. Each MVS profile defines a list of technical and soft skills required for the profile. Think on how to incorporate both aspects in your learning materials. -Go to MVS profiles catalogue +Go to the MVS profiles catalogue ### Structure is everything From 90195793602518969b9389d18ba999fb7aab563e Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 12:30:58 +0200 Subject: [PATCH 139/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 73 +++++++++++-------- 1 file changed, 41 insertions(+), 32 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 25798751306ba0..43a3ed99e10c24 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -319,15 +319,15 @@ Now it's time to brainstorm... ### Concept map -1. Build a concept map of your learning materials. +Step 1: Build a concept map of your learning materials. > More details on concept maps ... > [Read about Concept Maps in the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md#concept-maps %} ) {: .details} -2. Make sure you align your concept map with the MVS profiles. +Step 2: Make sure you align your concept map with the MVS profiles. -The aligned MVS profile can help you crystalise the learning objectives using the MVS taxonomy. +The aligned MVS profile can help you crystallize the learning objectives using the MVS taxonomy. Each MVS profile defines a list of technical and soft skills required for the profile. Think on how to incorporate both aspects in your learning materials. @@ -336,7 +336,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr ### Structure is everything > ->{%icon galaxy-gear %} Create an intuitive logical organisation of all learning materials. +>{%icon galaxy-gear %} Use an intuitive logical organisation of all learning materials. {: .comment} > @@ -344,51 +344,60 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .comment} > ->{%icon galaxy-dataset-map %} Use a hierarchical structure to combine learning units into larger compositions. +>{%icon galaxy-dataset-map %} Take advantage of a hierarchical structure to combine learning units into larger compositions. {: .comment} - >How to organise the files -> The diagram shows how to organise all files in folders and subfolders. Click on the links to discover and use pre-prepared templates. +> +> GTN defines a specific hierarchical structure that needs to be followed when developing learning materials. +> +> > Check out the following tutorials ... +> > [How to create a skeleton for a new learning topic]( {% link topics/contributing/tutorials/create-new-topic/tutorial.md#creating-a-new-topic-with-its-own-materials %} ) +> > +> > [How to create the skeleton of a new tutorial]( {% link topics/contributing/tutorials/create-new-tutorial/tutorial.md %} ) +> {: .details} +> {: .hands-on} -``` -├── README -├── CITATION.cff -├── LICENCE -├── resources -├───├── attachments -│ ├── Learning Unit1 -├───├───├── attachments -│ │ ├── assesment -│ │ ├── activities -│ ├── Learning Unit2 - -``` - >Syllabus is ready -> You should by now have the first draft of your syllabus. It contains all the fields from the RDA min metadata set plus the high level topics covered by the learning material. +> You should by now have the first draft of your syllabus. It contains all the fields from the RDA min metadata set plus the high level topics covered by the learning material. {: .comment} >Available feedback form -> The feedback form template is ready to be used as is. All you need to do is change the name of the training. It should be shared with training participants after the training, to gather quantitative and qualitative feedback. -{: .tip} - ->Available facilitation guide kit -> The facilitation guide should help prepare for the actual training. If you don't want to develop your own, use something that is already available such as the [TRIPLE project TRAINING TOOLKIT](https://project.gotriple.eu/project-deliverables/triple-training-toolkit/). +> GTN provides a readily available feedback form that is automatically added at the end of each tutorial. The feedback form is used to gather quantitative and qualitative feedback. +> +> > Learn more about feedback in training ... +> > [Follow the Assessment and feedback in training and teachings tutorial available on GTN]( {% link topics/teaching/tutorials/assessment/tutorial.md#dealing-with-feedback %} ) +> {: .details} +> {: .tip} ->Don't worry, we got you covered with templates -> All templates are readily available for use in the specialised [templates repository](https://github.com/FAIR-by-Design-Methodology/templates). See the detailed training on how to use it step by step. +>Facilitation guide kit +> A facilitation guide should help prepare for the actual training. +> +> The facilitation guide kit includes documentation of the process of organising and running a training. What different people need to have, know and do so that everything runs smoothly. +> +> > Learn more about facilitation ... +> > [Follow the Organizing a workshop tutorial available on GTN]( {% link topics/teaching/tutorials/organize-workshop/tutorial.md %} ) +> > +> > [Follow the Running a workshop as instructor tutorial available on GTN]( {% link topics/teaching/tutorials/running-workshop/tutorial.md#Checklists %} ) +> {: .details} +> +> Another option is to use something like the [TRIPLE project TRAINING TOOLKIT](https://project.gotriple.eu/project-deliverables/triple-training-toolkit/). +> {: .tip} >What about instructor notes? -> Need to be detailed enough so that anyone can reuse the slides properly. Don't put them in the slide deck. This is what the learning content file is for. +> They need to be detailed enough so that anyone can reuse the learning content, especially slides properly. +> +> Any specific information relevant for instructors that would like to organise a training based on your GTN tutorial content should be added in Details box. +> +> This practice significantly increases the reuse potential of the material. {: .question} ### How to develop the learning content -Use the Hunter Model +Read more about the Hunter Model ...
    @@ -489,7 +498,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -Go to FAIR-by-Design Methodology: Design stage.... +Go to the full description of FAIR-by-Design Methodology: Design stage.... ## Stage 4 - Produce From 8ae27fe61b0a61e39fc3ee1bf34de5357e2a51a9 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 13:36:23 +0200 Subject: [PATCH 140/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 75 ++++++++++++------- 1 file changed, 49 insertions(+), 26 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 43a3ed99e10c24..852c7ae46991ac 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -395,7 +395,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr > This practice significantly increases the reuse potential of the material. {: .question} -### How to develop the learning content +### How to design the learning content Read more about the Hunter Model ... @@ -507,27 +507,44 @@ Each MVS profile defines a list of technical and soft skills required for the pr ### Choose Tools & Formats > Collaborative environment for team work -> Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. Two examples are workplace or GitHub (find out more here). Replicate the folder tree in the environment and start using the provided templates to generate the content. +> Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. +> +> - GitHub is one of the most popular options at the moment (find out more here) +> - GTN is also based on GitHub and defines specific procedures on how one can contribute and collaborate using GitHub +> +> > GTN: collaboration using GitHub ... +> > [Follow the Contributing with GitHub via its interface tutorial available on GTN]( {% link topics/contributing/tutorials/github-interface-contribution/tutorial.md %} ) +> > +> > [Follow the Contributing with GitHub via command-line tutorial available on GTN]( {% link topics/contributing/tutorials/github-command-line-contribution/tutorial.md %} ) +> {: .details} {: .tip} > Granular versioning for easy rollback -> Versioning helps you maintain control over your changes. If the collaborative environment does not provide versioning and history retention then keep a history of the files by adopting a naming convention such as combining the file name with an increasing version number. +> - Versioning helps you maintain control over your changes. +> - GitHub natively provides versioning and history retention that help easy roll back to an earlier stable state. {: .tip} > Open file formats to foster reuse -> For other people to reuse your materials they should be made available using open file formats (docx, pptx, pdf, md, html, etc.). If you use close file formats then you MUST clearly state the tools that have been used for development in your README file. +> - For other people to reuse the materials they should be made available using open file formats +> - GTN promotes the use of the MD open file format for the main learning content empowered with open scientific notebooks and workflows. +> - If you use close file formats then you MUST clearly state the tools that have been used in more details. {: .tip} > Multimodal content to reach all audience -> Don't forget to include different types of multimedia to provide support for different learning modalities: read/write, auditory, visual, kinesthetic. +> - Don't forget to include different types of multimedia to provide support for different learning modalities: read/write, auditory, visual, kinesthetic. +> - In addition to hands-on exercises, GTN also provides support for audio and video modalities. {: .tip} > Two file sets: editable + final -> Always work with and keep a history of your editable files. These are what matters for you and other instructors. The second set of final files should be obtained from the editable when needed (before distributing them to the learners). The final files should be kept on the learning platform only. In this way you don't need to worry about keeping the versions in sync. +> - The MD and supporting files are the main files used for development of the content. These files are what matters for you and other instructors. +> - Based on the editable files, GTN automatically generates the final (non-editable version) in HTML (and PDF). These are shared with the learners. +> - GTN takes care of the revision numbering for you. {: .tip} -> Don't forget to support co-creation -> Truly FAIR learning materials should enable co-creation with external parties. If you don't use a collaborative environment that supports this from the start (such as GitHub), then think how are you going to enable this in the future and how are you going to deal with versioning then. +> Don't forget to take advantage of co-creation +> Truly FAIR learning materials enable co-creation with external parties. +> GitHub is a collaborative environment that supports co-creation in every step of the learning materials development and revision process. +> The GTN fork-and-pull process of contributing to the learning material is a clear example of co-creation implementation. {: .tip} @@ -535,20 +552,24 @@ Each MVS profile defines a list of technical and soft skills required for the pr #### Check the license -The existing materials is available under a CC license, but it is different than the one you plan to use for your materials... +The existing materials you are reusing are available under a CC license, but it is different than the one you plan to use for your materials... >I want to reuse it as a whole ->You can't use something that is licensed with ND (no derivatives). In this case you must follow the rules on combining and adapting CC material. +>- You can't use something that is licensed with ND (no derivatives). +>- In this case you must follow the rules on combining and adapting CC material. +> >[Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material) {: .details} >I want to reuse a small part of it -> No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. If the work is licensed with ND, do not modify it while reusing. +> No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. +> +> Remember that if the work is licensed with ND, you can not modify it while reusing. {: .details} ->Learn more about IPR +>Learn more about IPR ... >[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) -{: .details} +{: .tip} [{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) @@ -556,20 +577,24 @@ The existing materials is available under a CC license, but it is different than #### Attribute All CC licenses require that you attribute the author, and this rule is recommended even if the license is public domain CC-0. + If the work you are reusing has a copyright notice ('© some text') you need to reproduce it while you credit the work. + You should also be able to remove attribution upon request. -> Use the authors recommended attribution +##### How to attribute? + +> Use the authors recommended attribution > If the original author has provided a cite-as information, use it to attribute the work. -{: .details} +{: .solution} -> Use TASL +> Use TASL > Provide the Title, Author, Source and License of the work that you are reusing. > >- Source is the URL to the original work. >- If there is a URL to the author personal pages, provide it together with the name. >- Provide the name of the license and a URL to the license. -{: .details} +{: .solution} > Examples > Examples are taken from [Best Practices for Creative Commons attributions - how to attribute works you reuse under a Creative Commons license](https://www.newmediarights.org/guide/how_to/creative_commons/best_practices_creative_commons_attributions) submitted by [New Media Rights](https://www.newmediarights.org/) available under a [CC BY-NC 3.0 US DEED](https://creativecommons.org/licenses/by-nc/3.0/us/) @@ -585,24 +610,22 @@ You should also be able to remove attribution upon request. > - [Comcast protest](http://www.flickr.com/photos/ari/8503459/in/set-214952/)” by Flikr user [Steve Rhodes](http://www.flickr.com/photos/ari/) used under [Creative Commons Attribution 2.0 license](http://creativecommons.org/licenses/by/2.0/deed.en) {: .details} -> Learn more +> Read more about how to attribute ... > [{% icon point-right %} Attribution and Citing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#attribution-and-citing) +> +> [{% icon point-right %} How to handle attribution?](https://courses.lumenlearning.com/suny-oerguide/chapter/how-to-handle-attribution/) {: .details} -[{% icon point-right %} How to handle attribution?](https://courses.lumenlearning.com/suny-oerguide/chapter/how-to-handle-attribution/) - - ### Accessibility > +>![Universal access logo](../../images/universal-access-6602642_640.png) +>
    J S from Pixabay     +> >The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. {: .tip} -![Universal access logo](../../images/universal-access-6602642_640.png) - -
    -J S from Pixabay -     + #### Standards There are several standards that govern the rules on level of accessibility. Three conformance levels exist, you should aim for AA which is the middle one. From 172d1becaa5a6a2df8bc00d7cd64680cbfe0c911 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 13:44:59 +0200 Subject: [PATCH 141/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 28 ++++--------------- 1 file changed, 6 insertions(+), 22 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 852c7ae46991ac..b3e86e4d7ec25f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -626,7 +626,6 @@ You should also be able to remove attribution upon request. {: .tip} - #### Standards There are several standards that govern the rules on level of accessibility. Three conformance levels exist, you should aim for AA which is the middle one. @@ -634,30 +633,15 @@ Most commonly used is the PDF/UA (Universal Accessibility). -Learn more - - -#### Use accessibility evaluation tools! -Accessibility evaluation tools are not perfect. Even if they say that all is ok, it does not mean that your content is truly accessible. But they are a very good starting point. - -> Slides -> Use the integrated accessibility checker in Power Point: -> 1. Open an existing presentation in PowerPoint and review the content. -> 2. Select the Review tab. -> 3. Select Check Accessibility. -> 4. An Accessibility Checker pane will appear on the right with 'Inspection Results' displayed. -{: .details} +#### Accessibility guidelines -> Web content -> Choose from the [Web Accessibility Evaluation Tools List](https://www.w3.org/WAI/test-evaluate/tools/list/) developed by W3C. -{: .details} +General guidelines for development of accessible material -> PDF document -> Check accessibility in Adobe Acrobat Pro. -> -> Open the PDF and then from the All tools menu on the left, select View more and then select Prepare for accessibility. -{: .details} +>GTN Accessibility +> GTN has developed an < href="https://training.galaxyproject.org/training-material/accesibility.html"> accessibility mission aiming for WCAG 2.0 AA compliance by implementing a number of accessibility features. +> +{: .tip} ### Internal QA From db38fbe083e017be0c400aded23f3d7897bd47f8 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 13:49:26 +0200 Subject: [PATCH 142/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b3e86e4d7ec25f..701b938e24d91c 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -685,8 +685,10 @@ PDF document accessibility is measured with a separate technical specification <
    -Go to FAIR-by-Design Methodology: Produce stage.... +Go to the full FAIR-by-Design Methodology: Produce stage.... + ## Stage 5 - Publish + > Publishing is the art of working on a creative idea and turning it into a masterpiece​! {: .quote author="Unknown"} From 977dd2b2ea812ab0bb965715d0e47a921a0beb6c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 14:01:19 +0200 Subject: [PATCH 143/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 701b938e24d91c..14fb3fb38da8bd 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -571,6 +571,8 @@ The existing materials you are reusing are available under a CC license, but it >[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) {: .tip} +Still need help? + [{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) @@ -618,12 +620,11 @@ You should also be able to remove attribution upon request. ### Accessibility -> ->![Universal access logo](../../images/universal-access-6602642_640.png) ->
    J S from Pixabay     -> ->The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. -{: .tip} + +The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. + +![Universal access logo](../../images/universal-access-6602642_640.png) +J S from Pixabay #### Standards @@ -636,10 +637,10 @@ PDF document accessibility is measured with a separate technical specification < #### Accessibility guidelines -General guidelines for development of accessible material +Review some general guidelines for development of accessible material >GTN Accessibility -> GTN has developed an < href="https://training.galaxyproject.org/training-material/accesibility.html"> accessibility mission aiming for WCAG 2.0 AA compliance by implementing a number of accessibility features. +> GTN has developed an accessibility mission aiming for WCAG 2.0 AA compliance by implementing a number of accessibility features. > {: .tip} From 6ebf0de0a6442dd91b3076daa18a8f26d75351ad Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 14:04:31 +0200 Subject: [PATCH 144/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 14fb3fb38da8bd..f470aa0584915e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -640,7 +640,7 @@ PDF document accessibility is measured with a separate technical specification < Review some general guidelines for development of accessible material >GTN Accessibility -> GTN has developed an accessibility mission aiming for WCAG 2.0 AA compliance by implementing a number of accessibility features. +> GTN has developed an accessibility mission aiming for WCAG 2.0 AA compliance by implementing a number of accessibility features. > {: .tip} From 30b87b8d2479d57d71882e5b8f213253c5d3f4f4 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 14:12:57 +0200 Subject: [PATCH 145/262] Update tutorial.bib --- .../tutorials/fair-by-design/tutorial.bib | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.bib b/topics/contributing/tutorials/fair-by-design/tutorial.bib index e02cee25b764cb..11abe45a5c2e55 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.bib +++ b/topics/contributing/tutorials/fair-by-design/tutorial.bib @@ -48,4 +48,23 @@ @misc{filiposka_2023_8305540 version = {1.4}, doi = {10.5281/zenodo.8305540}, url = {https://doi.org/10.5281/zenodo.8305540} +} + +@misc{sanchez_2023_8305482, + author = {Sánchez, Marina and + Méndez, Eva and + Whyte, Angus and + Weisteen Bjerde, Katrine and + Martínez, Sara and + Bueno, Gema and + Ucar, Iñaki}, + title = {{D2.3 Community-endorsed quality assurance and + certification framework for professional training + and qualifications}}, + month = sep, + year = 2023, + publisher = {Zenodo}, + version = {1.3}, + doi = {10.5281/zenodo.8305482}, + url = {https://doi.org/10.5281/zenodo.8305482} } \ No newline at end of file From deef444ee73913ea174bbedf166985a93c258ad0 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 14:13:03 +0200 Subject: [PATCH 146/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 42 ++++++++++--------- 1 file changed, 22 insertions(+), 20 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index f470aa0584915e..0e43a8b5ad060b 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -800,25 +800,26 @@ PDF document accessibility is measured with a separate technical specification < >You are at the point when you should also consider making a record in a relevant training catalogue such as the EOSC training catalogue. {: .tip} -Go to FAIR-by-Design Methodology: Publish stage.... +Go to the full FAIR-by-Design Methodology: Publish stage.... ## Stage 6 - Verify > You will find it a very good practice always to verify your references, sir! {: .quote author="Martin Routh"} ### External QA > A fresh set of eyes -> Have someone who has not participated in the development of the learning materials review the final work. This will guarantee a review free of cognitive bias. +> - Have someone who has not participated in the development of the learning materials review the final work. This will guarantee a review free of cognitive bias. +> - GTN implements this automatically via the fork-and-pull request process. Before publication your new contribution is being reviewed by GTN peers. {: .tip} > Go through the QA checklists -> In Skills4EOSC T2.4 has developed a number of QA checklists that you and your external reviewer need to go through so that you can ensure high-quality learning materials. +> In Skills4EOSC T2.4 has developed a number of QA checklists that you and your external reviewer need to go through so that you can ensure high-quality learning materials {% cite sanchez_2023_8305482 %}. {: .tip} ### FAIR or not FAIR, that is the question... #### Measure FAIRness -Use the FAIR-by-Design methodology QA checklist to check if you have followed the most important aspects of the methodology and managed to produce FAIR learning materials. +Use the [FAIR-by-Design methodology QA checklist](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%206%20–%20Verify/19-Final%20QA%20check/19-finalQA/#fair-by-design-methodology-qa-checklist) to check if you have followed the most important aspects of the methodology and managed to produce FAIR learning materials. The questions marked as essential achieve bare minimum FAIRness. @@ -856,7 +857,7 @@ The questions marked as essential achieve bare minimum FAIRness. > Ensure that you actively and regularly gather feedback from both perspectives: the learners and the instructors. {: .comment} -Go to FAIR-by-Design Methodology: Verify stage.... +Go to the full FAIR-by-Design Methodology: Verify stage.... ## Stage 7 - Continuous Improvement > To improve is to change; to be perfect is to change often @@ -864,35 +865,36 @@ The questions marked as essential achieve bare minimum FAIRness. #### {% icon galaxy-download %} Gather -Gather feedback from all available internal & external sources. +- Gather feedback from all available internal & external sources. -Potential sources: -- Feedback form  -- QA recommendations  -- self-reflection after training  -- Survey  -- Direct mail contact  -- Other means of communication +- Potential sources: + - Feedback form  + - QA recommendations  + - self-reflection after training  + - Git Issues + - Gitter Chat + - Direct mail contact  + - Other means of communication #### {% icon galaxy-barchart %} Analyse -Analyse the gathered information in a structured way. +- Analyse the gathered information in a structured way. -Create a list of potential improvements with impact level (high, moderate, low). +- Create a list of potential improvements with impact level (high, moderate, low). #### {% icon galaxy-wf-edit %} Improve -Select items from the list that will be part of a new version. +- Select items from the list that will be part of a new version. -Choose items that make sense to be in the same new release. +- Choose items that make sense to be in the same new release. #### {% icon galaxy-history-refresh %} Repeat -Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. +- Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. -After the Verify stage, you will reenter continuous improvement with newly gathered information.... +- After the Verify stage, you will reenter continuous improvement with the newly gathered information.... -Go to FAIR-by-Design Methodology: Continuous Improvement stage.... +Go to the full FAIR-by-Design Methodology: Continuous Improvement .... # About From 08f838df06a2ba1ba8a91ccd4368034dd49ea9f9 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 12 Aug 2024 14:17:41 +0200 Subject: [PATCH 147/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 0e43a8b5ad060b..1ae05e24544d8d 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -790,7 +790,7 @@ PDF document accessibility is measured with a separate technical specification <
    -### Store in a repository +### Storing and indexing >Automated publishing >If you are working on GitHub using the provided templates repository then the "publish to Zenodo" step is fully automated for you. Just follow the [guide to publishing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%205%20%E2%80%93%20Publish/17-Zenodo%20Publishing/17-Zenodo%20Publishing/). @@ -870,7 +870,7 @@ The questions marked as essential achieve bare minimum FAIRness. - Potential sources: - Feedback form  - QA recommendations  - - self-reflection after training  + - Self-reflection after training  - Git Issues - Gitter Chat - Direct mail contact  From 8e8ad1c1a53a474bb8ee5998f6ca02a7b915bca1 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 09:44:45 +0200 Subject: [PATCH 148/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 45 ++++++++++--------- 1 file changed, 24 insertions(+), 21 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 1ae05e24544d8d..37ee5db53e9516 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -510,7 +510,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr > Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. > > - GitHub is one of the most popular options at the moment (find out more here) -> - GTN is also based on GitHub and defines specific procedures on how one can contribute and collaborate using GitHub +> - GTN is also based on GitHub and defines [specific procedures on how one can contribute and collaborate]( {% link CONTRIBUTING.md %}) using GitHub > > > GTN: collaboration using GitHub ... > > [Follow the Contributing with GitHub via its interface tutorial available on GTN]( {% link topics/contributing/tutorials/github-interface-contribution/tutorial.md %} ) @@ -696,13 +696,14 @@ PDF document accessibility is measured with a separate technical specification < >Publishing closed FAIR materials > Having FAIR learning materials does not always mean that the materials are open to everyone and there are no costs or access rules attached. In this case the bundle that is going to be published in an open repository such as Zenodo should contain the following: > 1. Syllabus - that contains all metadata that describe the materials and metadata should always be open -> 2. Accompanying files - optional - augment the description of the materials and describe the details when it comes to accessing and using the materials from a trainer perspective -> Another alternative is to publish the materials in a closed repository where the corresponding access rules can be implemented. +> 2. Accompanying information - optional - to augment the description of the materials and describe the details when it comes to accessing and using the materials from a trainer perspective +> +> The complete learning materials package itself should be published in a closed repository where the corresponding access rules (and costs) can be implemented. {: .warning} ### Final preparations ->Time to create the accompanying files ->These are files that are provided in the root of your learning materials and describe the content and define the rules of reuse. +>Time to provide the accompanying information +> Usually provided at (or near) the root of the learning materials, the purpose of the accompanying information is to further describe the content and define the rules of reuse. {: .tip}
    @@ -713,9 +714,11 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon text-document %} LICENSE

    - Plaintext file that defines the license of your learning materials. Just copy paste it from the official CC website. CC-BY-4.0 is the recommended license. + The license defines the potential of reuse of your learning materials together with the rules regarding their attribution by others.
    + CC-BY-4.0 is the recommended license, which is default in GTN.
    + If you choose a different license, it must be supplied in the tutorial header as metadata.
    - {% icon point-right %} CC license + {% icon point-right %} Browse through the available CC license types

    @@ -728,7 +731,7 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon sticky-note %} README

    - A README is a text file that introduces and explains the contents of your learning materials. It usually describes the context and defines how the materials may be reused or co-created. It is usually written in a plain text format. + A README is a text file that introduces and explains the contents of the learning topics and materials. It usually describes the context and written in a plain text format.
    GTN provides a README file on the level of each topic, where context information about the topic and its tutorials can be provided.
    {% icon point-right %} Make a README @@ -742,13 +745,13 @@ PDF document accessibility is measured with a separate technical specification <

    -
    {% icon references %} CITATION.cff
    +
    {% icon references %} CITATION

    - Citation files are plain text files with human- and machine-readable citation information that tells others how to cite or attribute your work. -
    -     - {% icon point-right %} Create a citation file - + It is best practice to provide information on how you want others to cite your learning materials when they are referenced to or reused.
    GTN does this automatically by appending the "Citing this Tutorial" section at the end of each tutorial. +
    + + {% icon point-right %} See an example citation +

    @@ -761,12 +764,12 @@ PDF document accessibility is measured with a separate technical specification <
    -
    {% icon license %} CODE_OF_CONDUCT
    +
    {% icon license %} CODE OF CONDUCT

    A code of conduct defines the rules for how to engage in a co-creation community. It is based on a premise of an inclusive environment that respects all contributions.
    - - {% icon point-right %} Code of conduct template + + {% icon point-right %} Read the Galaxy Project Code of Conduct

    @@ -777,12 +780,12 @@ PDF document accessibility is measured with a separate technical specification <
    -
    {% icon comment %} RELEASE NOTES
    +
    {% icon comment %} REVISIONS

    - A release note is a report published alongside new or updated version of your learning materials that details the changes in the new version. + Information about new or updated version of your learning materials helps others track the changes more easily.
    GTN automatically updates the Revision number of each tutorial after each release. This information combined with the commit message can provide more detailed information about the changes made in the new versions.
    - - {% icon point-right %} Creating Release Notes + + {% icon point-right %} Compare changes between GTN releases

    From fc6bd38c837e042a8cb87f44ddb6079d724485cb Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 09:58:02 +0200 Subject: [PATCH 149/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 26 +++++++++++++++---- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 37ee5db53e9516..c37bcfcf78eeeb 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -740,6 +740,24 @@ PDF document accessibility is measured with a separate technical specification <
    +
    + +
    + +
    +
    {% icon sticky-note %} CONTRIBUTORS
    +

    + In GTN CONTRIBUTORS is a YAML file that lists the information about all contributors of learning materials on the platform. +
    You must have a GitHub user to be listed as a contributor. Additional information such as ORCID can also be provided. +
    + [{% icon point-right %} Add to CONTRIBUTORS.yaml]( {% link /topics/contributing/tutorials/create-new-tutorial-content/tutorial.md#listing-contributors %}) +

    +
    +
    +
    +
    + +
    @@ -756,9 +774,6 @@ PDF document accessibility is measured with a separate technical specification <
    -
    - -
    @@ -766,7 +781,8 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon license %} CODE OF CONDUCT

    - A code of conduct defines the rules for how to engage in a co-creation community. It is based on a premise of an inclusive environment that respects all contributions. + A code of conduct defines the rules for how to engage in a co-creation community. +
    It is based on a premise of an inclusive environment that respects all contributions.
    {% icon point-right %} Read the Galaxy Project Code of Conduct @@ -782,7 +798,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon comment %} REVISIONS

    - Information about new or updated version of your learning materials helps others track the changes more easily.
    GTN automatically updates the Revision number of each tutorial after each release. This information combined with the commit message can provide more detailed information about the changes made in the new versions. + Information about new or updated version of your learning materials helps others track the changes more easily.
    GTN automatically updates the Revision number of each tutorial after each release.
    {% icon point-right %} Compare changes between GTN releases From 0b18244086d972add03f6d83daea805d97576792 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 10:06:19 +0200 Subject: [PATCH 150/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index c37bcfcf78eeeb..22f22843710049 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -750,7 +750,7 @@ PDF document accessibility is measured with a separate technical specification < In GTN CONTRIBUTORS is a YAML file that lists the information about all contributors of learning materials on the platform.
    You must have a GitHub user to be listed as a contributor. Additional information such as ORCID can also be provided.
    - [{% icon point-right %} Add to CONTRIBUTORS.yaml]( {% link /topics/contributing/tutorials/create-new-tutorial-content/tutorial.md#listing-contributors %}) + {% icon point-right %} [Add to CONTRIBUTORS.yaml]( {% link topics/contributing/tutorials/create-new-tutorial-content/tutorial.md#listing-contributors %})

    @@ -812,7 +812,9 @@ PDF document accessibility is measured with a separate technical specification < ### Storing and indexing >Automated publishing ->If you are working on GitHub using the provided templates repository then the "publish to Zenodo" step is fully automated for you. Just follow the [guide to publishing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%205%20%E2%80%93%20Publish/17-Zenodo%20Publishing/17-Zenodo%20Publishing/). +>If you are working on GTN following the provided rules and procedures, GTN will automatically publish the new tutorial once the full review and release process is completed. +> +>Just follow the [GTN guide to contributing via GitHub]( {% link /topics/contributing/#st-contribute %}). {: .tip} >To training catalogue From 9ede307e35bb4c97ebb82021c9e4db8915631016 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 10:10:13 +0200 Subject: [PATCH 151/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 22f22843710049..a5ee984067eed4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -750,7 +750,9 @@ PDF document accessibility is measured with a separate technical specification < In GTN CONTRIBUTORS is a YAML file that lists the information about all contributors of learning materials on the platform.
    You must have a GitHub user to be listed as a contributor. Additional information such as ORCID can also be provided.
    - {% icon point-right %} [Add to CONTRIBUTORS.yaml]( {% link topics/contributing/tutorials/create-new-tutorial-content/tutorial.md#listing-contributors %}) +     + {% icon point-right %} Add to CONTRIBUTORS.yaml +

    From b45f4ac5dedd8dd361bf253d18e68edffea77947 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 10:15:16 +0200 Subject: [PATCH 152/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index a5ee984067eed4..85cb4bec117be4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -7,6 +7,7 @@ abbreviations: EOSC: European Open Science Cloud CC: Creative Commons MVS: Minimum Viable Skills + TeSS: Training eSupport System zenodo_link: https://zenodo.org/records/11548062 questions: - How to develop FAIR learning materials? @@ -820,7 +821,9 @@ PDF document accessibility is measured with a separate technical specification < {: .tip} >To training catalogue ->You are at the point when you should also consider making a record in a relevant training catalogue such as the EOSC training catalogue. +>You are at the point when you should also consider making a record in a relevant training catalogue. +> +>GTN automatically creates a new record in the [Elixir TeSS training catalogue](https://tess.elixir-europe.org) that is the most relevant catalogue for its community. {: .tip} Go to the full FAIR-by-Design Methodology: Publish stage.... From c7cad573d0bac4c055b5eddf14dc64b65b22a65a Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 10:27:00 +0200 Subject: [PATCH 153/262] adding contributors --- CONTRIBUTORS.yaml | 44 ++++++++++++------- .../tutorials/fair-by-design/tutorial.md | 3 ++ 2 files changed, 32 insertions(+), 15 deletions(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index fc14b72f1c0906..59233fabdf821a 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -133,11 +133,6 @@ almahmoud: joined: 2019-06 orcid: 0000-0001-7271-6655 -amisev1971: - name: Anastas Mishev - joined: 2024-07 - orcid: 0000-0001-7271-6655 - andreacabibbe: name: Andrea Cabibbe affiliations: @@ -1187,11 +1182,6 @@ KlemensFroehlich: name: Klemens Fröhlich joined: 2021-08 -korvoj: - name: Vojdan Kjorveziroski - joined: 2024-07 - orcid: 0000-0003-0419-4300 - kostrykin: name: Leonid Kostrykin orcid: 0000-0003-1323-3762 @@ -1989,11 +1979,6 @@ sonalhenson: name: Sonal Henson joined: 2023-09 -sonjafiliposka: - name: Sonja Filiposka - joined: 2024-07 - orcid: 0000-0003-0034-2855 - Shians: name: Shian Su joined: 2019-02 @@ -2400,3 +2385,32 @@ ThibaudGlinez: affiliations: - pndb - elixir-europe + +sonjafiliposka: + name: Sonja Filiposka + joined: 2024-07 + orcid: 0000-0003-0034-2855 + +amisev1971: + name: Anastas Mishev + joined: 2024-07 + orcid: 0000-0001-7271-6655 + +korvoj: + name: Vojdan Kjorveziroski + joined: 2024-07 + orcid: 0000-0003-0419-4300 + +domlgreen: + name: Dominique Green + joined: 2024-07 + orcid: 0000-0002-9411-4281 + +isouyioul: + name: Irakleitos Souyioultzoglou + joined: 2024-07 + orcid: 0000-0002-9875-7196 + +CarolinLeister: + name: Carolin Leister + orcid: 0000-0002-6940-0024 \ No newline at end of file diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 85cb4bec117be4..760c5395305ec3 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -31,7 +31,10 @@ contributions: authorship: - sonjafiliposka - amisev1971 + - CarolinLeister - korvoj + - domlgreen + - isouyioul funding: - skills4eosc follow_up_training: From 489e6584bb7220976e8de7ede311512256b21da0 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 10:54:31 +0200 Subject: [PATCH 154/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 64 +++++++++++++++++-- 1 file changed, 59 insertions(+), 5 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 760c5395305ec3..da90a4c5bfc8c4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -275,7 +275,7 @@ Reusable materials can be found anywhere. These are just some examples: > GTN > [GTN learning resources](https://training.galaxyproject.org) > -> [TeSS Catalogue by Elixir](https://tess.elixir-europe.com) +> [TeSS Catalogue by Elixir](https://tess.elixir-europe.org) {: .code-in} > OER @@ -514,7 +514,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr > Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. > > - GitHub is one of the most popular options at the moment (find out more here) -> - GTN is also based on GitHub and defines [specific procedures on how one can contribute and collaborate]( {% link CONTRIBUTING.md %}) using GitHub +> - GTN is also based on GitHub and defines [specific procedures on how one can contribute and collaborate](https://github.com/galaxyproject/training-material/blob/main/CONTRIBUTING.md) using GitHub > > > GTN: collaboration using GitHub ... > > [Follow the Contributing with GitHub via its interface tutorial available on GTN]( {% link topics/contributing/tutorials/github-interface-contribution/tutorial.md %} ) @@ -722,7 +722,7 @@ PDF document accessibility is measured with a separate technical specification < CC-BY-4.0 is the recommended license, which is default in GTN.
    If you choose a different license, it must be supplied in the tutorial header as metadata.
    - {% icon point-right %} Browse through the available CC license types + {% icon point-right %} Browse through the available CC license types

    @@ -749,7 +749,7 @@ PDF document accessibility is measured with a separate technical specification <
    -
    {% icon sticky-note %} CONTRIBUTORS
    +
    {% icon cofest %} CONTRIBUTORS

    In GTN CONTRIBUTORS is a YAML file that lists the information about all contributors of learning materials on the platform.
    You must have a GitHub user to be listed as a contributor. Additional information such as ORCID can also be provided. @@ -763,6 +763,60 @@ PDF document accessibility is measured with a separate technical specification <

    +
    +
    + +
    + +
    +
    {% icon help %} FAQs
    +

    + In addition to the learning content the Frequently Asked Questions can further help both learners and instructors with specific information regarding the learning context or practicalities. +
    Consider adding tutorial specific FAQ to the GTN tutorial where in you can answer questions regarding the challenges when working with the hands on activities, or provide other hints and guidelines to instructors and learners. +
    + + {% icon point-right %} Create snippets + +

    +
    +
    +
    +
    + +
    + +
    +
    {% icon event-cost %} FUNDERS
    +

    + If the creation of the learning materials is funded by an organisation or another body, they should be attributed accordingly.
    + In GTN this can be accomplished by adding the funding information into the special FUNDERS.yaml file. +
    + + {% icon point-right %} Add to the Funders file + +

    +
    +
    +
    +
    + +
    + +
    +
    {% icon new-history %} OTHER
    +

    + Additional miscellaneous information should be provided if possible. +
    For an example, GTN also supports adding Organisations information. +
    + + {% icon point-right %} Add org info + +

    +
    +
    +
    +
    +
    @@ -820,7 +874,7 @@ PDF document accessibility is measured with a separate technical specification < >Automated publishing >If you are working on GTN following the provided rules and procedures, GTN will automatically publish the new tutorial once the full review and release process is completed. > ->Just follow the [GTN guide to contributing via GitHub]( {% link /topics/contributing/#st-contribute %}). +>Just follow the [GTN guide to contributing via GitHub]( {% link topics/contributing/#st-contribute %}). {: .tip} >To training catalogue From b0f018ad6eeec96c1134fb76671284e28967c54d Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 10:55:36 +0200 Subject: [PATCH 155/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index da90a4c5bfc8c4..41bc0512773266 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -1040,10 +1040,6 @@ This training has no certification or any recognition mechanism included. [https://doi.org/10.5281/zenodo.11548062](https://doi.org/10.5281/zenodo.11548062) -### Accessibility Mission - -Skills4EOSC is dedicated to ensuring that all produced learning materials are accessible to as many visitors as possible regardless of their ability or technology. We have an active commitment to increasing our learning materials accessibility. The main standards that we aim to comply with are WCAG v.2.1 Level AA criteria and PDF/UA (ISO 14289). - #### Acknowledgement These learning materials have been developed by following the [FAIR-by-Design Methodology](https://zenodo.org/records/8305540). From d4b45f4e04ee8f5197437d3c2045d7a02e3e39e5 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 13 Aug 2024 11:13:47 +0200 Subject: [PATCH 156/262] FAQs --- .../tutorials/fair-by-design/faqs/FAQ-C1.md | 11 +++++++++++ .../tutorials/fair-by-design/faqs/FAQ-C2.md | 11 +++++++++++ .../tutorials/fair-by-design/faqs/FAQ-L1.md | 13 +++++++++++++ .../tutorials/fair-by-design/faqs/FAQ1.md | 10 ---------- 4 files changed, 35 insertions(+), 10 deletions(-) create mode 100644 topics/contributing/tutorials/fair-by-design/faqs/FAQ-C1.md create mode 100644 topics/contributing/tutorials/fair-by-design/faqs/FAQ-C2.md create mode 100644 topics/contributing/tutorials/fair-by-design/faqs/FAQ-L1.md delete mode 100644 topics/contributing/tutorials/fair-by-design/faqs/FAQ1.md diff --git a/topics/contributing/tutorials/fair-by-design/faqs/FAQ-C1.md b/topics/contributing/tutorials/fair-by-design/faqs/FAQ-C1.md new file mode 100644 index 00000000000000..6438da544fcbd4 --- /dev/null +++ b/topics/contributing/tutorials/fair-by-design/faqs/FAQ-C1.md @@ -0,0 +1,11 @@ +--- +title: Can this tutorial be adapted to other instructional development platforms? +box_type: tip +layout: faq +contributors: [sonjafiliposka] +area: contributors +--- + +The tutorial has been specifically adapted to the rules and options available in GTN. However, the general FAIR-by-Design Methodology is platform agnostic and can be applied to any environment. + +Thus, the tutorial can be reused and carefully adapted to be applicable to other platforms, as long as the adaptation is based on the originally published FAIR-by-Design Methodology. diff --git a/topics/contributing/tutorials/fair-by-design/faqs/FAQ-C2.md b/topics/contributing/tutorials/fair-by-design/faqs/FAQ-C2.md new file mode 100644 index 00000000000000..e4b71c272311f8 --- /dev/null +++ b/topics/contributing/tutorials/fair-by-design/faqs/FAQ-C2.md @@ -0,0 +1,11 @@ +--- +title: Can the FAIR-by-Design Methodology be used for FAIR development of other types of resources? +box_type: tip +layout: faq +contributors: [amisev1971] +area: contributors +--- + +The FAIR-by-Design Methodology stages can be relatively easily adapted to the processes for designing other FAIR objects. + +For an example, the FAIR-by-Design Methodology can be adapted to create FAIR-by-Design software objects. This has been demonstrated on the IDCC24 W6 - FAIR-by-Design: introducing Skills4EOSC and FAIR-IMPACT workshop. The information regarding this example is available at [https://fair-by-design-methodology.github.io/IDCC24workshop/latest/](https://fair-by-design-methodology.github.io/IDCC24workshop/latest/). diff --git a/topics/contributing/tutorials/fair-by-design/faqs/FAQ-L1.md b/topics/contributing/tutorials/fair-by-design/faqs/FAQ-L1.md new file mode 100644 index 00000000000000..2330852963cf93 --- /dev/null +++ b/topics/contributing/tutorials/fair-by-design/faqs/FAQ-L1.md @@ -0,0 +1,13 @@ +--- +title: Is there a certification available for the FAIR-by-Design Methodology? +box_type: tip +layout: faq +contributors: [amisev1971] +area: learners +--- + +There is no specific certification regarding the implementation of the FAIR-by-Design Methodology when developing learning materials for GTN. + +There is, however, the possibility to obtain FAIR-by-Design per stages and overall badge based on the Training of Trainers learning materials prepared by the Skills4EOSC project. + +To obtain this certification follow the [FAIR-by-Design Learning Materials Methodology Course](https://learning.skills4eosc.eu/course/view.php?id=19) and make sure you successfully pass all of the assessments. \ No newline at end of file diff --git a/topics/contributing/tutorials/fair-by-design/faqs/FAQ1.md b/topics/contributing/tutorials/fair-by-design/faqs/FAQ1.md deleted file mode 100644 index 87053abffb1a0c..00000000000000 --- a/topics/contributing/tutorials/fair-by-design/faqs/FAQ1.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -title: How does one convert RAW files to MGF peak lists within Galaxy? -box_type: tip -layout: faq -contributors: [millen2223] -redirect_from: - - /topics/proteomics/faqs/convert_to_MGF ---- - -Galaxy has implemented msconvert tool so that RAW files from Thermo instruments can be converted into MGF or mzML formats. From b7d56922d0fa4561669f93e9909f76d3143156a4 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 16:08:09 +0200 Subject: [PATCH 157/262] Remove non-ASCII whitespace --- .../tutorials/fair-by-design/tutorial.md | 58 +++++++++---------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 41bc0512773266..bbda71d34c2b9f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -49,7 +49,7 @@ extra: URL_resource_type: "Permanent URL" learning_resource_type: "self-paced microlearning unit" access_cost: "No" - attribution: "This microlearning unit is based on Filiposka, Sonja, Mishev, Anastas. (2024). FAIR-by-Design Microlearning (1.0.0). https://doi.org/10.5281/zenodo.11548062" + attribution: "This microlearning unit is based on Filiposka, Sonja, Mishev, Anastas. (2024). FAIR-by-Design Microlearning (1.0.0). https://doi.org/10.5281/zenodo.11548062" --- @@ -248,7 +248,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > What competences will be gained after successful completing of the learning process? > > >Be SMART -> >Objectives should be specific, ​measurable, ​attainable, ​relevant and ​time-bound​. +> >Objectives should be specific, measurable, attainable, relevant and time-bound. > {: .tip} > > >Use Blooms Taxonomy @@ -295,11 +295,11 @@ Reusable materials can be found anywhere. These are just some examples: {: .code-in} > General -> [Creative Commons Search](https://search.creativecommons.org/) - content provided under a CC license +> [Creative Commons Search](https://search.creativecommons.org/) - content provided under a CC license > -> [Zenodo](https://zenodo.org/) - a multi-disciplinary open repository +> [Zenodo](https://zenodo.org/) - a multi-disciplinary open repository > -> [OSF](https://osf.io/) - a free, open research platform +> [OSF](https://osf.io/) - a free, open research platform {: .code-in} ### Potential for reuse @@ -507,7 +507,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr ## Stage 4 - Produce > To contrive is nothing! To construct is something! To produce is everything! -{: .quote author="Edward Rickenbacker​"} +{: .quote author="Edward Rickenbacker"} ### Choose Tools & Formats > Collaborative environment for team work @@ -694,7 +694,7 @@ PDF document accessibility is measured with a separate technical specification < ## Stage 5 - Publish -> Publishing is the art of working on a creative idea and turning it into a masterpiece​! +> Publishing is the art of working on a creative idea and turning it into a masterpiece! {: .quote author="Unknown"} >Publishing closed FAIR materials @@ -914,24 +914,24 @@ The questions marked as essential achieve bare minimum FAIRness. {: .details} >Optional requirements -> - Did you follow the stages of the backward instructional design process while developing the learning resource? -> -  Are controlled vocabularies (CVs) used for describing the resource characteristics aligned with the chosen metadata schema? -> -  Does the learning resource represent a complete learning object defined around minimum one learning objective? -> -  Does the resource incorporate an instructor kit that aids in facilitating the process of others reusing learning material by offering helpful how-to guides? -> -  facilitator guide -> -  activities description -> -  assessment activities and strategy to assess -> -  general learning content or instructor notes -> -  lesson unit plan -> -  syllabus -> -  Have you employed a versioning system to track and control changes in your materials? -> -  Are the resource access rules (how to access, e.g. registration procedure) explicitly communicated to learners? -> -  Is the learning resource searchable in at least one relevant catalogue?  -> -  Is it FAIR (can be searched based on metadata)? -> -  Does the course include the possibility to provide feedback or comments from users and-or trainers/designers?  -> -  If so, do you regularly gather and analyse that feedback? -> -  Does the resource adopt an open community approach regarding its quality and reachability? -> -  Has the learning resource been checked by a third party regarding its learning experience quality? +> - Did you follow the stages of the backward instructional design process while developing the learning resource? +> - Are controlled vocabularies (CVs) used for describing the resource characteristics aligned with the chosen metadata schema? +> - Does the learning resource represent a complete learning object defined around minimum one learning objective? +> - Does the resource incorporate an instructor kit that aids in facilitating the process of others reusing learning material by offering helpful how-to guides? +> - facilitator guide +> - activities description +> - assessment activities and strategy to assess +> - general learning content or instructor notes +> - lesson unit plan +> - syllabus +> - Have you employed a versioning system to track and control changes in your materials? +> - Are the resource access rules (how to access, e.g. registration procedure) explicitly communicated to learners? +> - Is the learning resource searchable in at least one relevant catalogue? +> - Is it FAIR (can be searched based on metadata)? +> - Does the course include the possibility to provide feedback or comments from users and-or trainers/designers? +> - If so, do you regularly gather and analyse that feedback? +> - Does the resource adopt an open community approach regarding its quality and reachability? +> - Has the learning resource been checked by a third party regarding its learning experience quality? {: .details} ### Feedback QA @@ -951,12 +951,12 @@ The questions marked as essential achieve bare minimum FAIRness. - Gather feedback from all available internal & external sources. - Potential sources: - - Feedback form  - - QA recommendations  - - Self-reflection after training  + - Feedback form + - QA recommendations + - Self-reflection after training - Git Issues - Gitter Chat - - Direct mail contact  + - Direct mail contact - Other means of communication #### {% icon galaxy-barchart %} Analyse From 10733fbdd390cf8d36398a6e62cb7f47699e5203 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 16:13:47 +0200 Subject: [PATCH 158/262] Remove unnecessary trailing whitespace --- .../tutorials/fair-by-design/tutorial.md | 94 +++++++++---------- 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index bbda71d34c2b9f..c64e2c95c0d044 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -86,7 +86,7 @@ Welcome to the FAIR-by-Design Methodology Microlearning GTN adapted tutorial. > - Use gathered feedback for continuous improvement >7. [Continuous Improvement](#stage-7---continuous-improvement) > - Create a list of potential improvements -> - Choose a set of improvements to be implemented +> - Choose a set of improvements to be implemented > - Start a new release cycle > >Review each stage and the essential steps that it includes. @@ -170,8 +170,8 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > Using metadata in GTN tutorials > ->- When developing materials in GTN, this information should be included in the Tutorial.md file header metadata. ->- Most of the fields are already defined in the GTN Tutorial metadata schema. The ones that are missing can be added using the "extra" field. +>- When developing materials in GTN, this information should be included in the Tutorial.md file header metadata. +>- Most of the fields are already defined in the GTN Tutorial metadata schema. The ones that are missing can be added using the "extra" field. > > > More details on the GTN Metadata ... > > [Follow the GTN Metadata tutorial]( {% link topics/contributing/tutorials/schemas/tutorial.md %} ) @@ -304,7 +304,7 @@ Reusable materials can be found anywhere. These are just some examples: ### Potential for reuse > Respect the licenses, to be respected! -> - Materials with non-permissible licenses can be used for inspiration only. +> - Materials with non-permissible licenses can be used for inspiration only. > - Materials with permissible licenses should be reused based on the license rules. {: .warning} @@ -377,7 +377,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .tip} >Facilitation guide kit -> A facilitation guide should help prepare for the actual training. +> A facilitation guide should help prepare for the actual training. > > The facilitation guide kit includes documentation of the process of organising and running a training. What different people need to have, know and do so that everything runs smoothly. > @@ -392,9 +392,9 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .tip} >What about instructor notes? -> They need to be detailed enough so that anyone can reuse the learning content, especially slides properly. +> They need to be detailed enough so that anyone can reuse the learning content, especially slides properly. > -> Any specific information relevant for instructors that would like to organise a training based on your GTN tutorial content should be added in Details box. +> Any specific information relevant for instructors that would like to organise a training based on your GTN tutorial content should be added in Details box. > > This practice significantly increases the reuse potential of the material. {: .question} @@ -409,7 +409,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon curriculum %} 1. Set Learning Objectives

    - ... what is the goal + ... what is the goal

    @@ -429,7 +429,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon galaxy-panelview %} 3. Plan

    - ... share the agenda + ... share the agenda

    @@ -442,7 +442,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon version %} 4. Hook

    - ... why is the content important + ... why is the content important

    @@ -462,7 +462,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon galaxy-rulebuilder-history %} 6. Practise

    - ... you help me do it, I'll watch you do it + ... you help me do it, I'll watch you do it

    @@ -506,12 +506,12 @@ Each MVS profile defines a list of technical and soft skills required for the pr ## Stage 4 - Produce -> To contrive is nothing! To construct is something! To produce is everything! +> To contrive is nothing! To construct is something! To produce is everything! {: .quote author="Edward Rickenbacker"} ### Choose Tools & Formats > Collaborative environment for team work -> Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. +> Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. > > - GitHub is one of the most popular options at the moment (find out more here) > - GTN is also based on GitHub and defines [specific procedures on how one can contribute and collaborate](https://github.com/galaxyproject/training-material/blob/main/CONTRIBUTING.md) using GitHub @@ -524,13 +524,13 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .tip} > Granular versioning for easy rollback -> - Versioning helps you maintain control over your changes. +> - Versioning helps you maintain control over your changes. > - GitHub natively provides versioning and history retention that help easy roll back to an earlier stable state. {: .tip} > Open file formats to foster reuse > - For other people to reuse the materials they should be made available using open file formats -> - GTN promotes the use of the MD open file format for the main learning content empowered with open scientific notebooks and workflows. +> - GTN promotes the use of the MD open file format for the main learning content empowered with open scientific notebooks and workflows. > - If you use close file formats then you MUST clearly state the tools that have been used in more details. {: .tip} @@ -540,33 +540,33 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .tip} > Two file sets: editable + final -> - The MD and supporting files are the main files used for development of the content. These files are what matters for you and other instructors. +> - The MD and supporting files are the main files used for development of the content. These files are what matters for you and other instructors. > - Based on the editable files, GTN automatically generates the final (non-editable version) in HTML (and PDF). These are shared with the learners. > - GTN takes care of the revision numbering for you. {: .tip} > Don't forget to take advantage of co-creation > Truly FAIR learning materials enable co-creation with external parties. -> GitHub is a collaborative environment that supports co-creation in every step of the learning materials development and revision process. +> GitHub is a collaborative environment that supports co-creation in every step of the learning materials development and revision process. > The GTN fork-and-pull process of contributing to the learning material is a clear example of co-creation implementation. {: .tip} -### Plan to reuse existing material? +### Plan to reuse existing material? #### Check the license The existing materials you are reusing are available under a CC license, but it is different than the one you plan to use for your materials... >I want to reuse it as a whole ->- You can't use something that is licensed with ND (no derivatives). ->- In this case you must follow the rules on combining and adapting CC material. +>- You can't use something that is licensed with ND (no derivatives). +>- In this case you must follow the rules on combining and adapting CC material. > >[Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material) {: .details} >I want to reuse a small part of it -> No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. +> No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. > > Remember that if the work is licensed with ND, you can not modify it while reusing. {: .details} @@ -575,7 +575,7 @@ The existing materials you are reusing are available under a CC license, but it >[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) {: .tip} -Still need help? +Still need help? [{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) @@ -588,22 +588,22 @@ If the work you are reusing has a copyright notice ('© some text') you need to You should also be able to remove attribution upon request. -##### How to attribute? +##### How to attribute? > Use the authors recommended attribution > If the original author has provided a cite-as information, use it to attribute the work. {: .solution} > Use TASL -> Provide the Title, Author, Source and License of the work that you are reusing. +> Provide the Title, Author, Source and License of the work that you are reusing. > >- Source is the URL to the original work. >- If there is a URL to the author personal pages, provide it together with the name. ->- Provide the name of the license and a URL to the license. +>- Provide the name of the license and a URL to the license. {: .solution} > Examples -> Examples are taken from [Best Practices for Creative Commons attributions - how to attribute works you reuse under a Creative Commons license](https://www.newmediarights.org/guide/how_to/creative_commons/best_practices_creative_commons_attributions) submitted by [New Media Rights](https://www.newmediarights.org/) available under a [CC BY-NC 3.0 US DEED](https://creativecommons.org/licenses/by-nc/3.0/us/) +> Examples are taken from [Best Practices for Creative Commons attributions - how to attribute works you reuse under a Creative Commons license](https://www.newmediarights.org/guide/how_to/creative_commons/best_practices_creative_commons_attributions) submitted by [New Media Rights](https://www.newmediarights.org/) available under a [CC BY-NC 3.0 US DEED](https://creativecommons.org/licenses/by-nc/3.0/us/) > - Webpage/Blog - Title (with link to original work), author (or username) (with link to author's website), and license (with link). > - [Undercover Vampire Policeman](https://chriszabriskie.bandcamp.com/album/undercover-vampire-policeman) by [Chris Zabriskie](https://chriszabriskie.bandcamp.com/), available under a [Creative Commons Attribution 4.0 License](http://creativecommons.org/licenses/by/4.0/) > - Book – Title, author, license written somewhere near the title and author if it’s a hard copy or if it’s an online book you should include a link to the licensed terms. @@ -628,7 +628,7 @@ You should also be able to remove attribution upon request. The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. ![Universal access logo](../../images/universal-access-6602642_640.png) -J S from Pixabay +J S from Pixabay #### Standards @@ -659,7 +659,7 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon congratulations %} QA Self-assessment

    - to check if everything is as it should be. + to check if everything is as it should be.

    @@ -683,7 +683,7 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon solution %} Qualitative

    - do all learning units provide materials to reach the learning objectives with different modalities. + do all learning units provide materials to reach the learning objectives with different modalities.

    @@ -700,7 +700,7 @@ PDF document accessibility is measured with a separate technical specification < >Publishing closed FAIR materials > Having FAIR learning materials does not always mean that the materials are open to everyone and there are no costs or access rules attached. In this case the bundle that is going to be published in an open repository such as Zenodo should contain the following: > 1. Syllabus - that contains all metadata that describe the materials and metadata should always be open -> 2. Accompanying information - optional - to augment the description of the materials and describe the details when it comes to accessing and using the materials from a trainer perspective +> 2. Accompanying information - optional - to augment the description of the materials and describe the details when it comes to accessing and using the materials from a trainer perspective > > The complete learning materials package itself should be published in a closed repository where the corresponding access rules (and costs) can be implemented. {: .warning} @@ -723,7 +723,7 @@ PDF document accessibility is measured with a separate technical specification < If you choose a different license, it must be supplied in the tutorial header as metadata.
    {% icon point-right %} Browse through the available CC license types - +

    @@ -751,7 +751,7 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon cofest %} CONTRIBUTORS

    - In GTN CONTRIBUTORS is a YAML file that lists the information about all contributors of learning materials on the platform. + In GTN CONTRIBUTORS is a YAML file that lists the information about all contributors of learning materials on the platform.
    You must have a GitHub user to be listed as a contributor. Additional information such as ORCID can also be provided.
    @@ -772,7 +772,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon help %} FAQs

    In addition to the learning content the Frequently Asked Questions can further help both learners and instructors with specific information regarding the learning context or practicalities. -
    Consider adding tutorial specific FAQ to the GTN tutorial where in you can answer questions regarding the challenges when working with the hands on activities, or provide other hints and guidelines to instructors and learners. +
    Consider adding tutorial specific FAQ to the GTN tutorial where in you can answer questions regarding the challenges when working with the hands on activities, or provide other hints and guidelines to instructors and learners.
    {% icon point-right %} Create snippets @@ -789,7 +789,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon event-cost %} FUNDERS

    If the creation of the learning materials is funded by an organisation or another body, they should be attributed accordingly.
    - In GTN this can be accomplished by adding the funding information into the special FUNDERS.yaml file. + In GTN this can be accomplished by adding the funding information into the special FUNDERS.yaml file.
    {% icon point-right %} Add to the Funders file @@ -805,8 +805,8 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon new-history %} OTHER

    - Additional miscellaneous information should be provided if possible. -
    For an example, GTN also supports adding Organisations information. + Additional miscellaneous information should be provided if possible. +
    For an example, GTN also supports adding Organisations information.
    {% icon point-right %} Add org info @@ -841,7 +841,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon license %} CODE OF CONDUCT

    - A code of conduct defines the rules for how to engage in a co-creation community. + A code of conduct defines the rules for how to engage in a co-creation community.
    It is based on a premise of an inclusive environment that respects all contributions.
    @@ -858,7 +858,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon comment %} REVISIONS

    - Information about new or updated version of your learning materials helps others track the changes more easily.
    GTN automatically updates the Revision number of each tutorial after each release. + Information about new or updated version of your learning materials helps others track the changes more easily.
    GTN automatically updates the Revision number of each tutorial after each release.
    {% icon point-right %} Compare changes between GTN releases @@ -872,7 +872,7 @@ PDF document accessibility is measured with a separate technical specification < ### Storing and indexing >Automated publishing ->If you are working on GTN following the provided rules and procedures, GTN will automatically publish the new tutorial once the full review and release process is completed. +>If you are working on GTN following the provided rules and procedures, GTN will automatically publish the new tutorial once the full review and release process is completed. > >Just follow the [GTN guide to contributing via GitHub]( {% link topics/contributing/#st-contribute %}). {: .tip} @@ -904,7 +904,7 @@ PDF document accessibility is measured with a separate technical specification < Use the [FAIR-by-Design methodology QA checklist](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%206%20–%20Verify/19-Final%20QA%20check/19-finalQA/#fair-by-design-methodology-qa-checklist) to check if you have followed the most important aspects of the methodology and managed to produce FAIR learning materials. -The questions marked as essential achieve bare minimum FAIRness. +The questions marked as essential achieve bare minimum FAIRness. >Essential requirements > - **Findable** = Is the complete learning resource (including instructors info) registered or indexed in at least one searchable repository? Is it in a FAIR repository? Is metadata for the resource provided in both human- and machine-readable format (e.g JSON, XMLor YAML? @@ -934,7 +934,7 @@ The questions marked as essential achieve bare minimum FAIRness. > - Has the learning resource been checked by a third party regarding its learning experience quality? {: .details} -### Feedback QA +### Feedback QA > Regularly gather feedback from learners and instructors > Ensure that you actively and regularly gather feedback from both perspectives: the learners and the instructors. @@ -950,13 +950,13 @@ The questions marked as essential achieve bare minimum FAIRness. - Gather feedback from all available internal & external sources. -- Potential sources: - - Feedback form - - QA recommendations - - Self-reflection after training +- Potential sources: + - Feedback form + - QA recommendations + - Self-reflection after training - Git Issues - Gitter Chat - - Direct mail contact + - Direct mail contact - Other means of communication #### {% icon galaxy-barchart %} Analyse @@ -973,7 +973,7 @@ The questions marked as essential achieve bare minimum FAIRness. #### {% icon galaxy-history-refresh %} Repeat -- Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. +- Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. - After the Verify stage, you will reenter continuous improvement with the newly gathered information.... From 21dc8342564ccdd446c2b4ab8a76c2abe7bc9c99 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 16:14:55 +0200 Subject: [PATCH 159/262] Remove colon from section heading --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index c64e2c95c0d044..e73414b1398d39 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -226,7 +226,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > - [Steps of the backward learning process](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#backward-instructional-design-process) {: .tip } -### Define: +### Define > Purpose > When and how the learning materials can be used and for what purposes? From 63c118879e3e92134fdffc79dbc9ef3f765a9b06 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 16:15:23 +0200 Subject: [PATCH 160/262] Highlight first letters of SMART explanation --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index e73414b1398d39..3b16f437f03189 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -248,7 +248,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > What competences will be gained after successful completing of the learning process? > > >Be SMART -> >Objectives should be specific, measurable, attainable, relevant and time-bound. +> >Objectives should be **s**pecific, **m**easurable, **a**ttainable, **r**elevant and **t**ime-bound. > {: .tip} > > >Use Blooms Taxonomy From d5d234e47d188cf280cb88e4f471fb6a4cb2eb65 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 16:16:00 +0200 Subject: [PATCH 161/262] Display OER sources in separate lines --- topics/contributing/tutorials/fair-by-design/tutorial.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 3b16f437f03189..8b07524cf0ceaa 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -280,11 +280,17 @@ Reusable materials can be found anywhere. These are just some examples: > OER > [DOAB](https://directory.doabooks.org/) +> > [MERLOT](https://www.merlot.org/merlot/index.htm) +> > [OASIS](https://oasis.geneseo.edu/index.php) +> > [OER Commons](https://www.oercommons.org/) +> > [OERTX CORA](https://www.projectcora.org/) +> > [GALILEO](https://oer.galileo.usg.edu/) +> > [FORRT](https://forrt.org/) {: .code-in} From 140309f9053565052f2f527d275b39116bd5d7bc Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 16:27:53 +0200 Subject: [PATCH 162/262] Use ellipses more consistent --- .../tutorials/fair-by-design/tutorial.md | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 8b07524cf0ceaa..a73b8138250138 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -186,7 +186,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} >- [FAIR learning objects](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-learning-objects) {: .details} -### Start Ideating... +### Start Ideating ...

    @@ -196,7 +196,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %}
    Think backward
    Step 1
    -

    What are your desired effects, i.e. learning outcomes...

    +

    What are your desired effects, i.e. learning outcomes ...

    @@ -206,7 +206,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %}
    Think backward
    Step 2
    -

    How are you going to assess the learners achievement....

    +

    How are you going to assess the learners achievement ...

    @@ -216,7 +216,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %}
    Think backward
    Step 3
    -

    How should you structure the material to provide effective learning experience...

    +

    How should you structure the material to provide effective learning experience ...

    @@ -262,7 +262,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > [Read about defining intended Learning Outcomes in the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md#define-intended-learning-outcomes-los %} ) {: .details} -Go to the full description of FAIR-by-Design Methodology: Prepare stage.... +Go to the full description of FAIR-by-Design Methodology: Prepare stage ... ## Stage 2 - Discover @@ -297,7 +297,7 @@ Reusable materials can be found anywhere. These are just some examples: > EOSC > [EOSC Training catalogue on the EOSC Marketplace](https://search.marketplace.eosc-portal.eu/search/training?q=*) > -> Most EOSC projects have their own training catalogues and/or platforms... +> Most EOSC projects have their own training catalogues and/or platforms ... {: .code-in} > General @@ -318,14 +318,14 @@ Reusable materials can be found anywhere. These are just some examples: Different learners have different learning modalities (read/write, auditory, visual, kinesthetic). To elevate the learning experience you should use all types of multimedia in your learning materials. -Go to the full description of FAIR-by-Design Methodology: Discover stage.... +Go to the full description of FAIR-by-Design Methodology: Discover stage ... ## Stage 3 - Design > Design is intelligence made visible. {: .quote author="Alina Wheeler"} -Now it's time to brainstorm... +Now it's time to brainstorm ... ### Concept map @@ -508,7 +508,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -Go to the full description of FAIR-by-Design Methodology: Design stage.... +Go to the full description of FAIR-by-Design Methodology: Design stage ... ## Stage 4 - Produce @@ -562,13 +562,13 @@ Each MVS profile defines a list of technical and soft skills required for the pr #### Check the license -The existing materials you are reusing are available under a CC license, but it is different than the one you plan to use for your materials... +The existing materials you are reusing are available under a CC license, but it is different than the one you plan to use for your materials ... >I want to reuse it as a whole >- You can't use something that is licensed with ND (no derivatives). >- In this case you must follow the rules on combining and adapting CC material. > ->[Read more...](https://creativecommons.org/faq/#combining-and-adapting-cc-material) +>[Read more ...](https://creativecommons.org/faq/#combining-and-adapting-cc-material) {: .details} >I want to reuse a small part of it @@ -696,7 +696,7 @@ PDF document accessibility is measured with a separate technical specification <
    -Go to the full FAIR-by-Design Methodology: Produce stage.... +Go to the full FAIR-by-Design Methodology: Produce stage ... ## Stage 5 - Publish @@ -889,7 +889,7 @@ PDF document accessibility is measured with a separate technical specification < >GTN automatically creates a new record in the [Elixir TeSS training catalogue](https://tess.elixir-europe.org) that is the most relevant catalogue for its community. {: .tip} -Go to the full FAIR-by-Design Methodology: Publish stage.... +Go to the full FAIR-by-Design Methodology: Publish stage ... ## Stage 6 - Verify > You will find it a very good practice always to verify your references, sir! @@ -904,7 +904,7 @@ PDF document accessibility is measured with a separate technical specification < > In Skills4EOSC T2.4 has developed a number of QA checklists that you and your external reviewer need to go through so that you can ensure high-quality learning materials {% cite sanchez_2023_8305482 %}. {: .tip} -### FAIR or not FAIR, that is the question... +### FAIR or not FAIR, that is the question ... #### Measure FAIRness @@ -946,7 +946,7 @@ The questions marked as essential achieve bare minimum FAIRness. > Ensure that you actively and regularly gather feedback from both perspectives: the learners and the instructors. {: .comment} -Go to the full FAIR-by-Design Methodology: Verify stage.... +Go to the full FAIR-by-Design Methodology: Verify stage ... ## Stage 7 - Continuous Improvement > To improve is to change; to be perfect is to change often @@ -981,9 +981,9 @@ The questions marked as essential achieve bare minimum FAIRness. - Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. -- After the Verify stage, you will reenter continuous improvement with the newly gathered information.... +- After the Verify stage, you will reenter continuous improvement with the newly gathered information. -Go to the full FAIR-by-Design Methodology: Continuous Improvement .... +Go to the full FAIR-by-Design Methodology: Continuous Improvement ... # About From 6c07b56bd6acfdbace7195fcd0fab2fcf0888087 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 17:34:31 +0200 Subject: [PATCH 163/262] Minor linguistic/format/style changes in 04 Produce --- .../tutorials/fair-by-design/tutorial.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index a73b8138250138..0ea7988427b7a4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -535,7 +535,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .tip} > Open file formats to foster reuse -> - For other people to reuse the materials they should be made available using open file formats +> - For other people to reuse the materials they should be made available using open file formats. > - GTN promotes the use of the MD open file format for the main learning content empowered with open scientific notebooks and workflows. > - If you use close file formats then you MUST clearly state the tools that have been used in more details. {: .tip} @@ -633,14 +633,15 @@ You should also be able to remove attribution upon request. The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. -![Universal access logo](../../images/universal-access-6602642_640.png) -J S from Pixabay +![Universal access logo](../../images/universal-access-6602642_640.png) +Image by J S from Pixabay #### Standards -There are several standards that govern the rules on level of accessibility. Three conformance levels exist, you should aim for AA which is the middle one. -Most commonly used is the W3C Web Content Accessibility Guidelines (WCAG) standard version 2.1. +There are several standards that govern the rules on level of accessibility. + +Most commonly used is the W3C Web Content Accessibility Guidelines (WCAG) standard version 2.1. Three conformance levels exist, you should aim for AA which is the middle one. PDF document accessibility is measured with a separate technical specification PDF/UA (Universal Accessibility). @@ -665,7 +666,7 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon congratulations %} QA Self-assessment

    - to check if everything is as it should be. + Check if everything is as it should be.

    @@ -677,7 +678,7 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon pref-list %} Quantitative

    - are all required elements produced + Are all required elements produced?

    @@ -689,7 +690,7 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon solution %} Qualitative

    - do all learning units provide materials to reach the learning objectives with different modalities. + Do all learning units provide materials to reach the learning objectives with different modalities?

    From 508797954a69642c4167954e2ebda0418717a7f5 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 17:35:26 +0200 Subject: [PATCH 164/262] Minor linguistic/format/style changes in 05 Publish --- .../tutorials/fair-by-design/tutorial.md | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 0ea7988427b7a4..a5761e6f1a087e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -706,8 +706,8 @@ PDF document accessibility is measured with a separate technical specification < >Publishing closed FAIR materials > Having FAIR learning materials does not always mean that the materials are open to everyone and there are no costs or access rules attached. In this case the bundle that is going to be published in an open repository such as Zenodo should contain the following: -> 1. Syllabus - that contains all metadata that describe the materials and metadata should always be open -> 2. Accompanying information - optional - to augment the description of the materials and describe the details when it comes to accessing and using the materials from a trainer perspective +> 1. Syllabus, that contains all metadata that describe the materials. Metadata should always be open. +> 2. Accompanying information (optional) to augment the description of the materials and describe the details when it comes to accessing and using the materials from a trainer perspective. > > The complete learning materials package itself should be published in a closed repository where the corresponding access rules (and costs) can be implemented. {: .warning} @@ -758,8 +758,8 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon cofest %} CONTRIBUTORS

    - In GTN CONTRIBUTORS is a YAML file that lists the information about all contributors of learning materials on the platform. -
    You must have a GitHub user to be listed as a contributor. Additional information such as ORCID can also be provided. + GTN CONTRIBUTORS is a YAML file that lists the information about all contributors of learning materials on the platform. +
    You must have a GitHub user to be listed as a contributor. Additional information such as ORCID can also be provided.
    {% icon point-right %} Add to CONTRIBUTORS.yaml @@ -778,8 +778,8 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon help %} FAQs

    - In addition to the learning content the Frequently Asked Questions can further help both learners and instructors with specific information regarding the learning context or practicalities. -
    Consider adding tutorial specific FAQ to the GTN tutorial where in you can answer questions regarding the challenges when working with the hands on activities, or provide other hints and guidelines to instructors and learners. + In addition to the learning content, the Frequently Asked Questions can further help both learners and instructors with specific information about the learning context or practicalities. +
    Consider adding a tutorial-specific FAQ to the GTN tutorial where you can answer questions about the challenges of working with the hands on activities, or provide other hints and guidelines to instructors and learners.
    {% icon point-right %} Create snippets @@ -813,7 +813,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon new-history %} OTHER

    Additional miscellaneous information should be provided if possible. -
    For an example, GTN also supports adding Organisations information. +
    For example, GTN also supports adding organisations information.
    {% icon point-right %} Add org info @@ -832,7 +832,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon references %} CITATION

    - It is best practice to provide information on how you want others to cite your learning materials when they are referenced to or reused.
    GTN does this automatically by appending the "Citing this Tutorial" section at the end of each tutorial. + It is best practice to provide information on how you want others to cite your learning materials when they are referenced or reused.
    GTN does this automatically by appending the "Citing this Tutorial" section at the end of each tutorial.
    {% icon point-right %} See an example citation @@ -849,7 +849,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon license %} CODE OF CONDUCT

    A code of conduct defines the rules for how to engage in a co-creation community. -
    It is based on a premise of an inclusive environment that respects all contributions. +
    It is based on the premise of an inclusive environment that respects all contributions.
    {% icon point-right %} Read the Galaxy Project Code of Conduct @@ -865,7 +865,7 @@ PDF document accessibility is measured with a separate technical specification <

    {% icon comment %} REVISIONS

    - Information about new or updated version of your learning materials helps others track the changes more easily.
    GTN automatically updates the Revision number of each tutorial after each release. + Information about new or updated versions of your learning materials helps others keep track of the changes more easily.
    GTN automatically updates the Revision number of each tutorial after each release.
    {% icon point-right %} Compare changes between GTN releases From a1ef5a143dfabe25fc78c81b5dace9fc10faf013 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 17:36:05 +0200 Subject: [PATCH 165/262] Minor linguistic/format/style changes in 06 Verify --- .../tutorials/fair-by-design/tutorial.md | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index a5761e6f1a087e..b8637a2315c4d3 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -893,9 +893,12 @@ PDF document accessibility is measured with a separate technical specification < Go to the full FAIR-by-Design Methodology: Publish stage ... ## Stage 6 - Verify + > You will find it a very good practice always to verify your references, sir! {: .quote author="Martin Routh"} + ### External QA + > A fresh set of eyes > - Have someone who has not participated in the development of the learning materials review the final work. This will guarantee a review free of cognitive bias. > - GTN implements this automatically via the fork-and-pull request process. Before publication your new contribution is being reviewed by GTN peers. @@ -914,10 +917,18 @@ Use the [FAIR-by-Design methodology QA checklist](https://fair-by-design-methodo The questions marked as essential achieve bare minimum FAIRness. >Essential requirements -> - **Findable** = Is the complete learning resource (including instructors info) registered or indexed in at least one searchable repository? Is it in a FAIR repository? Is metadata for the resource provided in both human- and machine-readable format (e.g JSON, XMLor YAML? -> - **Accessible** = Has an accessibility checker tool been utilised to improve the accessibility of all learning resource files (PDF, HTML, video, etc.)? Are access rules (authentication & authorisation) implemented for the learning resource? -> - **Interoperable** = Is the RDA minimal (or domain specific) metadata schema used for the learning material description? Is the resource available in open file formats which are tool agnostic and compatible with a wide variety of existing software? -> - **Reusable** = Is there clear attribution for all reused resources with compatible licenses? Has the learning resource been made available for use by defining a permissable license or policy information that allows derivations? +> - **Findable** +> - Is the complete learning resource (including instructors info) registered or indexed in at least one searchable repository? Is it in a FAIR repository? +> - Is metadata for the resource provided in both human- and machine-readable format (e.g JSON, XMLor YAML)? +> - **Accessible** +> - Has an accessibility checker tool been utilised to improve the accessibility of all learning resource files (PDF, HTML, video, etc.)? +> - Are access rules (authentication & authorisation) implemented for the learning resource? +> - **Interoperable** +> - Is the RDA minimal (or domain specific) metadata schema used for the learning material description? +> - Is the resource available in open file formats which are tool agnostic and compatible with a wide variety of existing software? +> - **Reusable** +> - Is there clear attribution for all reused resources with compatible licenses? +> - Has the learning resource been made available for use by defining a permissable license or policy information that allows derivations? {: .details} >Optional requirements From 1de5d5d924a0c843dcd9235f68c648eab1f8cdcc Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 17:36:36 +0200 Subject: [PATCH 166/262] Minor linguistic/format/style changes in 07 CI --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b8637a2315c4d3..2b9d4fe2699473 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -967,7 +967,6 @@ The questions marked as essential achieve bare minimum FAIRness. #### {% icon galaxy-download %} Gather - Gather feedback from all available internal & external sources. - - Potential sources: - Feedback form - QA recommendations @@ -980,19 +979,16 @@ The questions marked as essential achieve bare minimum FAIRness. #### {% icon galaxy-barchart %} Analyse - Analyse the gathered information in a structured way. - - Create a list of potential improvements with impact level (high, moderate, low). #### {% icon galaxy-wf-edit %} Improve - Select items from the list that will be part of a new version. - - Choose items that make sense to be in the same new release. #### {% icon galaxy-history-refresh %} Repeat - Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. - - After the Verify stage, you will reenter continuous improvement with the newly gathered information. Go to the full FAIR-by-Design Methodology: Continuous Improvement ... From a0b224613e0239928dcd38ca958d814d15ddb914 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 17:38:21 +0200 Subject: [PATCH 167/262] Always add an empty line after headings --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 2b9d4fe2699473..fb9c1f7b6ad59f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -103,6 +103,7 @@ May all your materials be FAIR! # Main stages ## Stage 1 - Prepare + > Before anything else, preparation is the key to success! {: .quote author="Alexander Graham Bell"} @@ -309,6 +310,7 @@ Reusable materials can be found anywhere. These are just some examples: {: .code-in} ### Potential for reuse + > Respect the licenses, to be respected! > - Materials with non-permissible licenses can be used for inspiration only. > - Materials with permissible licenses should be reused based on the license rules. @@ -516,6 +518,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr {: .quote author="Edward Rickenbacker"} ### Choose Tools & Formats + > Collaborative environment for team work > Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. > @@ -713,6 +716,7 @@ PDF document accessibility is measured with a separate technical specification < {: .warning} ### Final preparations + >Time to provide the accompanying information > Usually provided at (or near) the root of the learning materials, the purpose of the accompanying information is to further describe the content and define the rules of reuse. {: .tip} From 36ba1f3c8661158fb3d7dbc88ce8010992527b28 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 18:56:53 +0200 Subject: [PATCH 168/262] Remove most ellipses for consistency --- .../tutorials/fair-by-design/tutorial.md | 62 +++++++++---------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index fb9c1f7b6ad59f..87fe384237afbb 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -130,7 +130,7 @@ May all your materials be FAIR! >The learning material has a clear usage license (CC-BY-4.0 recommended) and accurate information on provenance. {: .solution } -> More details on the FAIR principles ... +> More details on the FAIR principles > [Follow the FAIR in a nutshell tutorial available on GTN]( {% link topics/fair/tutorials/fair-intro/tutorial.md %} ) > > [Follow the FAIR Galaxy Training Material tutorial available on GTN]( {% link topics/fair/tutorials/fair-gtn/tutorial.md %} ) @@ -174,20 +174,20 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} >- When developing materials in GTN, this information should be included in the Tutorial.md file header metadata. >- Most of the fields are already defined in the GTN Tutorial metadata schema. The ones that are missing can be added using the "extra" field. > -> > More details on the GTN Metadata ... +> > More details on the GTN Metadata > > [Follow the GTN Metadata tutorial]( {% link topics/contributing/tutorials/schemas/tutorial.md %} ) > {: .details} > {: .tip} ->Learn more about FAIR learning objects ... +>Learn more about FAIR learning objects >- [FAIR instructional design skills](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-instructional-design-skills) >- [FAIR guiding principles](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-guiding-principles) >- [FAIR learning objects](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/01-FAIR%20skills%20%26%20principles/01-FAIR%20skills%20%26%20principles/#fair-learning-objects) {: .details} -### Start Ideating ... +### Start Ideating

    @@ -197,7 +197,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %}
    Think backward
    Step 1
    -

    What are your desired effects, i.e. learning outcomes ...

    +

    What are your desired effects, i.e. learning outcomes?

    @@ -207,7 +207,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %}
    Think backward
    Step 2
    -

    How are you going to assess the learners achievement ...

    +

    How are you going to assess the learners achievement?

    @@ -217,13 +217,13 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %}
    Think backward
    Step 3
    -

    How should you structure the material to provide effective learning experience ...

    +

    How should you structure the material to provide effective learning experience?

    ->Learn more about the backward learning process ... +>Learn more about the backward learning process > - [Steps of the backward learning process](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#backward-instructional-design-process) {: .tip } @@ -259,7 +259,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > [Read more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) {: .question } -> More details on ideating learning outcomes and related information ... +> More details on ideating learning outcomes and related information > [Read about defining intended Learning Outcomes in the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md#define-intended-learning-outcomes-los %} ) {: .details} @@ -298,7 +298,7 @@ Reusable materials can be found anywhere. These are just some examples: > EOSC > [EOSC Training catalogue on the EOSC Marketplace](https://search.marketplace.eosc-portal.eu/search/training?q=*) > -> Most EOSC projects have their own training catalogues and/or platforms ... +> Most EOSC projects have their own training catalogues and/or platforms. {: .code-in} > General @@ -327,13 +327,13 @@ Different learners have different learning modalities (read/write, auditory, vis > Design is intelligence made visible. {: .quote author="Alina Wheeler"} -Now it's time to brainstorm ... +Now it's time to brainstorm. ### Concept map Step 1: Build a concept map of your learning materials. -> More details on concept maps ... +> More details on concept maps > [Read about Concept Maps in the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md#concept-maps %} ) {: .details} @@ -363,7 +363,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr > > GTN defines a specific hierarchical structure that needs to be followed when developing learning materials. > -> > Check out the following tutorials ... +> > Check out the following tutorials > > [How to create a skeleton for a new learning topic]( {% link topics/contributing/tutorials/create-new-topic/tutorial.md#creating-a-new-topic-with-its-own-materials %} ) > > > > [How to create the skeleton of a new tutorial]( {% link topics/contributing/tutorials/create-new-tutorial/tutorial.md %} ) @@ -378,7 +378,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr >Available feedback form > GTN provides a readily available feedback form that is automatically added at the end of each tutorial. The feedback form is used to gather quantitative and qualitative feedback. > -> > Learn more about feedback in training ... +> > Learn more about feedback in training > > [Follow the Assessment and feedback in training and teachings tutorial available on GTN]( {% link topics/teaching/tutorials/assessment/tutorial.md#dealing-with-feedback %} ) > {: .details} > @@ -389,7 +389,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr > > The facilitation guide kit includes documentation of the process of organising and running a training. What different people need to have, know and do so that everything runs smoothly. > -> > Learn more about facilitation ... +> > Learn more about facilitation > > [Follow the Organizing a workshop tutorial available on GTN]( {% link topics/teaching/tutorials/organize-workshop/tutorial.md %} ) > > > > [Follow the Running a workshop as instructor tutorial available on GTN]( {% link topics/teaching/tutorials/running-workshop/tutorial.md#Checklists %} ) @@ -409,7 +409,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr ### How to design the learning content -Read more about the Hunter Model ... +Read more about the Hunter Model.
    @@ -417,7 +417,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon curriculum %} 1. Set Learning Objectives

    - ... what is the goal + What is the goal?

    @@ -427,7 +427,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon pref-identities %} 2. Identify Needs

    - ... how to get there + How to get there?

    @@ -437,7 +437,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon galaxy-panelview %} 3. Plan

    - ... share the agenda + Share the agenda.

    @@ -450,7 +450,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon version %} 4. Hook

    - ... why is the content important + Why is the content important?

    @@ -460,7 +460,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon galaxy-wf-edit %} 5. Instruct

    - ... watch how I do it + Watch how I do it.

    @@ -470,7 +470,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon galaxy-rulebuilder-history %} 6. Practise

    - ... you help me do it, I'll watch you do it + You help me do it, I'll watch you do it.

    @@ -483,7 +483,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon galaxy-barchart %} 7. Wrap-Up

    - ... foster retention and reinforcement + Foster retention and reinforcement.

    @@ -493,7 +493,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon license %} 8. Evaluate

    - ... monitor progress + Monitor progress.

    @@ -503,7 +503,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    {% icon galaxy-history-answer %} 9. Reflect

    - .. how did it go? + How did it go?

    @@ -525,7 +525,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr > - GitHub is one of the most popular options at the moment (find out more here) > - GTN is also based on GitHub and defines [specific procedures on how one can contribute and collaborate](https://github.com/galaxyproject/training-material/blob/main/CONTRIBUTING.md) using GitHub > -> > GTN: collaboration using GitHub ... +> > GTN: collaboration using GitHub > > [Follow the Contributing with GitHub via its interface tutorial available on GTN]( {% link topics/contributing/tutorials/github-interface-contribution/tutorial.md %} ) > > > > [Follow the Contributing with GitHub via command-line tutorial available on GTN]( {% link topics/contributing/tutorials/github-command-line-contribution/tutorial.md %} ) @@ -565,13 +565,13 @@ Each MVS profile defines a list of technical and soft skills required for the pr #### Check the license -The existing materials you are reusing are available under a CC license, but it is different than the one you plan to use for your materials ... +The existing materials you are reusing are available under a CC license, but it is different than the one you plan to use for your materials. Depending on how you want to reuse the material, you will need to consider the following aspects. >I want to reuse it as a whole >- You can't use something that is licensed with ND (no derivatives). >- In this case you must follow the rules on combining and adapting CC material. > ->[Read more ...](https://creativecommons.org/faq/#combining-and-adapting-cc-material) +>[Read more](https://creativecommons.org/faq/#combining-and-adapting-cc-material) {: .details} >I want to reuse a small part of it @@ -580,7 +580,7 @@ The existing materials you are reusing are available under a CC license, but it > Remember that if the work is licensed with ND, you can not modify it while reusing. {: .details} ->Learn more about IPR ... +>Learn more about IPR >[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) {: .tip} @@ -625,7 +625,7 @@ You should also be able to remove attribution upon request. > - [Comcast protest](http://www.flickr.com/photos/ari/8503459/in/set-214952/)” by Flikr user [Steve Rhodes](http://www.flickr.com/photos/ari/) used under [Creative Commons Attribution 2.0 license](http://creativecommons.org/licenses/by/2.0/deed.en) {: .details} -> Read more about how to attribute ... +> Read more about how to attribute > [{% icon point-right %} Attribution and Citing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#attribution-and-citing) > > [{% icon point-right %} How to handle attribution?](https://courses.lumenlearning.com/suny-oerguide/chapter/how-to-handle-attribution/) @@ -912,7 +912,7 @@ PDF document accessibility is measured with a separate technical specification < > In Skills4EOSC T2.4 has developed a number of QA checklists that you and your external reviewer need to go through so that you can ensure high-quality learning materials {% cite sanchez_2023_8305482 %}. {: .tip} -### FAIR or not FAIR, that is the question ... +### FAIR or not FAIR, that is the question #### Measure FAIRness From 54df67a0e9858952050cae6afa001fefa4acb328 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 19:05:29 +0200 Subject: [PATCH 169/262] Fix some punctuation errors --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 87fe384237afbb..8780b296ec5c0a 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -612,7 +612,7 @@ You should also be able to remove attribution upon request. {: .solution} > Examples -> Examples are taken from [Best Practices for Creative Commons attributions - how to attribute works you reuse under a Creative Commons license](https://www.newmediarights.org/guide/how_to/creative_commons/best_practices_creative_commons_attributions) submitted by [New Media Rights](https://www.newmediarights.org/) available under a [CC BY-NC 3.0 US DEED](https://creativecommons.org/licenses/by-nc/3.0/us/) +> Examples are taken from [Best Practices for Creative Commons attributions - how to attribute works you reuse under a Creative Commons license](https://www.newmediarights.org/guide/how_to/creative_commons/best_practices_creative_commons_attributions) submitted by [New Media Rights](https://www.newmediarights.org/) available under a [CC BY-NC 3.0 US DEED](https://creativecommons.org/licenses/by-nc/3.0/us/). > - Webpage/Blog - Title (with link to original work), author (or username) (with link to author's website), and license (with link). > - [Undercover Vampire Policeman](https://chriszabriskie.bandcamp.com/album/undercover-vampire-policeman) by [Chris Zabriskie](https://chriszabriskie.bandcamp.com/), available under a [Creative Commons Attribution 4.0 License](http://creativecommons.org/licenses/by/4.0/) > - Book – Title, author, license written somewhere near the title and author if it’s a hard copy or if it’s an online book you should include a link to the licensed terms. @@ -783,7 +783,7 @@ PDF document accessibility is measured with a separate technical specification <
    {% icon help %} FAQs

    In addition to the learning content, the Frequently Asked Questions can further help both learners and instructors with specific information about the learning context or practicalities. -
    Consider adding a tutorial-specific FAQ to the GTN tutorial where you can answer questions about the challenges of working with the hands on activities, or provide other hints and guidelines to instructors and learners. +
    Consider adding a tutorial-specific FAQ to the GTN tutorial, where you can answer questions about the challenges of working with the hands on activities, or provide other hints and guidelines to instructors and learners.
    {% icon point-right %} Create snippets From 376773373d6a8f301e44b6e368755e202802f1c7 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Fri, 16 Aug 2024 19:08:18 +0200 Subject: [PATCH 170/262] Remove a line break --- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 8780b296ec5c0a..e45c8ddf34cfd8 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -584,9 +584,7 @@ The existing materials you are reusing are available under a CC license, but it >[How Intellectual Property Rights (IPR) protect the interests of the creators and owners by providing them with rights over their creation?](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#intellectual-property-rights-ipr) {: .tip} -Still need help? - -[{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) +Still need help? [{% icon point-right %} Go to CC licensing FAQ](https://creativecommons.org/faq/#before-using-cc-licensed-material) #### Attribute From 1e91048cf6066e2256c2e1695edc258895cc6870 Mon Sep 17 00:00:00 2001 From: achim-kit <178550642+achim-kit@users.noreply.github.com> Date: Tue, 20 Aug 2024 11:12:34 +0200 Subject: [PATCH 171/262] Remove tracking from Pixabay links --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index e45c8ddf34cfd8..ce8e507a23e63f 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -635,7 +635,7 @@ You should also be able to remove attribution upon request. The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. ![Universal access logo](../../images/universal-access-6602642_640.png) -Image by J S from Pixabay +"Universal Access Human" by J S from Pixabay #### Standards From 085ae7d185035614adfa857915eb974b1e3ca3ed Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Tue, 20 Aug 2024 14:26:52 +0200 Subject: [PATCH 172/262] new author added --- CONTRIBUTORS.yaml | 6 +++++- topics/contributing/tutorials/fair-by-design/tutorial.md | 1 + 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 59233fabdf821a..82aa35cbb035c3 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -2413,4 +2413,8 @@ isouyioul: CarolinLeister: name: Carolin Leister - orcid: 0000-0002-6940-0024 \ No newline at end of file + orcid: 0000-0002-6940-0024 + +achim-kit: + name: Achim Winandi + orcid: 0000-0003-4800-7925 \ No newline at end of file diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 41bc0512773266..af1acc58fde28e 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -35,6 +35,7 @@ contributions: - korvoj - domlgreen - isouyioul + - achim-kit funding: - skills4eosc follow_up_training: From f552a9db32e00fb9387ee387f3ea675d3cc65c87 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 22 Aug 2024 09:31:31 +0200 Subject: [PATCH 173/262] added contributors --- CONTRIBUTORS.yaml | 9 ++++++++- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 ++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 82aa35cbb035c3..825fc56b79b3d7 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -2417,4 +2417,11 @@ CarolinLeister: achim-kit: name: Achim Winandi - orcid: 0000-0003-4800-7925 \ No newline at end of file + orcid: 0000-0003-4800-7925 + +agCleo: + name: Аrnaud Gingold + +CRHAD26: + name: Christine Hadrossek + orcid: 0000-0002-2638-6373 \ No newline at end of file diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index ace2c4368f072b..b05e769bd88c26 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -36,6 +36,8 @@ contributions: - domlgreen - isouyioul - achim-kit + - agCleo + - CRHAD26 funding: - skills4eosc follow_up_training: From ecfe99dd10ed580de562eca04caa9fbed4b67ff4 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 23 Aug 2024 12:43:04 +0200 Subject: [PATCH 174/262] Update CONTRIBUTORS.yaml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- CONTRIBUTORS.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 825fc56b79b3d7..1c87b84c434eaa 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -131,8 +131,6 @@ alliecreason: almahmoud: name: Alex Mahmoud joined: 2019-06 - orcid: 0000-0001-7271-6655 - andreacabibbe: name: Andrea Cabibbe affiliations: From 19191d2d2a586cb6f1e44c46eb658e6a7ffa312a Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 23 Aug 2024 12:44:08 +0200 Subject: [PATCH 175/262] changes as required --- CONTRIBUTORS.yaml | 4 ++++ FUNDERS.yaml | 2 +- topics/contributing/tutorials/fair-by-design/tutorial.md | 4 ++-- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 825fc56b79b3d7..8596f6612b805f 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -2413,15 +2413,19 @@ isouyioul: CarolinLeister: name: Carolin Leister + joined: 2024-07 orcid: 0000-0002-6940-0024 achim-kit: name: Achim Winandi + joined: 2024-07 orcid: 0000-0003-4800-7925 agCleo: name: Аrnaud Gingold + joined: 2024-07 CRHAD26: name: Christine Hadrossek + joined: 2024-07 orcid: 0000-0002-2638-6373 \ No newline at end of file diff --git a/FUNDERS.yaml b/FUNDERS.yaml index 0d9632520c4690..5eddada3d0dd7b 100644 --- a/FUNDERS.yaml +++ b/FUNDERS.yaml @@ -299,7 +299,7 @@ skills4eosc: funding_system: cordis funder_name: Horizon Europe url: https://www.skills4eosc.eu/ - github: https://github.com/FAIR-by-Design-Methodology + github: false ukmrc: name: UK Medical Research Council diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index b05e769bd88c26..44157b3bd5c1b9 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -395,7 +395,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr > > Learn more about facilitation > > [Follow the Organizing a workshop tutorial available on GTN]( {% link topics/teaching/tutorials/organize-workshop/tutorial.md %} ) > > -> > [Follow the Running a workshop as instructor tutorial available on GTN]( {% link topics/teaching/tutorials/running-workshop/tutorial.md#Checklists %} ) +> > [Follow the Running a workshop as instructor tutorial available on GTN]( {% link topics/teaching/tutorials/running-workshop/tutorial.md %} ) > {: .details} > > Another option is to use something like the [TRIPLE project TRAINING TOOLKIT](https://project.gotriple.eu/project-deliverables/triple-training-toolkit/). @@ -839,7 +839,7 @@ PDF document accessibility is measured with a separate technical specification <

    It is best practice to provide information on how you want others to cite your learning materials when they are referenced or reused.
    GTN does this automatically by appending the "Citing this Tutorial" section at the end of each tutorial.
    - + {% icon point-right %} See an example citation

    From 534d98ed48ae897b5b4f0635f04f57967dd04a93 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 23 Aug 2024 12:45:47 +0200 Subject: [PATCH 176/262] Update CONTRIBUTORS.yaml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- CONTRIBUTORS.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 06f6f8fee56f8d..d4c4466a5ef0c5 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -1976,7 +1976,6 @@ sebastian-schaaf: sonalhenson: name: Sonal Henson joined: 2023-09 - Shians: name: Shian Su joined: 2019-02 From 040c8eedcd1ccab2e665c1f283deee4229b2c1db Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 23 Aug 2024 12:45:57 +0200 Subject: [PATCH 177/262] Update topics/contributing/tutorials/fair-by-design/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 44157b3bd5c1b9..013df6f93f3fa1 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -643,7 +643,7 @@ The developed learning materials should cover the widest range of learner variab #### Standards -There are several standards that govern the rules on level of accessibility. +There are several standards that govern the rules on the level of accessibility. Most commonly used is the W3C Web Content Accessibility Guidelines (WCAG) standard version 2.1. Three conformance levels exist, you should aim for AA which is the middle one. From f6a8ab817df2e27a03e08392617fe544fbaf30a7 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 23 Aug 2024 12:46:17 +0200 Subject: [PATCH 178/262] Update topics/contributing/tutorials/fair-by-design/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 013df6f93f3fa1..6da89fda4bb8e6 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -977,7 +977,7 @@ The questions marked as essential achieve bare minimum FAIRness. - QA recommendations - Self-reflection after training - Git Issues - - Gitter Chat + - Matrix Chat - Direct mail contact - Other means of communication From 235ac695e42ffd2ab6554c89316a2cfcbf9a9f30 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 23 Aug 2024 12:46:33 +0200 Subject: [PATCH 179/262] Update topics/contributing/tutorials/fair-by-design/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 6da89fda4bb8e6..f8fe6a4aa1fa34 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -1011,7 +1011,7 @@ The questions marked as essential achieve bare minimum FAIRness. ### Training Description -Short how to guide that guides you through the stages of the FAIR-by-Design methodology without any specific choice on tools and formats. +Short how-to that guides you through the stages of the FAIR-by-Design methodology without any specific choice on tools and formats. ### Target audience From eec476fe41449df801f5feb1d26bf86a69efe4dd Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 23 Aug 2024 12:50:43 +0200 Subject: [PATCH 180/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 44157b3bd5c1b9..02846573595c55 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -568,7 +568,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr #### Check the license -The existing materials you are reusing are available under a CC license, but it is different than the one you plan to use for your materials. Depending on how you want to reuse the material, you will need to consider the following aspects. +The existing materials you are reusing are available under a [CC license](https://creativecommons.org/share-your-work/cclicenses/), but it is different than the one you plan to use for your materials. Depending on how you want to reuse the material, you will need to consider the following aspects. >I want to reuse it as a whole >- You can't use something that is licensed with ND (no derivatives). From 211fd9836e0a89746b2a442cb840c909dbed84f2 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Fri, 23 Aug 2024 13:01:20 +0200 Subject: [PATCH 181/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index ba12c09f074a3c..2e398a8fdd1dea 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -969,7 +969,7 @@ The questions marked as essential achieve bare minimum FAIRness. > To improve is to change; to be perfect is to change often {: .quote author="Winston Churchill"} -#### {% icon galaxy-download %} Gather +### {% icon galaxy-download %} Gather - Gather feedback from all available internal & external sources. - Potential sources: @@ -981,17 +981,17 @@ The questions marked as essential achieve bare minimum FAIRness. - Direct mail contact - Other means of communication -#### {% icon galaxy-barchart %} Analyse +### {% icon galaxy-barchart %} Analyse - Analyse the gathered information in a structured way. - Create a list of potential improvements with impact level (high, moderate, low). -#### {% icon galaxy-wf-edit %} Improve +### {% icon galaxy-wf-edit %} Improve - Select items from the list that will be part of a new version. - Choose items that make sense to be in the same new release. -#### {% icon galaxy-history-refresh %} Repeat +### {% icon galaxy-history-refresh %} Repeat - Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. - After the Verify stage, you will reenter continuous improvement with the newly gathered information. From 3a5e55a2d34d19ee400f62a5982a34e01dce6287 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Mon, 2 Sep 2024 14:31:20 +0200 Subject: [PATCH 182/262] updated email link to MD --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 2e398a8fdd1dea..2c142acc3b8bb4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -98,7 +98,7 @@ Welcome to the FAIR-by-Design Methodology Microlearning GTN adapted tutorial. > {: .agenda} -If you have any questions at any stage on your journey do not hesitate to contact the FAIR-by-Design methodology team. +If you have any questions at any stage on your journey do not hesitate to [contact the FAIR-by-Design methodology team](mailto:sonja.filiposka@finki.ukim.mk). May all your materials be FAIR! From fe6ea88feb1dd4b31ad9205a535b8393933e0c4c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 12 Sep 2024 12:07:47 +0200 Subject: [PATCH 183/262] Update topics/contributing/tutorials/fair-by-design/tutorial.md Co-authored-by: Helena --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 2c142acc3b8bb4..d265f2e44010fb 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -323,7 +323,7 @@ Reusable materials can be found anywhere. These are just some examples: Different learners have different learning modalities (read/write, auditory, visual, kinesthetic). To elevate the learning experience you should use all types of multimedia in your learning materials. -Go to the full description of FAIR-by-Design Methodology: Discover stage ... +[Go to the full description of FAIR-by-Design Methodology: Discover stage ...](https://fair-by-design-methodology.github.io/FAIR-by-Design_Book/4%20-%20FAIR-by-design%20learning%20materials%20creation/4.1%20-%20Workflow%20stages%20description/412-discover/){: .btn.btn-dark.text-white.btn-lg.btn-block} ## Stage 3 - Design From c887c61b89d6f2905a2505d5e27d5ee99be19063 Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 19 Sep 2024 12:29:27 +0200 Subject: [PATCH 184/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 42 ++++++++++--------- 1 file changed, 22 insertions(+), 20 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index d265f2e44010fb..8f6d017f270756 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -112,26 +112,28 @@ May all your materials be FAIR! ### First things first: What is FAIR? - -> Findable -> The editable learning material has a unique and persistent identifier (PID) and is described with sufficiently detailed metadata. -{: .solution} - - -> Accessible -> The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. -{: .solution} - - -> Interoperable -> The metadata describing the learning material follows a the RDA minimum metadata schema combined with agreed-upon controlled vocabularies. -> Formal, accessible, shared, and broadly applicable language(s) and format(s) are used to develop the material. -{: .solution} - - -> Reusable ->The learning material has a clear usage license (CC-BY-4.0 recommended) and accurate information on provenance. -{: .solution } +> What is FAIR? +> +>> Findable +>> The editable learning material has a unique and persistent identifier (PID) and is described with sufficiently detailed metadata. +>{: .solution} +> +> +>> Accessible +>> The human and machine readable metadata and object are stored in a trusted repository with clear authentication and authorization procedures. +>{: .solution} +> +> +>> Interoperable +>> The metadata describing the learning material follows a the RDA minimum metadata schema combined with agreed-upon controlled vocabularies. +>> Formal, accessible, shared, and broadly applicable language(s) and format(s) are used to develop the material. +>{: .solution} +> +> +>> Reusable +>>The learning material has a clear usage license (CC-BY-4.0 recommended) and accurate information on provenance. +>{: .solution } +{: .question } > More details on the FAIR principles > [Follow the FAIR in a nutshell tutorial available on GTN]( {% link topics/fair/tutorials/fair-intro/tutorial.md %} ) From eb9edcdc3a61c564c63dee1573574c7666032e7c Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 19 Sep 2024 12:46:43 +0200 Subject: [PATCH 185/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 8f6d017f270756..1cd7a03c2ac1f4 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -145,7 +145,7 @@ May all your materials be FAIR! If you are not using a discipline specific metadata schema, then, to ensure that your learning materials are appropriately described using a common approach, you should adopt the: - Go to the RDA Minimal Metadata Set for Learning Resources description details + Go to the RDA Minimal Metadata Set for Learning Resources description details The following are the fields described in the RDA Minimal Metadata Set divided into three categories: @@ -268,7 +268,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > [Read about defining intended Learning Outcomes in the Design and plan session, course, materials tutorial available on GTN]( {% link topics/contributing/tutorials/design/tutorial.md#define-intended-learning-outcomes-los %} ) {: .details} -Go to the full description of FAIR-by-Design Methodology: Prepare stage ... +Go to the full description of FAIR-by-Design Methodology: Prepare stage ... ## Stage 2 - Discover @@ -414,7 +414,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr ### How to design the learning content -Read more about the Hunter Model. +Read more about the Hunter Model.
    @@ -515,7 +515,7 @@ Each MVS profile defines a list of technical and soft skills required for the pr
    -Go to the full description of FAIR-by-Design Methodology: Design stage ... +Go to the full description of FAIR-by-Design Methodology: Design stage ... ## Stage 4 - Produce @@ -703,7 +703,7 @@ PDF document accessibility is measured with a separate technical specification < -Go to the full FAIR-by-Design Methodology: Produce stage ... +Go to the full FAIR-by-Design Methodology: Produce stage ... ## Stage 5 - Publish @@ -897,7 +897,7 @@ PDF document accessibility is measured with a separate technical specification < >GTN automatically creates a new record in the [Elixir TeSS training catalogue](https://tess.elixir-europe.org) that is the most relevant catalogue for its community. {: .tip} -Go to the full FAIR-by-Design Methodology: Publish stage ... +Go to the full FAIR-by-Design Methodology: Publish stage ... ## Stage 6 - Verify @@ -965,7 +965,7 @@ The questions marked as essential achieve bare minimum FAIRness. > Ensure that you actively and regularly gather feedback from both perspectives: the learners and the instructors. {: .comment} -Go to the full FAIR-by-Design Methodology: Verify stage ... +Go to the full FAIR-by-Design Methodology: Verify stage ... ## Stage 7 - Continuous Improvement > To improve is to change; to be perfect is to change often @@ -998,7 +998,7 @@ The questions marked as essential achieve bare minimum FAIRness. - Start a new cycle of the FAIR-by-Design methodology that will implement the selected items. - After the Verify stage, you will reenter continuous improvement with the newly gathered information. -Go to the full FAIR-by-Design Methodology: Continuous Improvement ... +Go to the full FAIR-by-Design Methodology: Continuous Improvement ... # About From 7cf148eb83d2a667aa343a5bb7132f8fedba570e Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 19 Sep 2024 12:49:14 +0200 Subject: [PATCH 186/262] Update tutorial.md --- topics/contributing/tutorials/fair-by-design/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 1cd7a03c2ac1f4..d990d70d978fb7 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -325,7 +325,7 @@ Reusable materials can be found anywhere. These are just some examples: Different learners have different learning modalities (read/write, auditory, visual, kinesthetic). To elevate the learning experience you should use all types of multimedia in your learning materials. -[Go to the full description of FAIR-by-Design Methodology: Discover stage ...](https://fair-by-design-methodology.github.io/FAIR-by-Design_Book/4%20-%20FAIR-by-design%20learning%20materials%20creation/4.1%20-%20Workflow%20stages%20description/412-discover/){: .btn.btn-dark.text-white.btn-lg.btn-block} +[Go to the full description of FAIR-by-Design Methodology: Discover stage ...](https://fair-by-design-methodology.github.io/FAIR-by-Design_Book/4%20-%20FAIR-by-design%20learning%20materials%20creation/4.1%20-%20Workflow%20stages%20description/412-discover/){: .btn.btn-dark.text-white.stretched-link} ## Stage 3 - Design From 81693830d5cbbec1fe16c35ea156f67ac2a06c3b Mon Sep 17 00:00:00 2001 From: amisev1971 Date: Thu, 19 Sep 2024 12:55:45 +0200 Subject: [PATCH 187/262] Update tutorial.md --- .../tutorials/fair-by-design/tutorial.md | 54 ++++++++----------- 1 file changed, 22 insertions(+), 32 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index d990d70d978fb7..714eb379b6529b 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -278,41 +278,31 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} Reusable materials can be found anywhere. These are just some examples: -> GTN -> [GTN learning resources](https://training.galaxyproject.org) -> -> [TeSS Catalogue by Elixir](https://tess.elixir-europe.org) -{: .code-in} +**GTN** -> OER -> [DOAB](https://directory.doabooks.org/) -> -> [MERLOT](https://www.merlot.org/merlot/index.htm) -> -> [OASIS](https://oasis.geneseo.edu/index.php) -> -> [OER Commons](https://www.oercommons.org/) -> -> [OERTX CORA](https://www.projectcora.org/) -> -> [GALILEO](https://oer.galileo.usg.edu/) -> -> [FORRT](https://forrt.org/) -{: .code-in} +- [GTN learning resources](https://training.galaxyproject.org) +- [TeSS Catalogue by Elixir](https://tess.elixir-europe.org) -> EOSC -> [EOSC Training catalogue on the EOSC Marketplace](https://search.marketplace.eosc-portal.eu/search/training?q=*) -> -> Most EOSC projects have their own training catalogues and/or platforms. -{: .code-in} +**OER** -> General -> [Creative Commons Search](https://search.creativecommons.org/) - content provided under a CC license -> -> [Zenodo](https://zenodo.org/) - a multi-disciplinary open repository -> -> [OSF](https://osf.io/) - a free, open research platform -{: .code-in} +- [DOAB](https://directory.doabooks.org/) +- [MERLOT](https://www.merlot.org/merlot/index.htm) +- [OASIS](https://oasis.geneseo.edu/index.php) +- [OER Commons](https://www.oercommons.org/) +- [OERTX CORA](https://www.projectcora.org/) +- [GALILEO](https://oer.galileo.usg.edu/) +- [FORRT](https://forrt.org/) + +**EOSC** + +- [EOSC Training catalogue on the EOSC Marketplace](https://search.marketplace.eosc-portal.eu/search/training?q=*) +- Most EOSC projects have their own training catalogues and/or platforms. + +**General** + +- [Creative Commons Search](https://search.creativecommons.org/) - content provided under a CC license +- [Zenodo](https://zenodo.org/) - a multi-disciplinary open repository +- [OSF](https://osf.io/) - a free, open research platform ### Potential for reuse From 93a80b97e557553c241b44953b05449860db03c2 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 12:25:10 +0200 Subject: [PATCH 188/262] rename funders file to grants for clarity --- FUNDERS.yaml => GRANTS.yaml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename FUNDERS.yaml => GRANTS.yaml (100%) diff --git a/FUNDERS.yaml b/GRANTS.yaml similarity index 100% rename from FUNDERS.yaml rename to GRANTS.yaml From 53bd356bb5c82cc2367a4a7a5690fdb5d92b476e Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 12:30:08 +0200 Subject: [PATCH 189/262] update description --- GRANTS.yaml | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/GRANTS.yaml b/GRANTS.yaml index a39b2e6a50ca77..57b9dbe02c630a 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -1,24 +1,21 @@ -# List of funders related to contributors +# List of grants funding GTN activity # -# reference funders by their id in tutorial metadata files +# Can be added to contributions->funding metadata key of materials # # valid tags: -# name, email, linkedin, twitter, gitter, orcid, bio, joined, url, -# funder, funding_id, funding_system, funding_statement +# name, joined, url, github, funding_id, funding_system, funding_statement # -# collection names should be equal to github username, if not, add github: false tag --- -# funder1: -# name: Funder A +# Grant1: # should be equal to GitHub username if one exists for the grant/project +# name: Grant/Project name # joined: 2020-06 -# url: "https://example.com" -# funder: true +# url: "https://example.com" # homepage of the project # funding_id: 2020-1-NL01-KA203-064717 -# funding_system: erasmusplus +# funding_system: erasmusplus # database/page where your # funding_statement: "This project is funded with the support of .." +# github: false # add this if the id does not map to a GitHub account, -# our real funders <3 # please add in alphabetical order of the key (id) abromics: From c867df10465aef9fc174a8dbaf90f1235c46d39f Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 12:32:15 +0200 Subject: [PATCH 190/262] remove obsolete funder key --- GRANTS.yaml | 27 --------------------------- 1 file changed, 27 deletions(-) diff --git a/GRANTS.yaml b/GRANTS.yaml index 57b9dbe02c630a..697ebcb1a21426 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -24,7 +24,6 @@ abromics: joined: 2024-01 avatar: "/training-material/assets/images/abromics.png" url: https://www.abromics.fr/ - funder: true ai4life: name: AI4Life @@ -32,7 +31,6 @@ ai4life: joined: 2023-07 avatar: "/training-material/topics/ai4life/images/AI4Life-logo_giraffe-solid.png" url: https://ai4life.eurobioimaging.eu/ - funder: true funding_id: "101057970" funding_system: cordis funding_statement: | @@ -44,7 +42,6 @@ biont: joined: 2023-09 avatar: "/training-material/assets/images/BioNT_Logo.png" url: https://biont-training.eu/ - funder: true funding_id: "101100604" funding_system: cordis funding_statement: | @@ -53,7 +50,6 @@ biont: by-covid: name: BeYond-COVID joined: 2023-04 - funder: true funding_id: "101046203" funding_system: cordis funding_statement: | @@ -67,7 +63,6 @@ CINECA-Project: name: Common Infrastructure for National Cohorts in Europe, Canada, and Africa short_name: "CINECA" joined: 2023-03 - funder: true funding_id: "825775" funding_system: cordis funder_name: Horizon 2020 @@ -78,11 +73,9 @@ nfdi4plants: joined: 2024-07 url: https://www.nfdi4plants.de://www.nfdi4plants.de/ avatar: "/training-material/shared/images/logo-dataplant.svg" - funder: true deNBI: name: de.NBI - funder: true url: https://www.denbi.de/ elixir-converge: @@ -91,7 +84,6 @@ elixir-converge: joined: 2023-01 avatar: "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png" url: https://elixir-europe.org/about-us/how-funded/eu-projects/converge - funder: true funding_id: "871075" funding_system: cordis funding_statement: | @@ -104,7 +96,6 @@ edctp-eu: avatar: "/training-material/shared/images/edctp-eu.png" github: false url: https://www.edctp.org/ - funder: true funding_statement: | TB-CAPT, PanACEA and PANGenS are part of the EDCTP2 and EDCTP3 programs supported by the European Union. @@ -113,14 +104,12 @@ elixir-excelerate: url: https://www.elixir-europe.org/excelerate/ avatar: "/training-material/shared/images/Excelerate_whitebackground.png" github: false - funder: true elixir-fair-data: name: "ELIXIR-UK: FAIR Data Stewardship training" short_name: "ELIXIR Fair Data" github: false joined: 2023-06 - funder: true funding_id: MR/V038966/1 funding_system: ukri funding_statement: | @@ -133,7 +122,6 @@ elixir-uk-dash: github: false avatar: "/training-material/shared/images/dash.png" url: https://elixiruknode.org/projects/elixir-uk-dash/ - funder: true funding_system: ukri funding_id: MR/V038966/1 funding_statement: | @@ -144,7 +132,6 @@ eosc-life: github: false joined: 2023-04 avatar: "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png" - funder: true funding_id: "824087" funding_system: cordis funding_statement: | @@ -157,7 +144,6 @@ epsrc-training-grant: short_name: "EPSRC/OU" github: false joined: 2022-09 - funder: true funding_statement: The research internship was supported through EPSRC Training Grant DTP 2020-2021 Open University url: "https://www.open.ac.uk/" @@ -167,7 +153,6 @@ eurosciencegateway: joined: 2023-10 avatar: "/training-material/assets/images/eurosciencegateway.png" url: https://galaxyproject.org/projects/esg/ - funder: true funding_id: "101057388" funding_system: cordis funding_statement: | @@ -180,7 +165,6 @@ fairease: joined: 2023-10 avatar: "/training-material/assets/images/fair_ease_colour.png" url: https://fairease.eu/ - funder: true funding_id: "101058785" funding_system: cordis funding_statement: | @@ -192,7 +176,6 @@ fnso2019: joined: 2023-05 avatar: "/training-material/shared/images/fnso.png" github: false - funder: true url: "https://www.ouvrirlascience.fr/national-fund-for-open-science/" funder_name: National Fund for Open Science funding_id: AAPFNSO2019OpenMetaPaper-14026 @@ -209,7 +192,6 @@ gallantries: joined: 2020-09 avatar: "https://gallantries.github.io/assets/images/gallantries-logo.png" github: false - funder: true url: "https://www.erasmusplus.nl" funder_name: Erasmus+ Programme funding_id: 2020-1-NL01-KA203-064717 @@ -225,7 +207,6 @@ h2020-defend: short_name: DEFEND github: false joined: 2023-05 - funder: true funding_id: "773701" funding_system: cordis funding_statement: | @@ -239,7 +220,6 @@ madland: joined: 2024-07 url: https://madland.science avatar: "/training-material/shared/images/logo-madland.jpg" - funder: true github: false mwk: @@ -248,7 +228,6 @@ mwk: joined: 2024-08 url: https://mwk.baden-wuerttemberg.de/de/startseite avatar: "/training-material/assets/images/MWK.png" - funder: true github: false nhgri-anvil: @@ -258,7 +237,6 @@ nhgri-anvil: joined: 2023-06 avatar: https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png url: https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL - funder: true funding_id: U24HG010263 nhgri-gdscn: @@ -268,7 +246,6 @@ nhgri-gdscn: joined: 2023-06 avatar: https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png url: https://www.genome.gov/ - funder: true funding_id: 75N92022P00232 NIH: @@ -276,7 +253,6 @@ NIH: short_name: "NIH" avatar: /training-material/shared/images/nih.png url: https://nih.gov/ - funder: true github: false @@ -285,7 +261,6 @@ nsf: url: https://www.nsf.gov avatar: "/training-material/shared/images/nsf.gif" github: false - funder: true sfb992: @@ -293,7 +268,6 @@ sfb992: url: https://www.sfb992.uni-freiburg.de/ avatar: https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg github: false - funder: true ukmrc: @@ -301,6 +275,5 @@ ukmrc: url: https://mrc.ukri.org avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/master/logo.png github: false - funder: true From bd0ee81d62bb747ec7976533d57d0b37e8bd8b57 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 12:38:57 +0200 Subject: [PATCH 191/262] relabel funders to grants in scripts for clarity --- .github/workflows/ci-main.yml | 2 +- bin/gtn.rb | 4 ++-- bin/news.rb | 10 +++++----- bin/validate-contributors.rb | 10 +++++----- 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.github/workflows/ci-main.yml b/.github/workflows/ci-main.yml index 11d974a2c02da7..21993c3c2934a1 100644 --- a/.github/workflows/ci-main.yml +++ b/.github/workflows/ci-main.yml @@ -17,7 +17,7 @@ on: - 'news/**' - 'events/**' - CONTRIBUTORS.yaml - - FUNDERS.yaml + - GRANTS.yaml - ORGANISATIONS.yaml diff --git a/bin/gtn.rb b/bin/gtn.rb index 1de7f225e5e203..163650590ff914 100644 --- a/bin/gtn.rb +++ b/bin/gtn.rb @@ -2,7 +2,7 @@ CONTRIBUTORS = YAML.load_file('CONTRIBUTORS.yaml') ORGANISATIONS = YAML.load_file('ORGANISATIONS.yaml') -FUNDERS = YAML.load_file('FUNDERS.yaml') +GRANTS = YAML.load_file('GRANTS.yaml') def automagic_loading(f) # Remove our documentation @@ -18,7 +18,7 @@ def automagic_loading(f) repl = [] # If one of the elements in this array is CONTRIBUTORS, replace it with the same named variable repl << CONTRIBUTORS.keys if v.find { |x| x == 'CONTRIBUTORS' } - repl << FUNDERS.keys if v.find { |x| x == 'FUNDERS' } + repl << GRANTS.keys if v.find { |x| x == 'GRANTS' } repl << ORGANISATIONS.keys if v.find { |x| x == 'ORGANISATIONS' } v.replace repl.flatten if repl.length.positive? end diff --git a/bin/news.rb b/bin/news.rb index e8787c772108be..dfbdcc3a249dda 100755 --- a/bin/news.rb +++ b/bin/news.rb @@ -51,7 +51,7 @@ CONTRIBUTORS = safe_load_yaml('CONTRIBUTORS.yaml') ORGANISATIONS = safe_load_yaml('ORGANISATIONS.yaml') -FUNDERS = safe_load_yaml('FUNDERS.yaml') +GRANTS = safe_load_yaml('GRANTS.yaml') # new news # new slidevideos @@ -140,7 +140,7 @@ def isDraft(n) .split("\n").grep(/^\+[^ ]+:\s*$/).map { |x| x.strip[1..-2] }, organisations: `git diff --unified --ignore-all-space #{options[:previousCommit]} ORGANISATIONS.yaml` .split("\n").grep(/^\+[^ ]+:\s*$/).map { |x| x.strip[1..-2] }, - funders: `git diff --unified --ignore-all-space #{options[:previousCommit]} FUNDERS.yaml` + grants: `git diff --unified --ignore-all-space #{options[:previousCommit]} GRANTS.yaml` .split("\n").grep(/^\+[^ ]+:\s*$/).map { |x| x.strip[1..-2] }, } @@ -234,10 +234,10 @@ def build_news(data, filter: nil, updates: true, only_news: false) output += data[:organisations].map { |c| linkify("@#{c}", "hall-of-fame/#{c}") }.join("\n").gsub(/^/, '- ') end - if filter.nil? && data[:funders].length.positive? + if filter.nil? && data[:grants].length.positive? newsworthy = true - output += "\n\n## #{data[:funders].length} new funders!\n\n" - output += data[:funders].map { |c| linkify("@#{c}", "hall-of-fame/#{c}") }.join("\n").gsub(/^/, '- ') + output += "\n\n## #{data[:grants].length} new grants!\n\n" + output += data[:grants].map { |c| linkify("@#{c}", "hall-of-fame/#{c}") }.join("\n").gsub(/^/, '- ') end [output, newsworthy] diff --git a/bin/validate-contributors.rb b/bin/validate-contributors.rb index 17d8b0a89065e1..15f71c33746e4e 100755 --- a/bin/validate-contributors.rb +++ b/bin/validate-contributors.rb @@ -11,9 +11,9 @@ CONTRIBUTORS_SCHEMA = automagic_loading(CONTRIBUTORS_SCHEMA_UNSAFE) contribs_validator = Kwalify::Validator.new(CONTRIBUTORS_SCHEMA) -FUNDERS_SCHEMA_UNSAFE = YAML.load_file('bin/schema-funders.yaml') -FUNDERS_SCHEMA = automagic_loading(FUNDERS_SCHEMA_UNSAFE) -funders_validator = Kwalify::Validator.new(FUNDERS_SCHEMA) +GRANTS_SCHEMA_UNSAFE = YAML.load_file('bin/schema-grants.yaml') +GRANTS_SCHEMA = automagic_loading(GRANTS_SCHEMA_UNSAFE) +grants_validator = Kwalify::Validator.new(GRANTS_SCHEMA) ORGANISATIONS_SCHEMA_UNSAFE = YAML.load_file('bin/schema-organisations.yaml') ORGANISATIONS_SCHEMA = automagic_loading(ORGANISATIONS_SCHEMA_UNSAFE) @@ -43,8 +43,8 @@ def show_errors(file, errs) # This variable from bin/gtn.rb errs = validate_document(CONTRIBUTORS, contribs_validator) ec |= show_errors('CONTRIBUTORS.yaml', errs) -errs = validate_document(FUNDERS, funders_validator) -ec |= show_errors('FUNDERS.yaml', errs) +errs = validate_document(GRANTS, grants_validator) +ec |= show_errors('GRANTS.yaml', errs) errs = validate_document(ORGANISATIONS, organisations_validator) ec | show_errors('ORGANISATIONS.yaml', errs) From 8d68064e87f9049941c8a75cf028a06d7c679229 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 12:40:03 +0200 Subject: [PATCH 192/262] rename schema file --- bin/{schema-funders.yaml => schema-grants.yaml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename bin/{schema-funders.yaml => schema-grants.yaml} (100%) diff --git a/bin/schema-funders.yaml b/bin/schema-grants.yaml similarity index 100% rename from bin/schema-funders.yaml rename to bin/schema-grants.yaml From 69eb536d69af6e1c78e1210ab623527b2ca4aead Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 13:10:22 +0200 Subject: [PATCH 193/262] rename funders to grants --- _includes/funding-statement.md | 4 ++-- _layouts/news.html | 2 +- bin/schema-contributors.yaml | 4 ++-- bin/schema-event-external.yaml | 4 ++-- bin/schema-event.yaml | 4 ++-- bin/schema-learning-pathway.yaml | 2 +- bin/schema-news.yaml | 8 ++++---- bin/schema-slides.yaml | 8 ++++---- bin/schema-tutorial.yaml | 8 ++++---- metadata/funders.yaml | 1 - metadata/grants.yaml | 1 + metadata/schema-funders.yaml | 1 - metadata/schema-grants.yaml | 1 + topics/contributing/tutorials/schemas/tutorial.md | 4 ++-- 14 files changed, 26 insertions(+), 26 deletions(-) delete mode 120000 metadata/funders.yaml create mode 120000 metadata/grants.yaml delete mode 120000 metadata/schema-funders.yaml create mode 120000 metadata/schema-grants.yaml diff --git a/_includes/funding-statement.md b/_includes/funding-statement.md index d2f72e4526ebce..47bef4df50ea78 100644 --- a/_includes/funding-statement.md +++ b/_includes/funding-statement.md @@ -3,7 +3,7 @@ {% for id in include.funders %} {% assign name = site.data.contributors[id].name | default: id -%} - {% assign pfo = site.data.funders[id] | default: site.data.organisations[id] | default: site.data.contributors[id] | default: nil %} + {% assign pfo = site.data.grants[id] | default: site.data.organisations[id] | default: site.data.contributors[id] | default: nil %}
    {% if pfo.avatar %} Logo @@ -17,7 +17,7 @@
    {{ pfo.short_name | default: pfo.name | default: id }}
    - {{ site.data.funders[id].funding_statement | markdownify | strip_html }} + {{ site.data.grants[id].funding_statement | markdownify | strip_html }} {{ pfo.description }}
    diff --git a/_layouts/news.html b/_layouts/news.html index 7008c0d1f06381..8b6e4b1cb4ef29 100644 --- a/_layouts/news.html +++ b/_layouts/news.html @@ -59,7 +59,7 @@

    {{locale['references']| default: "References" }}

    {% if page.contributions %} {% if page.contributions.funding %}

    {{locale['references']| default: "Funding" }}

    -

    These individuals or organisations provided funding support for the development of this resource

    +

    These organisations or grants provided funding support for the development of this resource

    {% include _includes/funding-statement.md funders=page.contributions.funding %} {% endif %} {% endif %} diff --git a/bin/schema-contributors.yaml b/bin/schema-contributors.yaml index 0ecf767339915e..9ea70e54cb1135 100644 --- a/bin/schema-contributors.yaml +++ b/bin/schema-contributors.yaml @@ -101,7 +101,7 @@ mapping: required: true enum: - ORGANISATIONS - - FUNDERS + - GRANTS former_affiliations: type: seq description: "A set of organisations you were previously affiliated with" @@ -110,7 +110,7 @@ mapping: required: true enum: - ORGANISATIONS - - FUNDERS + - GRANTS elixir_node: type: str enum: diff --git a/bin/schema-event-external.yaml b/bin/schema-event-external.yaml index 6320791ef1d464..973c5b02d6e0a0 100644 --- a/bin/schema-event-external.yaml +++ b/bin/schema-event-external.yaml @@ -58,7 +58,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS funding: type: seq description: These entities provided funding support for the development of this resource @@ -66,7 +66,7 @@ mapping: - type: str enum: - ORGANISATIONS - - FUNDERS + - GRANTS translation: type: seq description: These entities did translation and localisation work on this resource diff --git a/bin/schema-event.yaml b/bin/schema-event.yaml index 0e792fbd26a11c..98d3437a5e2076 100644 --- a/bin/schema-event.yaml +++ b/bin/schema-event.yaml @@ -53,7 +53,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS funding: type: seq description: These entities provided funding support for the development of this resource @@ -61,7 +61,7 @@ mapping: - type: str enum: - ORGANISATIONS - - FUNDERS + - GRANTS translation: type: seq description: These entities did translation and localisation work on this resource diff --git a/bin/schema-learning-pathway.yaml b/bin/schema-learning-pathway.yaml index 7852cf67dbd301..018cbdd2596ad1 100644 --- a/bin/schema-learning-pathway.yaml +++ b/bin/schema-learning-pathway.yaml @@ -54,7 +54,7 @@ mapping: - type: str enum: - ORGANISATIONS - - FUNDERS + - GRANTS tags: type: seq description: Any relevant tags that would help a user discover this LP diff --git a/bin/schema-news.yaml b/bin/schema-news.yaml index d11e68de938776..e7ed0c10945eb2 100644 --- a/bin/schema-news.yaml +++ b/bin/schema-news.yaml @@ -35,7 +35,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS description: | List of tutorial contributors. Please use `contributions` instead as it provides more detailed accounting of tutorial history. _examples: @@ -104,7 +104,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS funding: type: seq description: These entities provided funding support for the development of this resource @@ -112,7 +112,7 @@ mapping: - type: str enum: - ORGANISATIONS - - FUNDERS + - GRANTS translation: type: seq description: These entities did translation and localisation work on this resource @@ -129,7 +129,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS cover: type: str description: | diff --git a/bin/schema-slides.yaml b/bin/schema-slides.yaml index dcde51fb887e9e..13249ef2bbac0e 100644 --- a/bin/schema-slides.yaml +++ b/bin/schema-slides.yaml @@ -83,7 +83,7 @@ mapping: required: true enum: - CONTRIBUTORS - - FUNDERS + - GRANTS - ORGANISATIONS description: | List of tutorial contributors. Please use `contributions` instead as it provides more detailed accounting of tutorial history. @@ -153,7 +153,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS funding: type: seq description: These entities provided funding support for the development of this resource @@ -161,7 +161,7 @@ mapping: - type: str enum: - ORGANISATIONS - - FUNDERS + - GRANTS translation: type: seq description: These entities did translation and localisation work on this resource @@ -178,7 +178,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS hands_on: type: str enum: diff --git a/bin/schema-tutorial.yaml b/bin/schema-tutorial.yaml index a0340c245f87a5..2c5d8547b85e64 100644 --- a/bin/schema-tutorial.yaml +++ b/bin/schema-tutorial.yaml @@ -83,7 +83,7 @@ mapping: required: true enum: - CONTRIBUTORS - - FUNDERS + - GRANTS - ORGANISATIONS description: | List of tutorial contributors. Please use `contributions` instead as it provides more detailed accounting of tutorial history. @@ -153,7 +153,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS funding: type: seq description: These entities provided funding support for the development of this resource @@ -161,7 +161,7 @@ mapping: - type: str enum: - ORGANISATIONS - - FUNDERS + - GRANTS translation: type: seq description: These entities did translation and localisation work on this resource @@ -178,7 +178,7 @@ mapping: enum: - CONTRIBUTORS - ORGANISATIONS - - FUNDERS + - GRANTS subtopic: type: str description: | diff --git a/metadata/funders.yaml b/metadata/funders.yaml deleted file mode 120000 index d0859efd5ab683..00000000000000 --- a/metadata/funders.yaml +++ /dev/null @@ -1 +0,0 @@ -../FUNDERS.yaml \ No newline at end of file diff --git a/metadata/grants.yaml b/metadata/grants.yaml new file mode 120000 index 00000000000000..3b511b7b8dfd63 --- /dev/null +++ b/metadata/grants.yaml @@ -0,0 +1 @@ +../GRANTS.yaml \ No newline at end of file diff --git a/metadata/schema-funders.yaml b/metadata/schema-funders.yaml deleted file mode 120000 index 31f74974b577e9..00000000000000 --- a/metadata/schema-funders.yaml +++ /dev/null @@ -1 +0,0 @@ -../bin/schema-funders.yaml \ No newline at end of file diff --git a/metadata/schema-grants.yaml b/metadata/schema-grants.yaml new file mode 120000 index 00000000000000..56c55875577c75 --- /dev/null +++ b/metadata/schema-grants.yaml @@ -0,0 +1 @@ +../bin/schema-grants.yaml \ No newline at end of file diff --git a/topics/contributing/tutorials/schemas/tutorial.md b/topics/contributing/tutorials/schemas/tutorial.md index 2990641537e206..0f365685665f17 100644 --- a/topics/contributing/tutorials/schemas/tutorial.md +++ b/topics/contributing/tutorials/schemas/tutorial.md @@ -60,6 +60,6 @@ contributors: {% assign kid_val = site.data['schema-organisations'] %} {% include _includes/schema-render.html key=kid_key value=kid_val %} -{% assign kid_key = "Funder Schema" %} -{% assign kid_val = site.data['schema-funders'] %} +{% assign kid_key = "Grant Schema" %} +{% assign kid_val = site.data['schema-grants'] %} {% include _includes/schema-render.html key=kid_key value=kid_val %} From 4396760858639c923a7150f160d4a214dc260b70 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 14:47:57 +0200 Subject: [PATCH 194/262] reword explanation --- ORGANISATIONS.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml index 102d6b324eb7e7..8e5a74bdcc2f19 100644 --- a/ORGANISATIONS.yaml +++ b/ORGANISATIONS.yaml @@ -1,13 +1,14 @@ --- -# List of contributing organisations +# List of contributing organisations and projects # -# reference maintainers/contributors by their id in tutorial metadata files +# Organisations can be listed as affiliations for contributors +# Organisations can be listed as funding contributors on training materials # # valid tags: name, email, linkedin, twitter, gitter, orcid, bio, joined # -# collection names should be equal to github username, if not, add github: false tag - -# our real contributing organisations <3 (please add them in alphabetical order) +# ID should be equal to github username if one exists, otherwise add 'github: false' +# +# Please add organisations in alphabetical order AustralianBioCommons: name: Australian BioCommons From dca55482c045afe9e57e7dcbd13b7217cced3498 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 14:48:24 +0200 Subject: [PATCH 195/262] more renaming of funders to grants --- _plugins/gtn.rb | 18 +++++++++--------- _plugins/gtn/contributors.rb | 12 ++++++------ 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/_plugins/gtn.rb b/_plugins/gtn.rb index 826c02e6cf58ec..945a42d34b3691 100644 --- a/_plugins/gtn.rb +++ b/_plugins/gtn.rb @@ -847,7 +847,7 @@ def find_learningpaths_including_topic(site, topic_id) ## # We're going to do some find and replace, to replace `@gtn:contributorName` with a link to their profile. Jekyll::Hooks.register :site, :pre_render do |site| - pfo_keys = site.data['contributors'].keys + site.data['funders'].keys + site.data['organisations'].keys + pfo_keys = site.data['contributors'].keys + site.data['grants'].keys + site.data['organisations'].keys site.posts.docs.each do |post| if post.content post.content = post.content.gsub(/@gtn:([a-zA-Z0-9_-]+)/) do |match| @@ -899,10 +899,10 @@ def find_learningpaths_including_topic(site, topic_id) end site.data['organisations'][affiliation]['members'] << name - elsif site.data['funders'].key?(affiliation) - site.data['funders'][affiliation]['members'] = [] if !site.data['funders'][affiliation].key?('members') + elsif site.data['grants'].key?(affiliation) + site.data['grants'][affiliation]['members'] = [] if !site.data['grants'][affiliation].key?('members') - site.data['funders'][affiliation]['members'] << name + site.data['grants'][affiliation]['members'] << name end end end @@ -915,12 +915,12 @@ def find_learningpaths_including_topic(site, topic_id) end site.data['organisations'][affiliation]['former_members'] << name - elsif site.data['funders'].key?(affiliation) - if !site.data['funders'][affiliation].key?('former_members') - site.data['funders'][affiliation]['former_members'] = [] + elsif site.data['grants'].key?(affiliation) + if !site.data['grants'][affiliation].key?('former_members') + site.data['grants'][affiliation]['former_members'] = [] end - site.data['funders'][affiliation]['former_members'] << name + site.data['grants'][affiliation]['former_members'] << name end end end @@ -947,7 +947,7 @@ def find_learningpaths_including_topic(site, topic_id) # Annotate symlinks site.pages.each do |page| - page.data['symlink'] = File.symlink?(page.path) + page.data['symlink'] = File.symlink?(page.path) # Elsewhere we checked more levels deep, maybe enable if needed. # || File.symlink?(File.dirname(page.path)) || File.symlink?(File.dirname(File.dirname(page.path))) end diff --git a/_plugins/gtn/contributors.rb b/_plugins/gtn/contributors.rb index acc232ae5fd5bb..5d718fdf2d907b 100644 --- a/_plugins/gtn/contributors.rb +++ b/_plugins/gtn/contributors.rb @@ -94,7 +94,7 @@ def self.get_non_authors(material) def self.get_funders(site, data) if data.key?('contributions') && data['contributions'].key?('funding') # The ones specifically in the Grants table - data['contributions']['funding'].reject{ |f| site.data['funders'].key?(f) } + data['contributions']['funding'].reject{ |f| site.data['grants'].key?(f) } else [] end @@ -110,7 +110,7 @@ def self.get_funders(site, data) def self.get_grants(site, data) if data.key?('contributions') && data['contributions'].key?('funding') # The ones specifically in the Grants table - data['contributions']['funding'].select{ |f| site.data['funders'].key?(f) } + data['contributions']['funding'].select{ |f| site.data['grants'].key?(f) } else [] end @@ -140,8 +140,8 @@ def self.fetch(site, c, warn: false) return ['contributor', site.data['contributors'][c]] elsif _load_file(site, 'organisations').key?(c) return ['organisation', site.data['organisations'][c]] - elsif _load_file(site, 'funders').key?(c) - return ['funder', site.data['funders'][c]] + elsif _load_file(site, 'grants').key?(c) + return ['funder', site.data['grants'][c]] else if ! warn Jekyll.logger.warn "Contributor #{c} not found" @@ -181,7 +181,7 @@ def self.fetch_name(site, c, warn: false) # +Hash+ of contributors, funders, organisations merged together def self.list(site) site.data['contributors'] - .merge(site.data['funders']) + .merge(site.data['grants']) .merge(site.data['organisations']) .reject { |c| c['halloffame'] == 'no' } end @@ -203,7 +203,7 @@ def self.person?(site, c) # Returns: # +Boolean+ of whether the contributor is a funder or not def self.funder?(site, c) - site.data['funders'].key?(c) + site.data['grants'].key?(c) end ## From 0fe6af8cea2601f02e806974d50700ffdf9a01de Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 15:12:34 +0200 Subject: [PATCH 196/262] move anything without funding_id to organisations --- GRANTS.yaml | 57 +++++------------------------------------ ORGANISATIONS.yaml | 64 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 71 insertions(+), 50 deletions(-) diff --git a/GRANTS.yaml b/GRANTS.yaml index 697ebcb1a21426..bedd698f865d75 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -12,18 +12,13 @@ # joined: 2020-06 # url: "https://example.com" # homepage of the project # funding_id: 2020-1-NL01-KA203-064717 -# funding_system: erasmusplus # database/page where your +# funding_system: cordis|ukri|erasmusplus # database/page where your project/grant is listed, if your project is not present in one of these portals, please ping us # funding_statement: "This project is funded with the support of .." # github: false # add this if the id does not map to a GitHub account, # please add in alphabetical order of the key (id) -abromics: - name: ABRomics - github: false - joined: 2024-01 - avatar: "/training-material/assets/images/abromics.png" - url: https://www.abromics.fr/ + ai4life: name: AI4Life @@ -68,15 +63,6 @@ CINECA-Project: funder_name: Horizon 2020 url: https://www.cineca-project.eu -nfdi4plants: - name: DataPLANT - joined: 2024-07 - url: https://www.nfdi4plants.de://www.nfdi4plants.de/ - avatar: "/training-material/shared/images/logo-dataplant.svg" - -deNBI: - name: de.NBI - url: https://www.denbi.de/ elixir-converge: name: ELIXIR-CONVERGE @@ -96,14 +82,11 @@ edctp-eu: avatar: "/training-material/shared/images/edctp-eu.png" github: false url: https://www.edctp.org/ + funding_id: "101103640" + funding_system: cordis funding_statement: | TB-CAPT, PanACEA and PANGenS are part of the EDCTP2 and EDCTP3 programs supported by the European Union. -elixir-excelerate: - name: Elixir Excelerate - url: https://www.elixir-europe.org/excelerate/ - avatar: "/training-material/shared/images/Excelerate_whitebackground.png" - github: false elixir-fair-data: name: "ELIXIR-UK: FAIR Data Stewardship training" @@ -144,9 +127,12 @@ epsrc-training-grant: short_name: "EPSRC/OU" github: false joined: 2022-09 + funding_id: "EP/T518165/1" + funding_system: ukri funding_statement: The research internship was supported through EPSRC Training Grant DTP 2020-2021 Open University url: "https://www.open.ac.uk/" + eurosciencegateway: name: EuroScienceGateway github: false @@ -215,21 +201,6 @@ h2020-defend: This work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 773701. url: https://www.defend2020.eu -madland: - name: MAdLand - joined: 2024-07 - url: https://madland.science - avatar: "/training-material/shared/images/logo-madland.jpg" - github: false - -mwk: - name: Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg - short_name: MWK - joined: 2024-08 - url: https://mwk.baden-wuerttemberg.de/de/startseite - avatar: "/training-material/assets/images/MWK.png" - github: false - nhgri-anvil: name: National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space short_name: "NHGRI ANVIL" @@ -248,20 +219,6 @@ nhgri-gdscn: url: https://www.genome.gov/ funding_id: 75N92022P00232 -NIH: - name: National Institutes of Health - short_name: "NIH" - avatar: /training-material/shared/images/nih.png - url: https://nih.gov/ - github: false - - -nsf: - name: National Science Foundation - url: https://www.nsf.gov - avatar: "/training-material/shared/images/nsf.gif" - github: false - sfb992: name: Collaborative Research Centre 992 diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml index 8e5a74bdcc2f19..ee735e2f9f637e 100644 --- a/ORGANISATIONS.yaml +++ b/ORGANISATIONS.yaml @@ -10,6 +10,13 @@ # # Please add organisations in alphabetical order +abromics: + name: ABRomics + github: false + joined: 2024-01 + avatar: "/training-material/assets/images/abromics.png" + url: https://www.abromics.fr/ + AustralianBioCommons: name: Australian BioCommons url: https://www.biocommons.org.au/ @@ -27,6 +34,10 @@ carpentries: joined: 2021-09 ror: "0356fgm10" +deNBI: + name: de.NBI + url: https://www.denbi.de/ + earlham: name: Earlham Institute joined: 2017-09 @@ -49,6 +60,13 @@ egi: github: false ror: "052jj4m32" + +elixir-excelerate: + name: Elixir Excelerate + url: https://www.elixir-europe.org/excelerate/ + avatar: "/training-material/shared/images/Excelerate_whitebackground.png" + github: false + elixir-europe: name: ELIXIR Europe joined: 2017-09 @@ -133,6 +151,13 @@ linq: avatar: "/training-material/shared/images/linq.jpg" github: false +madland: + name: MAdLand + joined: 2024-07 + url: https://madland.science + avatar: "/training-material/shared/images/logo-madland.jpg" + github: false + minnesotauni: name: University of Minnesota url: "https://twin-cities.umn.edu/" @@ -147,12 +172,39 @@ MPIIE: github: false ror: "058xzat49" +mwk: + name: Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg + short_name: MWK + joined: 2024-08 + url: https://mwk.baden-wuerttemberg.de/de/startseite + avatar: "/training-material/assets/images/MWK.png" + github: false + ncbi: name: National Center for Biotechnology Information url: "https://www.ncbi.nlm.nih.gov/" avatar: "/training-material/shared/images/ncbi.png" ror: "02meqm098" +nfdi4plants: + name: DataPLANT + joined: 2024-07 + url: https://www.nfdi4plants.de://www.nfdi4plants.de/ + avatar: "/training-material/shared/images/logo-dataplant.svg" + +NIH: + name: National Institutes of Health + short_name: "NIH" + avatar: /training-material/shared/images/nih.png + url: https://nih.gov/ + github: false + +nsf: + name: National Science Foundation + url: https://www.nsf.gov + avatar: "/training-material/shared/images/nsf.gif" + github: false + panacea: name: PanACEA description: Pan-African Consortium for the Evaluation of Antituberculosis Antibiotics @@ -214,6 +266,12 @@ sciensano: github: false ror: "04ejags36" +sfb992: + name: Collaborative Research Centre 992 + url: https://www.sfb992.uni-freiburg.de/ + avatar: https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg + github: false + societyprotectionundergroundnetworks: name: Society for the Protection of Underground Networks description: "SPUN is a scientific research organization founded to map mycorrhizal fungal communities and advocate for their protection." @@ -240,6 +298,12 @@ uga: github: false ror: "02rx3b187" +ukmrc: + name: UK Medical Research Council + url: https://mrc.ukri.org + avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/master/logo.png + github: false + uni-freiburg: name: University of Freiburg url: https://www.uni-freiburg.de/ From 1cc1abb2e856b6560e07b204a09a3c0b36ef0ebd Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 15:15:50 +0200 Subject: [PATCH 197/262] require funding_id for grants --- bin/schema-grants.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/schema-grants.yaml b/bin/schema-grants.yaml index 3f01d1ca52142d..2be9d7a46f5f85 100644 --- a/bin/schema-grants.yaml +++ b/bin/schema-grants.yaml @@ -101,6 +101,7 @@ mapping: - true funding_id: type: str + required: true description: The short identifier for your grant. _examples: - 2020-1-NL01-KA203-064717 From 82b4cb0223edaf5225b26ad6337b40e0b6c54016 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 15:16:51 +0200 Subject: [PATCH 198/262] support highergov for grant database --- _plugins/gtn/contributors.rb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_plugins/gtn/contributors.rb b/_plugins/gtn/contributors.rb index 5d718fdf2d907b..87991075236886 100644 --- a/_plugins/gtn/contributors.rb +++ b/_plugins/gtn/contributors.rb @@ -222,6 +222,8 @@ def self.fetch_funding_url(contributor) "https://erasmus-plus.ec.europa.eu/projects/search/details/#{contributor['funding_id']}" when 'ukri' "https://gtr.ukri.org/projects?ref=#{contributor['funding_id']}" + when 'highergov' + "https://www.highergov.com/contract/#{contributor['funding_id']}/" else Jekyll.logger.error "Unknown funding system #{contributor['funding_system']}" 'ERROR' From a930dfbdbd3b6d540e07c798082bcd15fc594bf3 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 15:20:35 +0200 Subject: [PATCH 199/262] rename funding_system to funding_database --- GRANTS.yaml | 43 +++++++++++++-------------------- _layouts/contributor_index.html | 2 +- _plugins/gtn/contributors.rb | 6 ++--- bin/schema-grants.yaml | 3 ++- 4 files changed, 23 insertions(+), 31 deletions(-) diff --git a/GRANTS.yaml b/GRANTS.yaml index bedd698f865d75..7aa3b60046bee0 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -3,7 +3,7 @@ # Can be added to contributions->funding metadata key of materials # # valid tags: -# name, joined, url, github, funding_id, funding_system, funding_statement +# name, joined, url, github, funding_id, funding_database, funding_statement # --- @@ -12,7 +12,7 @@ # joined: 2020-06 # url: "https://example.com" # homepage of the project # funding_id: 2020-1-NL01-KA203-064717 -# funding_system: cordis|ukri|erasmusplus # database/page where your project/grant is listed, if your project is not present in one of these portals, please ping us +# funding_database: cordis|highergov|ukri|erasmusplus # database where your project/grant is listed, if your project is not present in one of these portals, please ping us. EU grants are often listed in cordis, US grants in highergov # funding_statement: "This project is funded with the support of .." # github: false # add this if the id does not map to a GitHub account, @@ -27,7 +27,7 @@ ai4life: avatar: "/training-material/topics/ai4life/images/AI4Life-logo_giraffe-solid.png" url: https://ai4life.eurobioimaging.eu/ funding_id: "101057970" - funding_system: cordis + funding_database: cordis funding_statement: | AI4Life has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101057970. @@ -38,7 +38,7 @@ biont: avatar: "/training-material/assets/images/BioNT_Logo.png" url: https://biont-training.eu/ funding_id: "101100604" - funding_system: cordis + funding_database: cordis funding_statement: | Co-funded by the European Union @@ -46,7 +46,7 @@ by-covid: name: BeYond-COVID joined: 2023-04 funding_id: "101046203" - funding_system: cordis + funding_database: cordis funding_statement: | BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. @@ -59,7 +59,7 @@ CINECA-Project: short_name: "CINECA" joined: 2023-03 funding_id: "825775" - funding_system: cordis + funding_database: cordis funder_name: Horizon 2020 url: https://www.cineca-project.eu @@ -71,7 +71,7 @@ elixir-converge: avatar: "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png" url: https://elixir-europe.org/about-us/how-funded/eu-projects/converge funding_id: "871075" - funding_system: cordis + funding_database: cordis funding_statement: | ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement № 871075 @@ -83,7 +83,7 @@ edctp-eu: github: false url: https://www.edctp.org/ funding_id: "101103640" - funding_system: cordis + funding_database: cordis funding_statement: | TB-CAPT, PanACEA and PANGenS are part of the EDCTP2 and EDCTP3 programs supported by the European Union. @@ -94,7 +94,7 @@ elixir-fair-data: github: false joined: 2023-06 funding_id: MR/V038966/1 - funding_system: ukri + funding_database: ukri funding_statement: | This work has been funded by the ELIXIR-UK FAIR Data Stewardship training UKRI award (MR/V038966/1) @@ -105,7 +105,7 @@ elixir-uk-dash: github: false avatar: "/training-material/shared/images/dash.png" url: https://elixiruknode.org/projects/elixir-uk-dash/ - funding_system: ukri + funding_database: ukri funding_id: MR/V038966/1 funding_statement: | This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources. @@ -116,7 +116,7 @@ eosc-life: joined: 2023-04 avatar: "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png" funding_id: "824087" - funding_system: cordis + funding_database: cordis funding_statement: | EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087 url: https://www.eosc-life.eu @@ -128,7 +128,7 @@ epsrc-training-grant: github: false joined: 2022-09 funding_id: "EP/T518165/1" - funding_system: ukri + funding_database: ukri funding_statement: The research internship was supported through EPSRC Training Grant DTP 2020-2021 Open University url: "https://www.open.ac.uk/" @@ -140,7 +140,7 @@ eurosciencegateway: avatar: "/training-material/assets/images/eurosciencegateway.png" url: https://galaxyproject.org/projects/esg/ funding_id: "101057388" - funding_system: cordis + funding_database: cordis funding_statement: | EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963. @@ -152,7 +152,7 @@ fairease: avatar: "/training-material/assets/images/fair_ease_colour.png" url: https://fairease.eu/ funding_id: "101058785" - funding_system: cordis + funding_database: cordis funding_statement: | FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe. @@ -181,7 +181,7 @@ gallantries: url: "https://www.erasmusplus.nl" funder_name: Erasmus+ Programme funding_id: 2020-1-NL01-KA203-064717 - funding_system: erasmusplus + funding_database: erasmusplus funding_statement: | This project ([`2020-1-NL01-KA203-064717`](https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717)) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics. ![eu flag with the text: with the support of the erasmus programme of the european union](https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg) @@ -194,7 +194,7 @@ h2020-defend: github: false joined: 2023-05 funding_id: "773701" - funding_system: cordis + funding_database: cordis funding_statement: | DEFEND is Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe. @@ -218,19 +218,10 @@ nhgri-gdscn: avatar: https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png url: https://www.genome.gov/ funding_id: 75N92022P00232 + funding_database: highergov -sfb992: - name: Collaborative Research Centre 992 - url: https://www.sfb992.uni-freiburg.de/ - avatar: https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg - github: false -ukmrc: - name: UK Medical Research Council - url: https://mrc.ukri.org - avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/master/logo.png - github: false diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html index 38a24a80a4542b..14dba6728c5f7d 100644 --- a/_layouts/contributor_index.html +++ b/_layouts/contributor_index.html @@ -273,7 +273,7 @@

    External Links

    {% if entity.funding_id %} Grant ID: - {% if entity.funding_system %} + {% if entity.funding_database %} {% assign url = entity | fetch_funding_url %}     {{ entity.funding_id }} diff --git a/_plugins/gtn/contributors.rb b/_plugins/gtn/contributors.rb index 87991075236886..4449fc2c5911d6 100644 --- a/_plugins/gtn/contributors.rb +++ b/_plugins/gtn/contributors.rb @@ -213,9 +213,9 @@ def self.funder?(site, c) # Returns: # +Boolean+ of whether the contributor is a funder or not def self.fetch_funding_url(contributor) - return contributor['funding_id'] if !contributor.key?('funding_system') + return contributor['funding_id'] if !contributor.key?('funding_database') - case contributor['funding_system'] + case contributor['funding_database'] when 'cordis' "https://cordis.europa.eu/project/id/#{contributor['funding_id']}" when 'erasmusplus' @@ -225,7 +225,7 @@ def self.fetch_funding_url(contributor) when 'highergov' "https://www.highergov.com/contract/#{contributor['funding_id']}/" else - Jekyll.logger.error "Unknown funding system #{contributor['funding_system']}" + Jekyll.logger.error "Unknown funding system #{contributor['funding_database']}" 'ERROR' end end diff --git a/bin/schema-grants.yaml b/bin/schema-grants.yaml index 2be9d7a46f5f85..3d5a2a37e928f5 100644 --- a/bin/schema-grants.yaml +++ b/bin/schema-grants.yaml @@ -110,13 +110,14 @@ mapping: description: associated webpage (NOTE, funders only!) _examples: - "https://elixir-europe.org" - funding_system: + funding_database: type: str description: Automatically link to the grant's information in the appropriate funding system site. enum: - cordis - erasmusplus - ukri + - highergov funder_name: type: str description: A name for the agency providing the funding. From b595d77de0aa6b5ec131ee1edac4d763704bd0ae Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 15:29:08 +0200 Subject: [PATCH 200/262] update description --- GRANTS.yaml | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/GRANTS.yaml b/GRANTS.yaml index 7aa3b60046bee0..4d1d3eb67a5ec4 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -1,23 +1,26 @@ -# List of grants funding GTN activity +--- +# List of grants funding GTN contributions # -# Can be added to contributions->funding metadata key of materials +# Grants can be listed as affiliations for contributors +# Grants can be listed as funding contributors on training materials # # valid tags: # name, joined, url, github, funding_id, funding_database, funding_statement # ---- - +# EXAMPLE +# # Grant1: # should be equal to GitHub username if one exists for the grant/project # name: Grant/Project name +# github: false # add this if the id does not map to a GitHub account # joined: 2020-06 -# url: "https://example.com" # homepage of the project -# funding_id: 2020-1-NL01-KA203-064717 -# funding_database: cordis|highergov|ukri|erasmusplus # database where your project/grant is listed, if your project is not present in one of these portals, please ping us. EU grants are often listed in cordis, US grants in highergov -# funding_statement: "This project is funded with the support of .." -# github: false # add this if the id does not map to a GitHub account, - -# please add in alphabetical order of the key (id) - +# url: "https://example.com" # homepage of the project +# funding_statement: "This project is funded with the support of .." # optional, if you want a specific bit of text to appear +# funding_id: 2020-1-NL01-KA203-064717 # id of your grant, will be used in combination with funding_database to link to offical grant page +# funding_database: cordis|highergov|ukri|erasmusplus # Database where your project/grant is listed, +# # EU grants are often listed in cordis, US grants in highergov, UK grants in ukri +# # If your project is not present in one of these databases, please ping us. +# +# Please add in alphabetical order of the key (id) ai4life: From 7a1d243e1a2d9fa7717e9b880f7b81a49ac87e8d Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 16:04:43 +0200 Subject: [PATCH 201/262] add a bunch of short names --- ORGANISATIONS.yaml | 65 ++++++++++++++++++++++++++++++++-------------- 1 file changed, 45 insertions(+), 20 deletions(-) diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml index ee735e2f9f637e..a177399511dfde 100644 --- a/ORGANISATIONS.yaml +++ b/ORGANISATIONS.yaml @@ -23,6 +23,7 @@ AustralianBioCommons: avatar: "/training-material/shared/images/Australian-Biocommons-Favicon-RGB.png" avans-atgm: + short_name: Avans name: Avans Hogeschool joined: 2020-11 url: https://avans.nl @@ -46,8 +47,8 @@ earlham: ror: "018cxtf62" edctp: - name: EDCTP - description: The European & Developing Countries Clinical Trials Partnership + short_name: EDCTP + name: The European & Developing Countries Clinical Trials Partnership url: https://www.edctp.org/ avatar: "/training-material/shared/images/edctp.jpg" github: false @@ -62,7 +63,7 @@ egi: elixir-excelerate: - name: Elixir Excelerate + name: ELIXIR Excelerate url: https://www.elixir-europe.org/excelerate/ avatar: "/training-material/shared/images/Excelerate_whitebackground.png" github: false @@ -81,22 +82,23 @@ elixir-goblet-ttt: avatar: "/training-material/shared/images/elixir.png" embl-ebi: - name: EMBL-EBI - description: European Bioinformatics Institute + short_name: EMBL-EBI + name: European Bioinformatics Institute url: https://www.ebi.ac.uk avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/d0fccaa9dc8dc8615eb7146d6c5e96bd36f11f3a/EMBL_EBI_Logo_black.svg github: false ror: "02catss52" erasmusmc: - name: ErasmusMC - description: Erasmus Medical Center + short_name: ErasmusMC + name: Erasmus Medical Center url: https://www.erasmusmc.nl avatar: "/training-material/shared/images/logo-erasmusmc.png" github: false ror: "018906e22" eu: + short_name: EU name: The European Union url: https://european-union.europa.eu avatar: "/training-material/shared/images/EU-logo.jpg" @@ -104,14 +106,15 @@ eu: ror: "019w4f821" find: - name: FIND - description: The Foundation for Innovative New Diagnostics + short_name: FIND + name: The Foundation for Innovative New Diagnostics url: https://www.finddx.org/ avatar: "/training-material/shared/images/FIND.png" github: false ror: "05tcsqz68" ifb: + short_name: IFB name: Institut Français de Bioinformatique url: https://www.france-bioinformatique.fr/ avatar: "/training-material/shared/images/ifb.png" @@ -125,6 +128,7 @@ inab-certh: ror: "03bndpq63" irccs: + short_name: IRCCS name: IRCCS Ospedale San Raffaele url: "https://www.hsr.it/" avatar: "/training-material/shared/images/irccs.jpg" @@ -138,6 +142,7 @@ jetstream2: github: false johnshopkins: + short_name: JHU name: Johns Hopkins University url: "https://www.jhu.edu/" avatar: "/training-material/shared/images/hopkins.png" @@ -145,20 +150,22 @@ johnshopkins: ror: "00za53h95" linq: - name: LINQ - description: LINQ management GmbH - link: "https://linq-management.com/" + short_name: LINQ + name: LINQ management GmbH + url: "https://linq-management.com/" avatar: "/training-material/shared/images/linq.jpg" github: false madland: - name: MAdLand + short_name: MAdLand + name: "MAdLand - Molecular Adaptation to Land: plant evolution to change" joined: 2024-07 url: https://madland.science avatar: "/training-material/shared/images/logo-madland.jpg" github: false minnesotauni: + short_name: UMN name: University of Minnesota url: "https://twin-cities.umn.edu/" avatar: "/training-material/shared/images/minnesotauni.png" @@ -166,6 +173,7 @@ minnesotauni: ror: "017zqws13" MPIIE: + short_name: MPIEE name: Max Planck Institute of Immunology and Epigenetics url: https://www.ie-freiburg.mpg.de avatar: https://raw.githubusercontent.com/bgruening/presentations/master/shared/resources/img/14_MPI_IE_logo_mit_180.gif @@ -181,13 +189,15 @@ mwk: github: false ncbi: + short_name: NCBI name: National Center for Biotechnology Information url: "https://www.ncbi.nlm.nih.gov/" avatar: "/training-material/shared/images/ncbi.png" ror: "02meqm098" nfdi4plants: - name: DataPLANT + short_name: DataPLANT + name: NFDI4Plants/DataPLANT joined: 2024-07 url: https://www.nfdi4plants.de://www.nfdi4plants.de/ avatar: "/training-material/shared/images/logo-dataplant.svg" @@ -200,38 +210,42 @@ NIH: github: false nsf: + short_name: NSF name: National Science Foundation url: https://www.nsf.gov avatar: "/training-material/shared/images/nsf.gif" github: false panacea: - name: PanACEA - description: Pan-African Consortium for the Evaluation of Antituberculosis Antibiotics + short_name: PanACEA + name: Pan-African Consortium for the Evaluation of Antituberculosis Antibiotics url: https://panacea-tb.net/ avatar: "/training-material/shared/images/panacea.jpg" github: false pangens: - name: PANGenS - description: Pan-Africa network for genomic surveillance of poverty related diseases and emerging pathogens + short_name: PANGenS + name: Pan-Africa network for genomic surveillance of poverty related diseases and emerging pathogens url: https://pangens.org/ avatar: "/training-material/shared/images/pangens.jpg" github: false petermac: + short_name: PeterMac name: Peter MacCallum Cancer Centre url: "https://www.petermac.org/" avatar: "/training-material/shared/images/petermac.png" ror: "02a8bt934" pndb: + short_name: PNDB name: Pôle National de Données de Biodiversité url: https://www.pndb.fr/ avatar: "/training-material/shared/images/PNDB_sub.png" github: false psu: + short_name: PSU name: The Pennsylvania State University url: http://www.psu.edu avatar: "/training-material/shared/images/psu.png" @@ -239,20 +253,22 @@ psu: ror: "04p491231" qiime2: + short_name: QIIME2 name: QIIME2 url: https://qiime2.org/ avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4 sanbi: - name: SANBI/UWC + short_name: SANBI/UWC url: https://www.sanbi.org/ avatar: "/training-material/shared/images/sanbi.png" - description: "South African National Bioinformatics Institute, University of the Western Cape" + name: "South African National Bioinformatics Institute, University of the Western Cape" github: false ror: "005r3tp02" san-raffaele-uni: + short_name: UniSR name: Università Vita-Salute San Raffaele url: "https://www.unisr.it/" avatar: "/training-material/shared/images/uni_san_raffaele.svg" @@ -267,18 +283,21 @@ sciensano: ror: "04ejags36" sfb992: + short_name: CRC992 name: Collaborative Research Centre 992 url: https://www.sfb992.uni-freiburg.de/ avatar: https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg github: false societyprotectionundergroundnetworks: + short_name: SPUN name: Society for the Protection of Underground Networks description: "SPUN is a scientific research organization founded to map mycorrhizal fungal communities and advocate for their protection." url: "https://www.spun.earth" avatar: "/training-material/shared/images/spun-logo.png" swiss-tph: + short_name: SwissTPH name: Swiss Tropical and Public Health Institute url: https://www.swisstph.ch/en/ avatar: "/training-material/shared/images/swiss-tph.png" @@ -286,12 +305,14 @@ swiss-tph: ror: "03adhka07" tb-capt: + short_name: TB-CAPT name: TB-CAPT url: https://www.tb-capt.org/ avatar: "/training-material/shared/images/tb_capt.svg" github: false uga: + short_name: UGA name: Université Grenoble-Alpes url: https://www.univ-grenoble-alpes.fr/ avatar: /training-material/shared/images/logo-uga.svg @@ -299,12 +320,14 @@ uga: ror: "02rx3b187" ukmrc: + short_name: UKRI-MRC name: UK Medical Research Council url: https://mrc.ukri.org avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/master/logo.png github: false uni-freiburg: + short_name: UFR name: University of Freiburg url: https://www.uni-freiburg.de/ avatar: https://raw.githubusercontent.com/bgruening/presentations/a2e38e4b007994af798320db3a0131c4bb891c0e/shared/resources/img/logo_freiburg.jpg @@ -312,6 +335,7 @@ uni-freiburg: ror: "0245cg223" UTas: + short_name: UTas name: University of Tasmania url: https://www.utas.edu.au/ avatar: "/training-material/shared/images/UTas_logo.png" @@ -319,6 +343,7 @@ UTas: ror: "01nfmeh72" vib: + short_name: VIB name: Vlaams Instituut voor Biotechnologie url: https://vib.be/ avatar: "/training-material/shared/images/logo-vib.png" From eff839c28d79a1d3de4cb516d51d17b69a836805 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 16:05:02 +0200 Subject: [PATCH 202/262] update schemas --- bin/schema-grants.yaml | 6 ------ bin/schema-organisations.yaml | 25 +++++++++++++++++++------ 2 files changed, 19 insertions(+), 12 deletions(-) diff --git a/bin/schema-grants.yaml b/bin/schema-grants.yaml index 3d5a2a37e928f5..d858d72d713594 100644 --- a/bin/schema-grants.yaml +++ b/bin/schema-grants.yaml @@ -93,12 +93,6 @@ mapping: - "2020-01-01" avatar: type: str - funder: - type: bool - description: Set this to true if this entity is a funding agency. - required: true - enum: - - true funding_id: type: str required: true diff --git a/bin/schema-organisations.yaml b/bin/schema-organisations.yaml index a06af6d24fd72e..074e2b7a4623de 100644 --- a/bin/schema-organisations.yaml +++ b/bin/schema-organisations.yaml @@ -10,17 +10,30 @@ mapping: description: | This ideally is your GitHub handle. If you do not have, or do not wish to provide a GitHub username, you may make up another identifier here, but then you must set `github: false` as described below. mapping: + short_name: + type: str + description: | + Name of the organisation, as short as possible (e.g. acronyms) + _examples: + - EBI + - UFR + - NIH + name: type: str required: true description: | - Your preferred name. If you prefer an alias or another name, this is welcome, it does not need to be your legal name. + Full name of the organisation (e.g. acronyms expanded). _examples: - - 张三 - - Alice - - Jane Doe - - Madame Tout-le-Monde - - Γιάννης Παπαδόπουλος + - European Bioinformatics Institute + - University of Freiburg + - National Institutes of Health + + description: + type: str + description: | + A couple sentences of description about the organisation + email: type: str pattern: /@/ From 611b1b7f594b7d4d6ebf95e0a2a8d6ca4737d88b Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 16:37:55 +0200 Subject: [PATCH 203/262] add some funding contributors as suggested by bgruening in #4913 --- .../tutorials/ewas-suite/tutorial.md | 21 +- .../tutorials/hicexplorer/tutorial.md | 18 +- .../fair/tutorials/bioimage-REMBI/tutorial.md | 33 +- .../tutorials/bioimage-metadata/tutorial.md | 15 +- .../tutorials/amr-gene-detection/tutorial.md | 29 +- .../bacterial-genome-annotation/tutorial.md | 48 +-- .../tutorials/funannotate/tutorial.md | 1 + .../tutorials/functional/tutorial.md | 2 + .../tutorials/genome-annotation/tutorial.md | 10 +- .../hela-screen-analysis/tutorial.md | 9 +- .../imaging-introduction/tutorial.md | 11 +- .../multiplex-tissue-imaging-TMA/tutorial.md | 80 ++--- .../tutorial.md | 9 +- .../imaging/tutorials/tutorial-CP/tutorial.md | 9 +- .../galaxy-intro-101-everyone/tutorial.md | 20 +- .../tutorial.md | 12 +- .../galaxy-intro-peaks2genes/tutorial.md | 4 + .../tutorials/galaxy-reproduce/tutorial.md | 9 +- .../tutorials/lcms-dataprocessing/tutorial.md | 312 +++++++++--------- .../tutorials/lcms-preprocessing/tutorial.md | 13 +- .../metabolomics/tutorials/lcms/tutorial.md | 17 +- .../msi-analyte-distribution/tutorial.md | 73 ++-- 22 files changed, 413 insertions(+), 342 deletions(-) diff --git a/topics/epigenetics/tutorials/ewas-suite/tutorial.md b/topics/epigenetics/tutorials/ewas-suite/tutorial.md index 0896265bf4e9f8..ca03203c1734dd 100644 --- a/topics/epigenetics/tutorials/ewas-suite/tutorial.md +++ b/topics/epigenetics/tutorials/ewas-suite/tutorial.md @@ -13,10 +13,15 @@ objectives: key_points: - "Infinium Human Methylation BeadChip is an array based technology to generate DNA methylation profiling at individual CpG loci in the human genome based on Illumina’s bead technology." - "Time and cost efficiency followed by high sample output, and overall quantitative accuracy and reproducibility made Infinium Human Methylation BeadChip one of the most widely used arrays on the market." -contributors: - - kkamieniecka - - khaled196 - - poterlowicz-lab +contributions: + authorship: + - kkamieniecka + - khaled196 + - poterlowicz-lab + editing: + testing: + funding: + - elixir-europe --- This tutorial is based on Hugo W, Shi H, Sun L, Piva M et al.: Non-genomic and Immune Evolution of Melanoma Acquiring MAPKi Resistance {% cite Hugo2015 %}. @@ -112,7 +117,7 @@ The first step of the Infinium Human Methylation BeadChip array analysis is raw > > > After exporting the reference genome from UCSC, we need to make sure that it is in the right dataset build. -> +> > Click on the **Differentially_Methylated_Positions.bed** output in your history to expand it. \ > Set the database build of your dataset to `Human Feb. 2009 (GRCh37/hg19) (hg19)`(if it is not set automatically) > @@ -170,7 +175,7 @@ The main goal of the **Infinium Human Methylation BeadChip** analysis is to simp > {: .hands_on} -> +> > How do we define phenotype covariate? > > > > Phenotype covariate is the set of observable characteristics of an individual resulting from the gene-environment interactions @@ -201,11 +206,11 @@ In addition to downstream analysis users can annotate the differentially methyla > - *"Input Type Gene ID"*: `SYMBOL` > - *"Output Type Gene ID"*: `ENTREZID` > -> 5. Run a GO Enrichment Analysis using {% tool [clusterProfiler go](toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0) %} on the output of the {% tool [Cluster Profiler Bitr](toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0) %} +> 5. Run a GO Enrichment Analysis using {% tool [clusterProfiler go](toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0) %} on the output of the {% tool [Cluster Profiler Bitr](toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0) %} {: .hands_on} ![Functional annotations](../../images/funcann.jpg "Results of GO enrichments analysis for DMPs") - + ID | Description | pvalue | qvalue | geneID | Count --- | --- | --- | --- | --- | --- GO:0048732 | gland development | 1.38E-58 | 4.23E-55 | PTGS2 / KCNC1 / FZD1 /SLC22A18 /SLC22A3 (...) | 372 diff --git a/topics/epigenetics/tutorials/hicexplorer/tutorial.md b/topics/epigenetics/tutorials/hicexplorer/tutorial.md index 25d6e88454cddf..8d5698671590e7 100644 --- a/topics/epigenetics/tutorials/hicexplorer/tutorial.md +++ b/topics/epigenetics/tutorials/hicexplorer/tutorial.md @@ -12,11 +12,19 @@ key_points: - "Hi-C helps to investigate the 3D structure of the genome and to uncover folding principles of chromatin." - "In order to build a Hi-C contact matrix the reads have to be mapped to the reference genome." - "Based on a contact matrix open and closed chromatin (A/B compartments) and topological associating domains (TADs) can be computed." -contributors: - - joachimwolff - - fidelram - - vivekbhr - - polkhe +contributions: + authorship: + - joachimwolff + - fidelram + - vivekbhr + - polkhe + editing: + testing: + funding: + - elixir-europe + - deNBI + - uni-freiburg + - sfb992 --- diff --git a/topics/fair/tutorials/bioimage-REMBI/tutorial.md b/topics/fair/tutorials/bioimage-REMBI/tutorial.md index c90bf4ccdbcbf0..ced6d8392faa32 100644 --- a/topics/fair/tutorials/bioimage-REMBI/tutorial.md +++ b/topics/fair/tutorials/bioimage-REMBI/tutorial.md @@ -13,7 +13,7 @@ objectives: - Find out what REMBI is and why it is useful - Categorise what metadata belongs to each of the submodules of REMBI - Gather the metadata for an example bioimage dataset - + time_estimation: "15m" key_points: @@ -23,7 +23,7 @@ tags: - fair - data management - bioimaging - + priority: 5 contributions: @@ -34,6 +34,7 @@ contributions: - poterlowicz-lab funding: - elixir-uk-dash + - elixir-europe subtopic: fair-data requirements: @@ -67,7 +68,7 @@ REMBI (Recommended Metadata for Biological Images) was proposed as a draft metad > In the [REMBI paper](https://www.nature.com/articles/s41592-021-01166-8), the authors consider three potential user groups who require different metadata. Find out what are these three groups and their metadata requirements. > > > -> > The identified three user groups are: Biologists, Imaging scientists, Computer-vision researchers. +> > The identified three user groups are: Biologists, Imaging scientists, Computer-vision researchers. > > - A research biologist may be interested in the biological sample that has been imaged to compare it to similar samples that they are working with. > > - An imaging scientist may be interested in how the image was acquired so they can improve upon current image acquisition techniques. > > - A computer vision researcher may be interested in annotated ground-truth segmentations, that can be obtained from the image, so they can develop faster and more accurate algorithms. @@ -78,11 +79,11 @@ REMBI (Recommended Metadata for Biological Images) was proposed as a draft metad > Instructor Note > > If you're an instructor leading this training, you might ask people to work in small groups for this exercise and encourage the discussion. Ask group members to share which of the user groups they identify as and what metadata they would want. -> +> {: .tip} -# Categories of metadata -REMBI covers different categories of metadata, such as: +# Categories of metadata +REMBI covers different categories of metadata, such as: - study - study component - biosample @@ -92,9 +93,9 @@ REMBI covers different categories of metadata, such as: - image correlation - analyzed data -Within each module, there are attributes that should be included to make the published data FAIR. We will explore all the modules and attributes suggested by REMBI and we'll show some examples as well. +Within each module, there are attributes that should be included to make the published data FAIR. We will explore all the modules and attributes suggested by REMBI and we'll show some examples as well. -## Study +## Study The first module of REMBI metadata describes the Study and should include: - Study type - Study description @@ -173,11 +174,11 @@ This should include all the information that relates to all the data in the proj A study component can be thought of as an experiment, both the physical experiment and subsequent data analysis, or a series of experiments that have been conducted with the same aim in mind. -The associated metadata should describe the imaging method used and include a description of the image dataset. The REMBI guidelines store high-level metadata in the study component and then divide the more detailed metadata into other modules. +The associated metadata should describe the imaging method used and include a description of the image dataset. The REMBI guidelines store high-level metadata in the study component and then divide the more detailed metadata into other modules. Within the Study component we include the Imaging Method which should describe the techniques used to acquire the raw data. This could be one or multiple methods, which should be part of a relevant ontology. For Confocal Microscopy data, we can use the Biological Imaging Methods Ontology, although it is also present in a number of other ontologies. -The description of the study component should include an overview of what was imaged as well as any processed data that is created during analysis. +The description of the study component should include an overview of what was imaged as well as any processed data that is created during analysis. > Example > @@ -195,7 +196,7 @@ The description of the study component should include an overview of what was im > Storing metadata > -> You could either choose to store the metadata in the same file as your study data or have a new file for each study component. This could be stored in the same place as your study metadata, or you could create a subdirectory structure. +> You could either choose to store the metadata in the same file as your study data or have a new file for each study component. This could be stored in the same place as your study metadata, or you could create a subdirectory structure. {: .tip} ## Biosample @@ -278,9 +279,9 @@ You can leave out some of the variables if they are not part of your experiment. ## Image acquisition Here you should include all the information about the instrument you used and how it was set up. Like with the specimen metadata, describe this information as though you are speaking to someone who already knows how to use a similar instrument. What would they need to know to produce the same image data? - + Check with your facility manager if they have any guidelines for what details need to be recorded for your particular instrument. Make sure that the parameters you record can actually be used by someone else if they don’t have exactly the same instrument or setup. For example, don’t say that you used a certain percentage of laser power, as this doesn’t tell you how much power was used unless you also provide the total power of the laser. If the instrument software has automatically generated a metadata file, remember to save this. Depending on its content, this may be sufficient. - + Start with the details of the equipment for the Instrument Attributes. If this is commercial equipment, include the make and model, a short description of what type of instrument it is and details about its configuration. If the instrument is bespoke, you will need to include more details. Next, you should include image acquisition parameters. These relate to how the instrument was set up for the particular experiment. Some of these may be captured automatically by the instrument’s software, so make things easy for yourself and check if a file is generated and what’s in it. If a file is generated, then you only need to manually record anything that is missing from the file. > Example @@ -318,8 +319,8 @@ Start with the details of the equipment for the Instrument Attributes. If this i > Helpful resources > -> To help you collect the information for your own data, you might have a look at the local resources from your institution or universities. For example, at Warwick University, there are [webpages](https://warwick.ac.uk/fac/sci/med/research/biomedical/facilities/camdu/methodsreporting/) describing the metadata that needs to be collected for some of the microscopes. -> +> To help you collect the information for your own data, you might have a look at the local resources from your institution or universities. For example, at Warwick University, there are [webpages](https://warwick.ac.uk/fac/sci/med/research/biomedical/facilities/camdu/methodsreporting/) describing the metadata that needs to be collected for some of the microscopes. +> {: .tip} ## Image data @@ -424,4 +425,4 @@ This section should not include metadata for any image data, including processed For more examples, check out REMBI Supplementary Information - either in [pdf](https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-021-01166-8/MediaObjects/41592_2021_1166_MOESM1_ESM.pdf) or [spreadsheet](https://docs.google.com/spreadsheets/d/1Ck1NeLp-ZN4eMGdNYo2nV6KLEdSfN6oQBKnnWU6Npeo/edit#gid=1023506919). -At first glance, it might seem to be quite a stretch to collect all that metadata! But don’t get discouraged - following those guidelines will ensure better communication between the scientists and will make your research FAIR: Findable, Accessible, Interoperable, Reusable. During big data era when we are surrounded by so much resources, it’s crucial to get good data management habits, share them with others and hence contribute to the development of Science toghether. +At first glance, it might seem to be quite a stretch to collect all that metadata! But don’t get discouraged - following those guidelines will ensure better communication between the scientists and will make your research FAIR: Findable, Accessible, Interoperable, Reusable. During big data era when we are surrounded by so much resources, it’s crucial to get good data management habits, share them with others and hence contribute to the development of Science toghether. diff --git a/topics/fair/tutorials/bioimage-metadata/tutorial.md b/topics/fair/tutorials/bioimage-metadata/tutorial.md index 1fd87b7a0ba238..d67b976d9be946 100644 --- a/topics/fair/tutorials/bioimage-metadata/tutorial.md +++ b/topics/fair/tutorials/bioimage-metadata/tutorial.md @@ -25,7 +25,7 @@ tags: - fair - data management - bioimaging - + priority: 4 contributions: @@ -36,6 +36,7 @@ contributions: - poterlowicz-lab funding: - elixir-uk-dash + - elixir-europe subtopic: fair-data requirements: @@ -44,7 +45,7 @@ requirements: tutorials: - fair-intro - data-management - + follow_up_training: - @@ -55,7 +56,7 @@ follow_up_training: - type: "internal" topic_name: imaging - + --- # FAIR Bioimaging @@ -76,7 +77,7 @@ But the question remains: where can I submit my data? Currently the main reposit > - [IDR: Image Data Repository](https://idr.openmicroscopy.org/) > - [EMPIAR: Electron Microscopy Public Image Archive](https://www.ebi.ac.uk/empiar/) > - [BioImage Archive](https://www.ebi.ac.uk/bioimage-archive/) -> +> > Visit their websites and find out what their scope is or what sorts of datasets they accept. > > > @@ -91,7 +92,7 @@ But the question remains: where can I submit my data? Currently the main reposit > Repositories everywhere > > As well as these repositories, your Institute may have their own repository. For example, at the Warwick University, there is also [OMERO](https://warwick.ac.uk/fac/sci/med/research/biomedical/facilities/camdu/training/omero-warwick-guide_2.pdf) and [WRAP](https://wrap.warwick.ac.uk/). -> +> {: .tip} @@ -117,7 +118,7 @@ Now we know what repositories are available, but how to decide which one is best > > 2. It is strongly recommended that submitters make their datasets available under [CC-BY](https://creativecommons.org/licenses/by/4.0/) license. > > 3. As specified on the [IDR website](https://idr.openmicroscopy.org/about/submission.html), dataset size is typically not an issue, but for sizes significantly larger than 1000 GB special planning may be needed. > > - **EMPIAR: Electron Microscopy Public Image Archive**: -> > 1. Provide image data in the formats in which they are uploaded, but recommended is the use of common formats in the field including MRC, MRCS, TIFF, DM4, IMAGIC, SPIDER, MRC FEI, RAW FEI and BIG DATA VIEWER HDF5. +> > 1. Provide image data in the formats in which they are uploaded, but recommended is the use of common formats in the field including MRC, MRCS, TIFF, DM4, IMAGIC, SPIDER, MRC FEI, RAW FEI and BIG DATA VIEWER HDF5. > > 2. All data in EMPIAR is freely and publicly available to the global community under the [CC0](https://creativecommons.org/share-your-work/public-domain/cc0/) license. > > 3. As specified on the [EMPIAR page](https://www.ebi.ac.uk/empiar/deposition/manual/#manIntro), typically having more than 4000 files in a directory has a tendency to slow down access considerably. It is recommended in this case to sub-divide the directory into subdirectories with no more than 4000 files each. If you have a single file larger than 1 TB, contact EMPAIR in advance. > > To find out more, check the [FAQ page](https://www.ebi.ac.uk/empiar/faq). @@ -128,7 +129,7 @@ Now we know what repositories are available, but how to decide which one is best > > - Less than 50 GB total size, less than 20GB per file – use submission tool > > - Up to 1TB total size – use FTP > > - Anything larger – use Aspera -> > +> > > > To find out more, check the [FAQ page](https://www.ebi.ac.uk/bioimage-archive/help-faq/). > {: .solution} > diff --git a/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md b/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md index fd77f245dcc2a7..37ccaf4a532fb0 100644 --- a/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md +++ b/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md @@ -43,6 +43,7 @@ contributions: funding: - avans-atgm - abromics + - elixir-europe follow_up_training: - type: internal topic_name: visualisation @@ -69,9 +70,9 @@ recordings: Antimicrobial resistance (AMR) is a global phenomenon with no geographical or species boundaries, which poses an important threat to human, animal and environmental health. It is a complex and growing problem that compromises our ability to treat bacterial infections. -AMR gene content can be assessed from whole genome sequencing to detect known resistance mechanisms and potentially identify novel mechanisms. +AMR gene content can be assessed from whole genome sequencing to detect known resistance mechanisms and potentially identify novel mechanisms. -To illustrate the process to identify AMR gene in a bacterial genome, we take an assembly of a bacterial genome (KUN1163 sample) generated by following a [bacterial genome assembly tutorial]({% link topics/assembly/tutorials/mrsa-illumina/tutorial.md %}) from data produced in "Complete Genome Sequences of Eight Methicillin-Resistant *Staphylococcus aureus* Strains Isolated from Patients in Japan" ({% cite Hikichi_2019 %}). +To illustrate the process to identify AMR gene in a bacterial genome, we take an assembly of a bacterial genome (KUN1163 sample) generated by following a [bacterial genome assembly tutorial]({% link topics/assembly/tutorials/mrsa-illumina/tutorial.md %}) from data produced in "Complete Genome Sequences of Eight Methicillin-Resistant *Staphylococcus aureus* Strains Isolated from Patients in Japan" ({% cite Hikichi_2019 %}). > Methicillin-resistant *Staphylococcus aureus* (MRSA) is a major pathogen > causing nosocomial infections, and the clinical manifestations of MRSA @@ -146,13 +147,13 @@ To identify AMR genes in contigs, tools like ABRicate or staramr ({% cite bharat * __Plasmid__: Plasmid types that were found for the isolate. * __Scheme__: The MLST scheme used - MLST stands for MultiLocus Sequence Typing. It is a technique for the typing of multiple loci, using DNA sequences of internal fragments of multiple housekeeping genes to characterize isolates of microbial species. + MLST stands for MultiLocus Sequence Typing. It is a technique for the typing of multiple loci, using DNA sequences of internal fragments of multiple housekeeping genes to characterize isolates of microbial species. Here, **starmr** uses [mlst](https://github.com/tseemann/mlst) to scan the contig files against traditional [PubMLST](https://pubmlst.org/) typing schemes. The correspondance between the scheme and the bacteria genus and species is accessible in the [map](https://github.com/tseemann/mlst/blob/master/db/scheme_species_map.tab) * __Sequence Type__: The sequence type that's assigned when combining all allele types * __Genome Length__: The isolate/genome file(s) genome length(s) - * __N50 value__: The isolate/genome file(s) N50 value(s) + * __N50 value__: The isolate/genome file(s) N50 value(s) * __Number of Contigs Greater Than Or Equal To 300 bp__: The number of contigs greater or equal to 300 base pair in the isolate/genome file(s) * __Quality Module Feedback__: The isolate/genome file(s) detailed feedback for the quality metrics @@ -174,7 +175,7 @@ To identify AMR genes in contigs, tools like ABRicate or staramr ({% cite bharat > > 1. There is one genome (1 line) > > 2. The genome has failed the quality (column 2), because the genome length is not within the acceptable length range (last column). > > 3. We can summarize starmr output and Table 1 in {% cite Hikichi_2019 %}: - > > + > > > > Antibiotic name | Abbreviation | staramr | {% cite Hikichi_2019 %} > > --- | --- | --- | --- > > Amikacin | | Yes | @@ -190,7 +191,7 @@ To identify AMR genes in contigs, tools like ABRicate or staramr ({% cite bharat > > Spectinomycin | | Yes | > > Tetracycline | | Yes | > > Tobramycin | | Yes | - > > + > > > > 4. The scheme is saureus, so *Staphylococcus aureus* (given the [scheme genus map](https://github.com/tseemann/mlst/blob/master/db/scheme_species_map.tab)), which is coherent with MRSA > {: .solution} > @@ -227,8 +228,8 @@ To identify AMR genes in contigs, tools like ABRicate or staramr ({% cite bharat > > Inspect the staramr output > > > > 1. There are: - > > - 1 MSLT - > > - 5 plasmid *rep* genes + > > - 1 MSLT + > > - 5 plasmid *rep* genes > > - 7 resistance genes > > 2. The plasmid genes are on contig00019 (3 genes - coherent with {% cite Lozano_2012 %}), contig00024, and contig00002. > > 3. The resistance genes are: @@ -301,7 +302,7 @@ CARD can be very helpful to check all the resistance genes and check if it is lo # Visualization of the ARGs and plasmid genes in their genomic context -We would like to look at the ARGs and plasmid genes in their genomic context. To do that, we will usie [JBrowse](https://jbrowse.org/jb2/) ({% cite diesh2023jbrowse %}) with several information: +We would like to look at the ARGs and plasmid genes in their genomic context. To do that, we will usie [JBrowse](https://jbrowse.org/jb2/) ({% cite diesh2023jbrowse %}) with several information: 1. Assembly as the reference 2. ARGs location @@ -330,13 +331,13 @@ The first step is to extract the location of the ARGs and plasmid genes on the c > {: .solution} {: .question} -This table can not be used directly in JBrowse. It first needs to be transformed in a standard format: GFF3, a file format used for describing genes and other features of DNA, RNA and protein sequences. +This table can not be used directly in JBrowse. It first needs to be transformed in a standard format: GFF3, a file format used for describing genes and other features of DNA, RNA and protein sequences. > GFF3 file format -> +> > A GFF is a tab delimited file with 9 fields per line: -> 1. **seqid**: The name of the sequence where the feature is located. +> 1. **seqid**: The name of the sequence where the feature is located. > 2. **source**: The algorithm or procedure that generated the feature. This is typically the name of a software or database. > 3. **type**: The feature type name, like "gene" or "exon". In a well structured GFF file, all the children features always follow their parents in a single block (so all exons of a transcript are put after their parent "transcript" feature line and before any other parent transcript line). In GFF3, all features and their relationships should be compatible with the standards released by the Sequence Ontology Project. > 4. **start**: Genomic start of the feature, with a 1-base offset. This is in contrast with other 0-offset half-open sequence formats, like BED. @@ -344,7 +345,7 @@ This table can not be used directly in JBrowse. It first needs to be transformed > 6. **score**: Numeric value that generally indicates the confidence of the source in the annotated feature. A value of "." (a dot) is used to define a null value. > 7. **strand**: Single character that indicates the strand of the feature. This can be "+" (positive, or 5'->3'), "-", (negative, or 3'->5'), "." (undetermined), or "?" for features with relevant but unknown strands. > 8. **phase**: phase of CDS features; it can be either one of 0, 1, 2 (for CDS features) or "." (for everything else). See the section below for a detailed explanation. -> 9. **attributes**: A list of tag-value pairs separated by a semicolon with additional information about the feature. +> 9. **attributes**: A list of tag-value pairs separated by a semicolon with additional information about the feature. {: .comment} > Create a GFF file @@ -391,7 +392,7 @@ In addition to the ARGs and plasmid genes, it would be good to have extra inform
    -**Bakta** is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. +**Bakta** is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. > Annotate the contigs > diff --git a/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md b/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md index 4570d4324dc994..9585e2649ca1d6 100644 --- a/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md +++ b/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md @@ -37,6 +37,8 @@ contributions: - bebatut funding: - abromics + - elixir-europe + - ifb follow_up_training: - type: internal topic_name: genome-annotation @@ -66,11 +68,11 @@ recordings: --- -After sequencing and assembly, a genome can be annotated. It is an essential step to describe the genome. +After sequencing and assembly, a genome can be annotated. It is an essential step to describe the genome. Genome annotation consists in describing the structure and function of the components of the genome, by predicting, analyzing, and interpreting them in order to extract their biological significance and understand the biological processes in which they participate. Among other things, it identifies the locations of genes and all the coding regions in a genome (*structural annotation*) and determines what those genes do (*functional annotation*). -To illustrate the process to annotate a bacterial genome, we take an assembly of a bacterial genome (KUN1163 sample) generated by following a [bacterial genome assembly tutorial]({% link topics/assembly/tutorials/mrsa-illumina/tutorial.md %}) from data produced in "Complete Genome Sequences of Eight Methicillin-Resistant *Staphylococcus aureus* Strains Isolated from Patients in Japan" ({% cite Hikichi_2019 %}). +To illustrate the process to annotate a bacterial genome, we take an assembly of a bacterial genome (KUN1163 sample) generated by following a [bacterial genome assembly tutorial]({% link topics/assembly/tutorials/mrsa-illumina/tutorial.md %}) from data produced in "Complete Genome Sequences of Eight Methicillin-Resistant *Staphylococcus aureus* Strains Isolated from Patients in Japan" ({% cite Hikichi_2019 %}). > Methicillin-resistant *Staphylococcus aureus* (MRSA) is a major pathogen > causing nosocomial infections, and the clinical manifestations of MRSA @@ -119,11 +121,11 @@ Any analysis should get its own Galaxy history. So let's start by creating a new For annotating the contigs, several tools exists to do that: Prokka ({% cite seemann2014prokka %}), Bakta ({% cite schwengers2021bakta %}), etc. Here, we use **Bakta** as recommended by {% include _includes/contributor-badge.html id="tseemann" %} as the successor of **Prokka**. -**Bakta** is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and metagenome-assembled genomes (MAGs). It implements a comprehensive annotation workflow for coding and non-coding genes (*i.e.* tRNA, rRNA). +**Bakta** is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and metagenome-assembled genomes (MAGs). It implements a comprehensive annotation workflow for coding and non-coding genes (*i.e.* tRNA, rRNA). ![Flow diagram of Bakta. It depicts the sequential steps and connections involved in its functioning.](./images/bakta_wf.png "Overview of the Bakta annotation workflow ({% cite schwengers2021bakta %})") -It is also able to detect and annotate small proteins (sORF). Predicted CDS are annotated using an alignment-free protein sequence identification approach with cross-references to public databases via stable identifiers. +It is also able to detect and annotate small proteins (sORF). Predicted CDS are annotated using an alignment-free protein sequence identification approach with cross-references to public databases via stable identifiers. > Contig annotation > @@ -135,7 +137,7 @@ It is also able to detect and annotate small proteins (sORF). Predicted CDS are > - In *"Optional annotation"*: > - *"Keep original contig header"*: `Yes` > - In *"Selection of the output files"*: -> - *"Output files selection"*: +> - *"Output files selection"*: > - `Annotation file in TSV` > - `Annotation and sequence in GFF3` > - `Feature nucleotide sequences as FASTA` @@ -153,7 +155,7 @@ It is also able to detect and annotate small proteins (sORF). Predicted CDS are > 2. How long is the draft genome? > 3. How many CDSs have been found? > 4. How many small proteins? - > 5. Which other components have been found? + > 5. Which other components have been found? > > How does it compare to results for KUN1163 in [Table 1](https://journals.asm.org/doi/10.1128/mra.01212-19#tab1) in {% cite Hikichi_2019 %}? > @@ -164,9 +166,9 @@ It is also able to detect and annotate small proteins (sORF). Predicted CDS are > > 3. 2,717 CDSs, a bit more than the expected 2,704 CDSs in [Table 1](https://journals.asm.org/doi/10.1128/mra.01212-19#tab1) in {% cite Hikichi_2019 %} > > 4. 5 sORFs. There is no information about sORFs in {% cite Hikichi_2019 %} > > 5. Other components - > > + > > > > Components | Bakta | {% cite Hikichi_2019 %} - > > --- | --- | --- + > > --- | --- | --- > > tRNAs | 57 | 61 > > Transfer-messenger RNA (tmRNAs) | 1 | 1 > > rRNAs | 9 | 5 @@ -224,7 +226,7 @@ It is also able to detect and annotate small proteins (sORF). Predicted CDS are GFF is a file format used for describing genes and other features of DNA, RNA and protein sequences. It is a tab delimited file with 9 fields per line: - 1. **seqid**: The name of the sequence where the feature is located. + 1. **seqid**: The name of the sequence where the feature is located. 2. **source**: The algorithm or procedure that generated the feature. This is typically the name of a software or database. 3. **type**: The feature type name, like "gene" or "exon". In a well structured GFF file, all the children features always follow their parents in a single block (so all exons of a transcript are put after their parent "transcript" feature line and before any other parent transcript line). In GFF3, all features and their relationships should be compatible with the standards released by the Sequence Ontology Project. 4. **start**: Genomic start of the feature, with a 1-base offset. This is in contrast with other 0-offset half-open sequence formats, like BED. @@ -232,7 +234,7 @@ It is also able to detect and annotate small proteins (sORF). Predicted CDS are 6. **score**: Numeric value that generally indicates the confidence of the source in the annotated feature. A value of "." (a dot) is used to define a null value. 7. **strand**: Single character that indicates the strand of the feature. This can be "+" (positive, or 5'->3'), "-", (negative, or 3'->5'), "." (undetermined), or "?" for features with relevant but unknown strands. 8. **phase**: phase of CDS features; it can be either one of 0, 1, 2 (for CDS features) or "." (for everything else). See the section below for a detailed explanation. - 9. **attributes**: A list of tag-value pairs separated by a semicolon with additional information about the feature. + 9. **attributes**: A list of tag-value pairs separated by a semicolon with additional information about the feature. > > @@ -246,12 +248,12 @@ It is also able to detect and annotate small proteins (sORF). Predicted CDS are {: .question} - Plot of the annotation as circular genome annotation - + ![A circular plot showcasing the draft genome, providing a visual representation of its genetic information.](./images/bakta_plot.png) > > - > 1. What the 2 rings in the center? + > 1. What the 2 rings in the center? > 2. How are plotted the features? > > > @@ -282,7 +284,7 @@ To identify plasmids in our contigs, we use **PlasmidFinder** ({% cite carattoli - `raw_results.txt`: A text file containing the result table and alignments - `results.tsv`: A tabular file with the following columns: - + - **Database** - **Plasmid**: Plasmid against which the input genome has been aligned. - **Identity**: Percent identity in the alignment between the best matching plasmid in the database and the corresponding sequence in the inputgenome (also called the high-scoring segment pair (HSP)). A perfect alignment is 100%, but must also cover the entire length of the plasmid in the database (compare example 1 and 3). @@ -307,7 +309,7 @@ To identify plasmids in our contigs, we use **PlasmidFinder** ({% cite carattoli > > - CP000737, AP003139 (2 times) correspond to *Staphylococcus aureus* plasmids > > - AF503772 corresponds to a *Enterococcus faecalis* plasmid > > - CP003584 corresponds to a *Enterococcus faecium* plasmid - > > + > > > > 4. All plasmid sequences corresponding to *Staphylococcus aureus* plasmids are all on contig00019, making this contig likely a plasmid. In addition, this contig has a length of 30,347 bp, which is similar to the expected length of the plasmid for KUN1163 in [Table 1](https://journals.asm.org/doi/10.1128/mra.01212-19#tab1) in {% cite Hikichi_2019 %} > {: .solution} {: .question} @@ -335,7 +337,7 @@ To detect integrons, we will use **IntegronFinder** ({% cite neron2022integronfi - Complete integron: Integron with integron integrase nearby attC site(s) - In0 element: Integron integrase only, without any attC site nearby - - CALIN element: Cluster of attC sites Lacking INtegrase nearby + - CALIN element: Cluster of attC sites Lacking INtegrase nearby > Integron identification > @@ -392,7 +394,7 @@ To detect IS elements, we will use **ISEScan** ({% cite xie2017isescan %}). **IS > > > > 1. 20 > > 2. Using {% tool [Group data by a column](Grouping1) %} to group and count on 1st column, we find: - > > + > > > > Contig | IS element number > > --- | --- > > contig00001 | 2 @@ -408,17 +410,17 @@ To detect IS elements, we will use **ISEScan** ({% cite xie2017isescan %}). **IS > > contig00019 | 3 > > contig00027 | 1 > > contig00032 | 1 - > > contig00037 | 1 + > > contig00037 | 1 > > > > 3. As for previous question, when grouping and counting on 2nd column, we find 5 IS families: - > > + > > > > IS families | Identified IS elements > > --- | --- > > IS1182 | 4 > > IS21 | 7 > > IS3 | 3 > > IS6 | 5 - > > ISL3 | 1 + > > ISL3 | 1 > > > {: .solution} {: .question} @@ -431,7 +433,7 @@ To detect IS elements, we will use **ISEScan** ({% cite xie2017isescan %}). **IS # Visualisation of the annotation -We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/) ({% cite diesh2023jbrowse %}) with several information: +We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/) ({% cite diesh2023jbrowse %}) with several information: 1. Annotations identified by **Bakta** 2. Plasmid sequences identified by **PlasmidFinder** @@ -492,11 +494,11 @@ We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/ > Transform IntegronFinder output to GFF if integrons found > **IntegronFinder** tabular output can be transformed to GFF by: -> +> > 1. Replace `NA` values on column 7 by `0` > 2. Remove the first two lines > 3. Transform to GFF3 -> +> > > Transform IntegronFinder to GFF > > 1. {% tool [Replace Text in a specific column](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1) %} with the following parameters: > > - {% icon param-file %} *"File to process"*: tabular output of **IntegronFinder** @@ -596,7 +598,7 @@ If it takes too long to build the JBrowse instance, you can view an embedded one > > > > > -> > 1. Yes all sequences in the **PlasmidFinder** track are also in the **Bakta** track. For +> > 1. Yes all sequences in the **PlasmidFinder** track are also in the **Bakta** track. For > > 2. All Insertion Sequences in the **ISEScan** track are also in the **Bakta** track, but the Terminanl Inverted repeats are not in the **Bakta** track > {: .solution} {: .question} diff --git a/topics/genome-annotation/tutorials/funannotate/tutorial.md b/topics/genome-annotation/tutorials/funannotate/tutorial.md index fb5462249d12b5..ab6fa724b8d955 100644 --- a/topics/genome-annotation/tutorials/funannotate/tutorial.md +++ b/topics/genome-annotation/tutorials/funannotate/tutorial.md @@ -36,6 +36,7 @@ contributions: funding: - gallantries - eurosciencegateway + - elixir-europe abbreviations: NMDS: Non-metric multidimensional scaling diff --git a/topics/genome-annotation/tutorials/functional/tutorial.md b/topics/genome-annotation/tutorials/functional/tutorial.md index 2cf6c7bc3d7bd5..3fdadbaadb9977 100644 --- a/topics/genome-annotation/tutorials/functional/tutorial.md +++ b/topics/genome-annotation/tutorials/functional/tutorial.md @@ -20,6 +20,8 @@ contributions: funding: - gallantries - eurosciencegateway + - elixir-europe + - ifb subtopic: eukaryote priority: 6 --- diff --git a/topics/genome-annotation/tutorials/genome-annotation/tutorial.md b/topics/genome-annotation/tutorials/genome-annotation/tutorial.md index 275a7d0882fd80..a19eac923b1597 100644 --- a/topics/genome-annotation/tutorials/genome-annotation/tutorial.md +++ b/topics/genome-annotation/tutorials/genome-annotation/tutorial.md @@ -11,9 +11,13 @@ objectives: time_estimation: "2H" level: Introductory key_points: -contributors: - - erxleben - - bgruening +contributions: + authorship: + - erxleben + - bgruening + funding: + - eurosciencegateway + - elixir-europe subtopic: prokaryote --- diff --git a/topics/imaging/tutorials/hela-screen-analysis/tutorial.md b/topics/imaging/tutorials/hela-screen-analysis/tutorial.md index 521803cb12e3d9..55b9fdcf9661cd 100644 --- a/topics/imaging/tutorials/hela-screen-analysis/tutorial.md +++ b/topics/imaging/tutorials/hela-screen-analysis/tutorial.md @@ -34,9 +34,12 @@ follow_up_training: tutorials: - machinelearning time_estimation: "1H" -contributors: - - thomaswollmann - - kostrykin +contributions: + authorship: + - thomaswollmann + - kostrykin + funding: + - elixir-europe tags: - HeLa diff --git a/topics/imaging/tutorials/imaging-introduction/tutorial.md b/topics/imaging/tutorials/imaging-introduction/tutorial.md index 9e9837e8b31fca..68b84a17d01001 100644 --- a/topics/imaging/tutorials/imaging-introduction/tutorial.md +++ b/topics/imaging/tutorials/imaging-introduction/tutorial.md @@ -24,10 +24,13 @@ follow_up_training: topic_name: imaging tutorials: - hela-screen-analysis -contributors: - - thomaswollmann - - shiltemann - - kostrykin +contributions: + authorship: + - thomaswollmann + - shiltemann + - kostrykin + funding: + - elixir-europe tags: - HeLa diff --git a/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md b/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md index ea2ee661b59307..6d72adafef7d53 100644 --- a/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md +++ b/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md @@ -8,7 +8,7 @@ questions: - What tools are available for downstream analysis of multiplex tissue images in Galaxy? - How do I pre-process and analyze Tissue Microarray data? - How can I visualize multiplex tissue images and associated data? -- How can I assign phenotypes to cells in an MTI dataset? +- How can I assign phenotypes to cells in an MTI dataset? objectives: - Understand the tools available in Galaxy for multiplex tissue imaging analysis - Analyze and visualize publicly available TMA data using Galaxy @@ -19,10 +19,10 @@ key_points: - There are powerful interactive visualization tools available in Galaxy that can combine the real images with associated data - Tissue Microarray data can be analyzed using workflows that invoke MTI tools in batch - Segmentation quality can vary significantly depending on features of the input image, tool used, and parameters -contributors: -- CameronFRWatson -- alliecreason - +contributions: + authorship: + - CameronFRWatson + - alliecreason --- @@ -77,8 +77,8 @@ Multiplex tissue images come in a variety of forms and file-types depending on t {: .hands_on} > **Imaging platform differences** -> -> The Exemplar-002 raw images are in *ome.tiff* format; however, commonly seen raw file-types are *ome.tiff*, *tiff*, *czi*, and *svs*. If your input images are not *ome.tiff* or *tiff*, you may have to edit the dataset attributes in Galaxy to allow tools to recognize them as viable inputs. +> +> The Exemplar-002 raw images are in *ome.tiff* format; however, commonly seen raw file-types are *ome.tiff*, *tiff*, *czi*, and *svs*. If your input images are not *ome.tiff* or *tiff*, you may have to edit the dataset attributes in Galaxy to allow tools to recognize them as viable inputs. > {: .warning} @@ -91,7 +91,7 @@ The raw files for each round (10 in total) of the exemplar-002 data are availabl Commonly, raw MTI data will consist of one image per round of imaging. These individual round images are frequently captured in tiles, and there can be slight variations in how each tile was illuminated across the course of imaging. Prior to tile stitching and image registration, the tiles have to undergo illumination correction with **BaSiC Illumination** ({% cite Peng2017 %}) to account for this. Unlike many of the other tools in this workflow, BaSiC has no extra parameters to think about: Just input the collection of raw images and press *go*! -Two new list collections will appear in the history upon completion: +Two new list collections will appear in the history upon completion: - BaSiC Illumination on Collection `X`: FFP (flat-field) - BaSiC Illumination on Collection `X`: DFP (deep-field) @@ -107,11 +107,11 @@ Two new list collections will appear in the history upon completion: # Stitching and registration with **ASHLAR** -After illumination is corrected across round tiles, the tiles must be stitched together, and subsequently, each round mosaic must be registered together into a single pyramidal OME-TIFF file. **ASHLAR** ({% cite Muhlich2022 %}) from MCMICRO provides both of these functions. +After illumination is corrected across round tiles, the tiles must be stitched together, and subsequently, each round mosaic must be registered together into a single pyramidal OME-TIFF file. **ASHLAR** ({% cite Muhlich2022 %}) from MCMICRO provides both of these functions. > Important detail: Marker File > -> **ASHLAR** optionally reads a marker metadata file to name the channels in the output OME-TIFF image. This marker file will also be used in later steps. Make sure that the marker file is comma-separated and has the `marker_names` as the third column (Figure 3.). +> **ASHLAR** optionally reads a marker metadata file to name the channels in the output OME-TIFF image. This marker file will also be used in later steps. Make sure that the marker file is comma-separated and has the `marker_names` as the third column (Figure 3.). > > ![screenshot of the markers table](../../images/multiplex-tissue-imaging-TMA/ex2_markersFile.png "Markers file, used both in ASHLAR and downstream steps. Critically, the marker_names are in the third column.") > @@ -131,16 +131,16 @@ After illumination is corrected across round tiles, the tiles must be stitched t > {: .hands_on} -> **Imaging platform differences** -> -> ASHLAR, among other tools in the MCMICRO and Galaxy-ME pre-processing tools have some parameters that are specific to the +> **Imaging platform differences** +> +> ASHLAR, among other tools in the MCMICRO and Galaxy-ME pre-processing tools have some parameters that are specific to the > imaging patform used. By default, ASHLAR is oriented to work with images from RareCyte scanners. AxioScan scanners render images > in a different orientation. Because of this, when using ASHLAR on AxioScan images, it is important to select the **Flip Y-Axis** > parameter to *Yes* -> +> > ASHLAR will work for most imaging modalities; however, certain modalities require different tools to be registered. For example, -> multiplex immunohistochemistry (mIHC) images must use an aligner that registers each moving image to a reference Hematoxylin image. -> For this, Galaxy-ME includes the alternative registration tool {% tool **PALOM** %}. +> multiplex immunohistochemistry (mIHC) images must use an aligner that registers each moving image to a reference Hematoxylin image. +> For this, Galaxy-ME includes the alternative registration tool {% tool **PALOM** %}. > {: .warning} @@ -169,7 +169,7 @@ UNetCoreograph will output images (used for downstream steps), masks, and a prev # Nuclear segmentation with **Mesmer** -Cell segmentation is the basis for all downstream single-cell analyses. Different segmentation tools work highly variably depending on the imaging modality or platform used. Because of this, Galaxy-ME has incorporated several cell segmentation tools so users may find the tool that works optimally for their data. +Cell segmentation is the basis for all downstream single-cell analyses. Different segmentation tools work highly variably depending on the imaging modality or platform used. Because of this, Galaxy-ME has incorporated several cell segmentation tools so users may find the tool that works optimally for their data. Available segmentation tools in Galaxy-ME: @@ -178,11 +178,11 @@ Available segmentation tools in Galaxy-ME: - Cellpose ({% cite Stringer2020 %}) - ilastik ({% cite Berg2019 %}) -In this tutorial, we use **Mesmer** because it tends to perform generally well on a diverse range of image types, and has a limited number of parameters to understand. +In this tutorial, we use **Mesmer** because it tends to perform generally well on a diverse range of image types, and has a limited number of parameters to understand. > Important detail: Running images in batches > -> Now that each image has been split into individual core images, downstream tools must be run on the images separately. Luckily, Galaxy makes this easy by including the option to run each tool in batch across a collection of inputs. Next to the input for the tool, select {% icon param-collection %} (**Dataset collection**) as the input type, and pass the collection output by UNetCoreograph as input. +> Now that each image has been split into individual core images, downstream tools must be run on the images separately. Luckily, Galaxy makes this easy by including the option to run each tool in batch across a collection of inputs. Next to the input for the tool, select {% icon param-collection %} (**Dataset collection**) as the input type, and pass the collection output by UNetCoreograph as input. > {: .comment} @@ -193,7 +193,7 @@ In this tutorial, we use **Mesmer** because it tends to perform generally well o > - *"Resolution of the image in microns-per-pixel"*: `0.65` > - *"Compartment for segmentation prediction:"*: `Nuclear` > -> > np.squeeze +> > np.squeeze > > > > The **np.squeeze** parameter is very important to select as `Yes` to make the output compatible with next steps > {: .comment} @@ -201,19 +201,19 @@ In this tutorial, we use **Mesmer** because it tends to perform generally well o {: .hands_on} > Imaging platform differences: Image resolution** -> -> A crucial parameter for Mesmer and other segmentation tools is the **Image resolution**. This is reported in microns/pixel, and can vary depending on the imaging platform used and the settings at image acquisition. Mesmer accepts the resolution in microns/pixel; however, if using UnMICST, the resolution must be reported as a ratio of the resolution of UnMICST's training images (0.65). For example, when using UnMICST, if your images were captured at a resolution of 0.65, then the UnMICST value would be 1, but if your images were captured at 0.325 microns/pixel, then the value you would enter for UnMICST would be 0.5. +> +> A crucial parameter for Mesmer and other segmentation tools is the **Image resolution**. This is reported in microns/pixel, and can vary depending on the imaging platform used and the settings at image acquisition. Mesmer accepts the resolution in microns/pixel; however, if using UnMICST, the resolution must be reported as a ratio of the resolution of UnMICST's training images (0.65). For example, when using UnMICST, if your images were captured at a resolution of 0.65, then the UnMICST value would be 1, but if your images were captured at 0.325 microns/pixel, then the value you would enter for UnMICST would be 0.5. > {: .warning} # Calculate single-cell features with **Quantification** -After generating a segmentation mask, the mask and the original registered image can be used to extract mean intensities for each marker in the panel, spatial coordinates, and morphological features for every cell. This step is performed by MCMICRO's **Quantification** module. +After generating a segmentation mask, the mask and the original registered image can be used to extract mean intensities for each marker in the panel, spatial coordinates, and morphological features for every cell. This step is performed by MCMICRO's **Quantification** module. -Once again, as this is a TMA, we will be running this in batch mode for every core image and its segmentation mask. +Once again, as this is a TMA, we will be running this in batch mode for every core image and its segmentation mask. -The quantification step will produce a CSV cell feature table for every image in the batch. +The quantification step will produce a CSV cell feature table for every image in the batch. > Quantification > @@ -224,7 +224,7 @@ The quantification step will produce a CSV cell feature table for every image in > - {% icon param-collection %} *"Additional Cell Masks "*: `Nothing Selected` (Other tools may produce multiple mask types) > - {% icon param-file %} *"Marker channels"*: Comma-separated markers file with marker_names in third column > -> > Mask metrics and Intensity metrics +> > Mask metrics and Intensity metrics > > > > Leaving the *"mask metrics"* and *"intensity metrics"* blank will by default run all available metrics > > @@ -235,7 +235,7 @@ The quantification step will produce a CSV cell feature table for every image in # **Convert McMicro Output to Anndata** -Anndata ({% cite Virshup2021 %}) is a Python package and file format schema for working with annotated data matrices that has gained popularity in the single-cell analysis community. Many downstream analysis tools, including Scimap from MCMICRO, Scanpy ({% cite Wolf2018 %}), and Squidpy ({% cite Palla2022 %}) are built around anndata format files (h5ad). This tool splits the marker intensity data into a separate dataframe (`X`), and places all observational data (spatial coordinates, morphological features, etc.) in the cell feature table into a separate dataframe (`obs`) that shares the same indices as `X`. In downstream analyses, new categorical variables, such as phenotype assignments for each cell, are stored in the `obs` dataframe. +Anndata ({% cite Virshup2021 %}) is a Python package and file format schema for working with annotated data matrices that has gained popularity in the single-cell analysis community. Many downstream analysis tools, including Scimap from MCMICRO, Scanpy ({% cite Wolf2018 %}), and Squidpy ({% cite Palla2022 %}) are built around anndata format files (h5ad). This tool splits the marker intensity data into a separate dataframe (`X`), and places all observational data (spatial coordinates, morphological features, etc.) in the cell feature table into a separate dataframe (`obs`) that shares the same indices as `X`. In downstream analyses, new categorical variables, such as phenotype assignments for each cell, are stored in the `obs` dataframe. Learn more about this file format at the [anndata documentation](https://anndata.readthedocs.io/en/latest/index.html). @@ -248,9 +248,9 @@ Learn more about this file format at the [anndata documentation](https://anndata > - *"Whether to remove the DNA channels from the final output"*: `No` > - *"Whether to use unique name for cells/rows"*: `No` > -> > Important parameter: Unique names for cells/rows +> > Important parameter: Unique names for cells/rows > > -> > Setting *"Whether to use unique name for cells/rows"* to `No` to ensures that downstream interactive visualizations will be able to map observational features to the mask CellIDs. +> > Setting *"Whether to use unique name for cells/rows"* to `No` to ensures that downstream interactive visualizations will be able to map observational features to the mask CellIDs. > {: .warning} > {: .hands_on} @@ -275,10 +275,10 @@ There are several ways to classify cells available in Galaxy-ME. Unsupervised ap > > > Limitations of GMM automated phenotyping > > -> > When manual gates are not provided, Scimap fits a GMM to determine a threshold between positive and negative cells. This automated gating works well when markers are highly abundant within the tissue, and the data shows a bimodal distribution (Figure 6A.). GMM gating can lead to spurious thresholds, however, when the data does not appear to be bimodal (Figure 6B.). This tends to happen when the marker is not highly abundant in the tissue, so there isn't a large positive population. Markers that have a highly continuous range of intensity, like certain functional markers, can also be problematic with GMM gating. It is recommended to always look at the GMM plots output by Scimap, and validate any potentially spurious gates manually. +> > When manual gates are not provided, Scimap fits a GMM to determine a threshold between positive and negative cells. This automated gating works well when markers are highly abundant within the tissue, and the data shows a bimodal distribution (Figure 6A.). GMM gating can lead to spurious thresholds, however, when the data does not appear to be bimodal (Figure 6B.). This tends to happen when the marker is not highly abundant in the tissue, so there isn't a large positive population. Markers that have a highly continuous range of intensity, like certain functional markers, can also be problematic with GMM gating. It is recommended to always look at the GMM plots output by Scimap, and validate any potentially spurious gates manually. > > > > ![Two bar plots with overlain curves. Left in A shows a bimodal distribution of CD3D, right in B shows a unimodal distribution in CD11B.](../../images/multiplex-tissue-imaging-TMA/ex2_example_GMMs.png "Scimap automatic gating GMMs for two markers. (A) An example of a marker with a bimodal distribution and a reasonable looking gate. (B) An example of a marker with a unimodal distribution that is not ideal for fitting with a GMM, and would be a candidate for manual validation and gating.") -> > +> > > {: .comment} > {: .hands_on} @@ -286,15 +286,15 @@ There are several ways to classify cells available in Galaxy-ME. Unsupervised ap # Interactive visualization of multiplex tissue images -Visual analysis is an important part of multiplex tissue imaging workflows. Galaxy-ME has several tools that make interactive visualization easy, and can be used at various stages of analysis. +Visual analysis is an important part of multiplex tissue imaging workflows. Galaxy-ME has several tools that make interactive visualization easy, and can be used at various stages of analysis. ## Converting UNetCoreograph images to OME-TIFF using the **Convert image** tool -UNetCoreograph outputs each individual core image in `tiff` format. Interactive visualization tools, such as **Vitessce** and **Avivator** require the images to be in `OME-TIFF` format to be viewed. Galaxy-ME includes a conversion tool that can accomodate this, along with many other useful conversion functions. +UNetCoreograph outputs each individual core image in `tiff` format. Interactive visualization tools, such as **Vitessce** and **Avivator** require the images to be in `OME-TIFF` format to be viewed. Galaxy-ME includes a conversion tool that can accomodate this, along with many other useful conversion functions. > Convert image > -> 1. {% tool [Convert image](toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0) %} with the following parameters: +> 1. {% tool [Convert image](toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0) %} with the following parameters: > - {% icon param-collection %} *"Input Image"*: `UNetCoreograph Images` > - *"Output data type"*: `OME TIFF` > - *"Tile image"*: `Tile image` @@ -305,7 +305,7 @@ UNetCoreograph outputs each individual core image in `tiff` format. Interactive ## **Rename OME-TIFF Channels** -Some tools can cause the channel names in an OME-TIFF image to be lost. To fix this, or to change the channel names to whatever the user prefers, the **Rename OME-TIFF Channels** tool can be invoked using a markers file similar to the one used in previous steps. +Some tools can cause the channel names in an OME-TIFF image to be lost. To fix this, or to change the channel names to whatever the user prefers, the **Rename OME-TIFF Channels** tool can be invoked using a markers file similar to the one used in previous steps. > Rename channels > @@ -332,7 +332,7 @@ For any `OME-TIFF` image in a Galaxy-ME history, there will be an option to view ## Generating an interactive visualization dashboard with **Vitessce** -**Vitessce** is a powerful visualization tool that creates interactive dashboards (Figure 8.) to look at a multiplex `OME-TIFF` images in conjunction with data generated during analysis and stored in an anndata file. The segmentation mask can be overlaid onto the image to qualitatively assess the segmentation performance. The mask can then be colored with associated observational data (Figure 9A.), such as `phenotype`, with the same colors appearing in barplots (Figure 9B.), UMAP representations, heatmaps, and marker intensity violin plots for comrehensive data exploration. +**Vitessce** is a powerful visualization tool that creates interactive dashboards (Figure 8.) to look at a multiplex `OME-TIFF` images in conjunction with data generated during analysis and stored in an anndata file. The segmentation mask can be overlaid onto the image to qualitatively assess the segmentation performance. The mask can then be colored with associated observational data (Figure 9A.), such as `phenotype`, with the same colors appearing in barplots (Figure 9B.), UMAP representations, heatmaps, and marker intensity violin plots for comrehensive data exploration. ![Screenshot of the vitessce dashboard.](../../images/multiplex-tissue-imaging-TMA/ex2_fullVitessce.png "A Full view of a vitesse dashboard for one core from Exemplar-002.") @@ -354,7 +354,7 @@ For any `OME-TIFF` image in a Galaxy-ME history, there will be an option to view # Next steps: Compositional and spatial analyses -Galaxy-ME includes additional tools from **Scimap** and tools from the **Squidpy** package ({% cite Palla2022 %}) that can be used to perform a variety of downstream analyses. For example, once phenotypes have been assigned to individual cells, **Squidpy** has several methods for understanding the spatial organization of the tissue. Using **Squidpy**, a spatial neighborhood graph is first generated, from which the organization of specific phenotype groups and their interactions can be quantified. +Galaxy-ME includes additional tools from **Scimap** and tools from the **Squidpy** package ({% cite Palla2022 %}) that can be used to perform a variety of downstream analyses. For example, once phenotypes have been assigned to individual cells, **Squidpy** has several methods for understanding the spatial organization of the tissue. Using **Squidpy**, a spatial neighborhood graph is first generated, from which the organization of specific phenotype groups and their interactions can be quantified. > Spatial analysis with Squidpy > @@ -371,7 +371,7 @@ Galaxy-ME includes additional tools from **Scimap** and tools from the **Squidpy > > > Neighborhood enrichment plot > > -> > **Squidpy** was used to calculate neighborhood enrichments for each phenotype in core 2 of exemplar 2 (Figure 10.). This shows which phenotypes co-locate most frequently within the tissue. +> > **Squidpy** was used to calculate neighborhood enrichments for each phenotype in core 2 of exemplar 2 (Figure 10.). This shows which phenotypes co-locate most frequently within the tissue. > > > > ![Heatmap showing phenotype vs neighbourhood enrichment. Most of the heatmap is blue/green (low) but one cell under epithelial is bright yellow (high)](../../images/multiplex-tissue-imaging-TMA/ex2_squidpy_enrichment.png "The output of Squidpy's neighborhood enrichment on core 2 from Exemplar-002.") > > @@ -387,9 +387,9 @@ Galaxy-ME includes additional tools from **Scimap** and tools from the **Squidpy > - In *"Plotting Options"*: > - *"Ripley's statistic to be plotted"*: `L` > -> > Ripley's L plot +> > Ripley's L plot > > -> > **Squidpy** was used to calculate Ripley's L curves for each phenotype in core 2 of exemplar 2 (Figure 11.). This shows the overall organization of each phenotype in the tissue. If the curve for a given phenotype lies above the light grey null line (Example: Epithelial cells in Figure 11.), the phenotype is statistically significantly clustered. If the curve lies on the null line (Example: Myeloid lineage in Figure 11.), it's spatial distribution within the tissue is random. If the curve is underneath the null line (Example: T cells in Figure 11.), it's spatial distribution is statistically significantly dispersed. +> > **Squidpy** was used to calculate Ripley's L curves for each phenotype in core 2 of exemplar 2 (Figure 11.). This shows the overall organization of each phenotype in the tissue. If the curve for a given phenotype lies above the light grey null line (Example: Epithelial cells in Figure 11.), the phenotype is statistically significantly clustered. If the curve lies on the null line (Example: Myeloid lineage in Figure 11.), it's spatial distribution within the tissue is random. If the curve is underneath the null line (Example: T cells in Figure 11.), it's spatial distribution is statistically significantly dispersed. > > > > ![Graph of Ripley's L. Value is plotted against bins, all of which show cursves starting at 0 and increasing as bins increase. Epithelial is the highest curve.](../../images/multiplex-tissue-imaging-TMA/ex2_squidpy_ripleys.png "The output of Squidpy's Ripley's L curve on core 2 from Exemplar-002.") > > diff --git a/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.md b/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.md index 842b5a4d12d0b2..fdc646ce47bfd7 100644 --- a/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.md +++ b/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.md @@ -17,11 +17,12 @@ objectives: time_estimation: 1H key_points: - CellProfiler in Galaxy can be used to track objects in time-lapse microscopy images -contributors: -- sunyi000 -- beatrizserrano -- jkh1 +contributions: + authorship: + - sunyi000 + - beatrizserrano + - jkh1 --- diff --git a/topics/imaging/tutorials/tutorial-CP/tutorial.md b/topics/imaging/tutorials/tutorial-CP/tutorial.md index ea48402b0af5f6..da796d919591b6 100644 --- a/topics/imaging/tutorials/tutorial-CP/tutorial.md +++ b/topics/imaging/tutorials/tutorial-CP/tutorial.md @@ -24,9 +24,12 @@ key_points: time points, z-stack positions and crop the image in different ways. - CellProfiler in Galaxy can segment and extract features of any object of interest. - The features and masks can be exported for further analysis. -contributors: -- beatrizserrano -- jkh1 + +contributions: + authorship: + - beatrizserrano + - jkh1 + zenodo_link: '' --- diff --git a/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.md b/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.md index 8ae72e5c797f64..dc8e8c7d90177d 100644 --- a/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.md @@ -23,14 +23,18 @@ key_points: - "Galaxy provides ways to share your results and methods with others" subtopic: core priority: 2 -contributors: - - annefou - - nagoue - - chrisbarnettster - - michelemaroni89 - - olanag1 - - tnabtaf - - shiltemann + +contributions: + authorship: + - annefou + - nagoue + - chrisbarnettster + - michelemaroni89 + - olanag1 + - tnabtaf + - shiltemann + funding: + - elixir-europe recordings: - captioners: diff --git a/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.md b/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.md index dead7b0fb87f1a..40cbaef93e6a4e 100644 --- a/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.md @@ -19,11 +19,13 @@ key_points: - "One can retrieve NGS data from Sequence Read Archive" - "Galaxy can analyze massive amounts of data and make them suitable for secondary analysis" subtopic: next-steps -contributors: - - nekrut - - mvdbeek - - tnabtaf - - blankenberg + +contributions: + authorship: + - nekrut + - mvdbeek + - tnabtaf + - blankenberg recordings: - captioners: diff --git a/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md b/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md index 1203b608e6b86a..e538af9eac945f 100644 --- a/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md @@ -34,6 +34,10 @@ contributions: - hexylena editing: - teresa-m + funding: + - elixir-europe + - deNBI + - uni-freiburg --- diff --git a/topics/introduction/tutorials/galaxy-reproduce/tutorial.md b/topics/introduction/tutorials/galaxy-reproduce/tutorial.md index db807ac4688e2c..a9cd0ebcfb42be 100644 --- a/topics/introduction/tutorials/galaxy-reproduce/tutorial.md +++ b/topics/introduction/tutorials/galaxy-reproduce/tutorial.md @@ -17,9 +17,12 @@ key_points: - "Galaxy provides ways to inspect and re-use Galaxy histories" - "Galaxy provides an easy way to re-run tasks from histories" subtopic: next-steps -contributors: - - foellmelanie - - annefou +contributions: + authorship: + - foellmelanie + - annefou + funding: + - uni-freiburg --- This training will demonstrate how to reproduce analyses performed in the Galaxy framework. Before we start with the hands-on part, we would like to give you some information about Galaxy. diff --git a/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md b/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md index 9eea73324e5de5..b15ee612543c2d 100644 --- a/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md +++ b/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md @@ -16,10 +16,14 @@ key_points: - Data processing is a key step in untargeted Metabolomics analyses. The question of data filtering and correction must be addressed in all projects, even thought in some cases it may lead to the decision of no action on data. In particular, blank filtering, pool variation study and signal drift correction are common aspects to consider when dealing with LC-MS. - Although some main steps are standard, various ways to combine tools exist. Remember that depending on your context (type of samples, protocol specificities...) specific filters/normalisations may be needed, independently of standards ones. - A variety of tools is available in Galaxy, but do not forget that you need appropriate knowledge to decide what to use depending on your data. -contributors: -- melpetera -- workflow4metabolomics +contributions: + authorship: + - melpetera + - workflow4metabolomics + editing: + funding: + - elixir-europe --- @@ -28,9 +32,9 @@ Metabolomics is a *-omic* science known for being one of the most closely relate It involves the study of different types of matrices, such as blood, urine, tissues, in various organisms including plants. It focuses on studying the very small molecules which are called *metabolites*, to better understand matters linked to the metabolism. -Metabolomics analyses can be quite complex to conduct, especially when dealing with untargeted approaches. -**Liquid-Chromatography Mass Spectrometry** (LC-MS) is one of the three main technologies used to perform this kind of approach. -Data analysis for this technology requires a large variety of steps, ranging from extracting information from the raw data to statistical analysis and annotation. +Metabolomics analyses can be quite complex to conduct, especially when dealing with untargeted approaches. +**Liquid-Chromatography Mass Spectrometry** (LC-MS) is one of the three main technologies used to perform this kind of approach. +Data analysis for this technology requires a large variety of steps, ranging from extracting information from the raw data to statistical analysis and annotation. One of these steps is called "data processing". It takes place after the pre-processing step (extraction of the peak list from raw data) and before any statistical analysis. You can get an overview of a complete LC-MS untargeted metabolomic workflow by following [the dedicated training material]({% link topics/metabolomics/tutorials/lcms/tutorial.md %}). @@ -49,7 +53,7 @@ What should you do to ensure the quality of your tables? This tutorial will show # Overview and data upload -Data processing covers a large range of actions. They can generally be described as transformation (*e.g.* normalisation) or filter (*e.g.* removal of unwanted ions). +Data processing covers a large range of actions. They can generally be described as transformation (*e.g.* normalisation) or filter (*e.g.* removal of unwanted ions). In this tutorial we will focus on three main types of processing: - Removing "trash" signals - Correcting intensities @@ -62,7 +66,7 @@ The different Galaxy tools that will be used in this tutorial are given in the f ![The picture is composed of 3 main boxes linked by arrows from left to right. In each of the first and last boxes, labelled '3 tabulars', are found 3 files named sampleMetadata, variableMetadata and dataMatrix. In the middle box labelled 'Quality Control' is found the workflow used in this tutorial, represented as tiny boxes with tool names, linked with arrows following the tutorial order.](../../images/tutorial-lcms-proc-wf.png "The full tutorial workflow") All these modules are part of the [Wokflow4Metabolomics](http://workflow4metabolomics.org/) tool suit ({% cite Giacomoni2014 %}, {% cite Guitton2017 %}). -They are compatible with the whole data analysis solution maintained by the W4M team. +They are compatible with the whole data analysis solution maintained by the W4M team. > Workflow4Metabolomics public history > @@ -76,42 +80,42 @@ They are compatible with the whole data analysis solution maintained by the W4M ## Dataset description To illustrate the steps in this tutorial, a dataset has been built purposely. -It is composed of 3 files. They are text files of tables with tabulation as separator. +It is composed of 3 files. They are text files of tables with tabulation as separator. The *dataMatrix* file is a table containing the intensities of measured variables (ions, in lines) for every samples (in column). The first column is for ions' identifiers while the first line is for samples' identifiers. -The *variableMetadata* file is a table containing information about the ions. -The first column is for ions' identifiers while the other columns gather information about m/z and retention time (rt). +The *variableMetadata* file is a table containing information about the ions. +The first column is for ions' identifiers while the other columns gather information about m/z and retention time (rt). -The *sampleMetadata* file is a table containing information about the samples. +The *sampleMetadata* file is a table containing information about the samples. The first column is for samples' identifiers while the other columns gather analytical and biological information -such as the order of injection in the analytical sequence and the biological groups of interest for the supposed study. +such as the order of injection in the analytical sequence and the biological groups of interest for the supposed study. The simulated design is composed of 30 biological samples (tagged "sample" in the *sampleType* column), completed with 8 quality-control pooled samples (tagged "pool" in the *sampleType* column) -and 6 extraction solvent samples (tagged "blank" in the *sampleType* column). +and 6 extraction solvent samples (tagged "blank" in the *sampleType* column). The samples have been supposedly injected in two distinct sequences (tagged "B1" and "B2" in the *batch* column), -the injection order being given in the *injectionOrder* column. +the injection order being given in the *injectionOrder* column. Two sample characteristics are given: - The *Group* column represents two groups "A" and "B", supposedly two biological groups (*e.g.* phenotypes, treatment groups...). -- The *Osmo* column represents a measurement of supposed osmolarity, imagining that the samples may be urine samples. +- The *Osmo* column represents a measurement of supposed osmolarity, imagining that the samples may be urine samples. ## Data upload -To perform the different exercices of this tutorial, you need to create a new history and upload the dedicated dataset. +To perform the different exercices of this tutorial, you need to create a new history and upload the dedicated dataset. > Data upload > > 1. Create a new history for this tutorial -> 2. Import the 3 starting files in your history. Two possibilities: +> 2. Import the 3 starting files in your history. Two possibilities: > - Option 1: from a shared data library (ask your instructor) > - Option 2: from [Zenodo](https://zenodo.org/record/5179809) using the URLs given below: > > ``` > https://zenodo.org/record/5179809/files/Dataprocessing_dataMatrix.txt > https://zenodo.org/record/5179809/files/Dataprocessing_sampleMetadata.txt -> https://zenodo.org/record/5179809/files/Dataprocessing_variableMetadata.txt +> https://zenodo.org/record/5179809/files/Dataprocessing_variableMetadata.txt > ``` > > {% snippet faqs/galaxy/datasets_import_via_link.md %} @@ -120,7 +124,7 @@ To perform the different exercices of this tutorial, you need to create a new hi > > {% snippet faqs/galaxy/datasets_rename.md %} > -> 4. Check that the datatype is "tabular". If not, you may change it. +> 4. Check that the datatype is "tabular". If not, you may change it. > > {% snippet faqs/galaxy/datasets_change_datatype.md datatype="datatypes" %} > @@ -134,17 +138,17 @@ To perform the different exercices of this tutorial, you need to create a new hi # Removing "trash" signals -Data are often affected by various sources of unwanted variability. This can be found in your tables in different ways, -two common ones being the presence of unwanted ions, and the effect of biological or analytical variables on intensity measures. -This unwanted information can limit the effectiveness of statistical methods, leading sometimes to difficulties in revealing investigated effects. -Thus, identifying such variability can help analysing your data at its full potential. -Yet, getting rid of such information may not be a trivial problem. It requires different elements to be completed successfully. +Data are often affected by various sources of unwanted variability. This can be found in your tables in different ways, +two common ones being the presence of unwanted ions, and the effect of biological or analytical variables on intensity measures. +This unwanted information can limit the effectiveness of statistical methods, leading sometimes to difficulties in revealing investigated effects. +Thus, identifying such variability can help analysing your data at its full potential. +Yet, getting rid of such information may not be a trivial problem. It requires different elements to be completed successfully. -In this section we will adress the question of "trash" signal filtering. +In this section we will adress the question of "trash" signal filtering. By this we mean ions that are present in the extracted peak list we have, but that do not correspond to relevant compounds to analyse. -This can be for example noise, or ions from compounds that are not present in the original biological samples. +This can be for example noise, or ions from compounds that are not present in the original biological samples. -To make it clearer, we will illustrate this with two examples: a "simple" one first and a more advanced one in a second time. +To make it clearer, we will illustrate this with two examples: a "simple" one first and a more advanced one in a second time. ## Filtering signals at given retention times @@ -152,9 +156,9 @@ When using a chromatography column for MS analysis, you may want to exclude some For example, you may want to exclude the dead volume, a calibration zone at the begining or the end, or to exclude a column flush. In this tutorial, let's suppose the data are from some LC-QTOF analysis with a dead volume between 0 and 0.4 minutes and a column flush from 16 minutes. -Then we may want to exclude ions that may be found at theses specific retention time (rt) ranges. +Then we may want to exclude ions that may be found at theses specific retention time (rt) ranges. A quick check at the variableMetadata file reveals that a retention time column is available ("rt") with values in minutes. -We can then use this column to filter the dataset. +We can then use this column to filter the dataset. > Using Generic_filter to filter ions found at specific retention times > @@ -181,9 +185,9 @@ We can then use this column to filter the dataset. > {: .hands_on} -The **Generic Filter** {% icon tool %} tool generates 3 tables. They correspond to the 3 original tables, -except the content has been filtered according to the specified parameters. -By "filtering", it means removing from the dataset some variables (ions) and/or samples according to the defined filters. +The **Generic Filter** {% icon tool %} tool generates 3 tables. They correspond to the 3 original tables, +except the content has been filtered according to the specified parameters. +By "filtering", it means removing from the dataset some variables (ions) and/or samples according to the defined filters. > > @@ -201,7 +205,7 @@ By "filtering", it means removing from the dataset some variables (ions) and/or {: .question} This was a relatively easy task to do. The key point to perform the filter was to know the ranges of rt that needed to be filter, -since the information about rt values was already explicitly found in the dataset. +since the information about rt values was already explicitly found in the dataset. However, sometimes filtering requires more steps to be able to perform the wanted processing. This will be illustrated with the next example. @@ -210,25 +214,25 @@ This will be illustrated with the next example. As mentioned before, measured signals using mass spectrometry may not always be all of interest. Some can be noise, or compounds not characteristic of the analysed biological samples. There are several ways to reduce there impact on gathered data. -But one key point is always, as a starting point, to identify the issue. +But one key point is always, as a starting point, to identify the issue. In the previous example we knew there were retention time ranges of values where signals were not relevant. -But they may also be some signals that represent noise, found at no specific retention times. -So a question can be "how do we identify these signals?". +But they may also be some signals that represent noise, found at no specific retention times. +So a question can be "how do we identify these signals?". -One possible procedure is the use of blanks to estimate the noise, as a reference. +One possible procedure is the use of blanks to estimate the noise, as a reference. The idea is to compare blanks’ intensities with other samples’ intensities. If there is no subtantial difference, we can assume that the concerned signal is noise. Of course, to be able to do so, you need to inject reference blanks along with your biological samples to get these intensities in your dataMatrix. -Thus, you need to anticipate it when you define your injection sequence. -Ideally, the blanks to use are extraction blanks, but you can also use injection solvent depending on your protocols. +Thus, you need to anticipate it when you define your injection sequence. +Ideally, the blanks to use are extraction blanks, but you can also use injection solvent depending on your protocols. When blanks are available in your dataset, another thing to consider is "how do I formalise the information needed to be able to filter?". One common way to compare may be to set a minimum difference between means or medians, or to test for significant difference with a statistical test. -In this tutorial, we will choose to calculate a mean fold change between blanks and non-blank samples, and to set a threshold value for filtering. +In this tutorial, we will choose to calculate a mean fold change between blanks and non-blank samples, and to set a threshold value for filtering. -The mean fold change ("fold") for each ion can be calculated using the **Intensity Check** {% icon tool %} tool. +The mean fold change ("fold") for each ion can be calculated using the **Intensity Check** {% icon tool %} tool. > Using Intensity Check to generate the information needed to filter > @@ -252,8 +256,8 @@ The mean fold change ("fold") for each ion can be calculated using the **Intensi {: .hands_on} This module generates two outputs: a pdf file for plots (that is not of interest in our example) -and a table corresponding to the variableMetadata file used as input, completed with new columns depending on the selected parameters. -In our case, it generated a column named *fold_Other_VS_blank* that we will use for filtering. +and a table corresponding to the variableMetadata file used as input, completed with new columns depending on the selected parameters. +In our case, it generated a column named *fold_Other_VS_blank* that we will use for filtering. > > @@ -264,21 +268,21 @@ In our case, it generated a column named *fold_Other_VS_blank* that we will use > > > > > > Since *"Selected class"*=`blank`, the samples are devided in two groups: the blank samples on one hand -> > and all the other samples on the other hand. -> > To calculate a mean fold change (*i.e.* a ratio of means) between the two classes, we need to define which mean will be used as numerator -> > and which one will be used as denominator. Since we defined that the selected class should be the denominator, the values we will get are -> > (mean of non-blank samples)/(mean of blank samples). -> > Thus, a value of "4" for a given ion means that the ion has a mean 4-times higher in non-blank samples compared to blank samples. +> > and all the other samples on the other hand. +> > To calculate a mean fold change (*i.e.* a ratio of means) between the two classes, we need to define which mean will be used as numerator +> > and which one will be used as denominator. Since we defined that the selected class should be the denominator, the values we will get are +> > (mean of non-blank samples)/(mean of blank samples). +> > Thus, a value of "4" for a given ion means that the ion has a mean 4-times higher in non-blank samples compared to blank samples. > > > {: .solution} > {: .question} The **Intensity Check** {% icon tool %} tool generates additional information about your dataset, but do not perform any filter. -We can now define a threshold for filtering, and use the **Generic Filter** {% icon tool %} tool again to remove noise signal. +We can now define a threshold for filtering, and use the **Generic Filter** {% icon tool %} tool again to remove noise signal. Here we will use a threshold value of "4". What we want is to remove ions having a fold value lower than 4, meaning that the mean values of biological samples' intensities for theses ions are not sufficiently high compared to blanks to be considered -to be resulting from relevant compounds. +to be resulting from relevant compounds. > Using Generic_filter to filter ions with insuffisant mean contrast with blank samples > @@ -303,7 +307,7 @@ to be resulting from relevant compounds. > {: .hands_on} -As for the previous use of **Generic Filter**, we now have a dataset filtered from noise signals. +As for the previous use of **Generic Filter**, we now have a dataset filtered from noise signals. > > @@ -312,22 +316,22 @@ As for the previous use of **Generic Filter**, we now have a dataset filtered fr > > > > > > From a dataset containing originally 200 ions, the two successive filters lead to a dataset containing only 131 ions. -> > The number of samples did not change, so we still have 30 biological samples, 8 QC pools and 6 blanks. +> > The number of samples did not change, so we still have 30 biological samples, 8 QC pools and 6 blanks. > > > {: .solution} > {: .question} -At that point we will not use the blank samples anymore. However, before removing them from the dataset, it is always interesting to -get an overview of the dataset including blanks. +At that point we will not use the blank samples anymore. However, before removing them from the dataset, it is always interesting to +get an overview of the dataset including blanks. ## Filtered dataset overview The idea here is to have a glance at what the dataset looks like at a macro scale. For this tutorial, we consider that at this step what we have in our dataset are ions only resulting from compounds originally present in the biological samples. -Thus, there are some assumptions we can begin to make, that we can try to check using graphical tools. +Thus, there are some assumptions we can begin to make, that we can try to check using graphical tools. -Here, we will use a tool that is called **Quality Metrics** to have an overview of our dataset through the generation of a pdf file containing some plots. +Here, we will use a tool that is called **Quality Metrics** to have an overview of our dataset through the generation of a pdf file containing some plots. > Using Quality Metrics to get an overview of the dataset > @@ -352,17 +356,17 @@ This tool generates several outputs (some of them are going to be used in a late On the top left of the picture, we can see the two first components of a Principal Component Analysis (PCA) with the projection of samples on it, colored by sample type. We can see that the main variability in the dataset distinguishes the blank samples (on the left in black) from the other ones (red for pools and green for samples). -This is awaited since blanks are supposed to have very low intensities compared to biological samples. +This is awaited since blanks are supposed to have very low intensities compared to biological samples. This observation is consistant with the top middle plot which represents the sum of intensities for each sample (plotting according to the injection order), -where blank samples have very low values. +where blank samples have very low values. -This kind of plots is a good way to detect samples that may have abnormally low profiles: +This kind of plots is a good way to detect samples that may have abnormally low profiles: if a sample is positioned at the same area as the blanks, it is suspicious and a special attention should be given to the concerned sample. In this tutorial dataset, no atypical sample is observed, so no special attention needs to be paid on specific samples. -Since the blank samples are of no use anymore, we can remove them from the dataset. -Again, this can be done running the **Generic Filter** {% icon tool %} tool, using the *sampleType* column of the sampleMetadata table. +Since the blank samples are of no use anymore, we can remove them from the dataset. +Again, this can be done running the **Generic Filter** {% icon tool %} tool, using the *sampleType* column of the sampleMetadata table. > Using Generic_filter to remove blank samples from the dataset > @@ -390,7 +394,7 @@ Again, this can be done running the **Generic Filter** {% icon tool %} tool, usi > {: .hands_on} -This step leads to a dataset containing 131 ions and 38 samples (from which 8 pools). +This step leads to a dataset containing 131 ions and 38 samples (from which 8 pools). You may have noticed that from module to module, output names tend to become longer and longer. To prevent very long and not-so-informative names due to successive use of modules, we highly recommand to regularly rename the outputs. @@ -409,31 +413,31 @@ Now we are ready to investigate another type of data processing: correcting inte # Signal drift and batch effect correction -Here we will illustrate an example of data processing that is not about filtering, but about correcting. +Here we will illustrate an example of data processing that is not about filtering, but about correcting. Indeed, when it comes to performing statistics comparing biological samples, it is crucial for the intensity values used to be reflecting -relevant variability between samples. +relevant variability between samples. In untargeted Metabolomics studies, we manipulate measures that are relative abundancies. Although we have no unit attached to the intensities, we at least assume that, for a given ion, an intensity value for one sample being higher than the one from another sample means that the compound from which the ion is generated is originally found in higher abundance in the biological sample from -the first sample compared to the other. +the first sample compared to the other. This assumption may seem trivial, but truth is it is not when dealing with LC-MS data. -It is known that when injecting successively a large number of samples, the LC-MS system tends to get dirty. This may cause a measure drift. +It is known that when injecting successively a large number of samples, the LC-MS system tends to get dirty. This may cause a measure drift. To prevent inability to catch signal anymore, in case of large injection series, the sequence is generally divided into several batches and the source is cleaned between batches. -Unfortunately, these signal drift and batch design can add significant variability in the data. -It makes sample comparison complicated, since the assumption stated previously about abundance in biological samples may not be true anymore. -In case data is impacted by these effects, we need a way to normalise the data to obtain something reliable for statistical analysis. +Unfortunately, these signal drift and batch design can add significant variability in the data. +It makes sample comparison complicated, since the assumption stated previously about abundance in biological samples may not be true anymore. +In case data is impacted by these effects, we need a way to normalise the data to obtain something reliable for statistical analysis. ## [Optional step] Checking batch effect on data -You may have noticed in the **Quality Metrics** output PDF that appart from blanks, samples seemed to be seperated in two groups. +You may have noticed in the **Quality Metrics** output PDF that appart from blanks, samples seemed to be seperated in two groups. Truth is it is indeed. However, the best would be to confirm it, in particular by finding out what these groups are linked to. -Here dices are already rolled, and given the fact that in this section we are adressing signal drift and batch effects, -one could suppose that the groups may have something to do with it. +Here dices are already rolled, and given the fact that in this section we are adressing signal drift and batch effects, +one could suppose that the groups may have something to do with it. -Let's confirm it by performing a PCA, with the specificity to colour the sample projections according to the supposed effect: the batch information. -This can be done using the **Multivariate** {% icon tool %} tool. +Let's confirm it by performing a PCA, with the specificity to colour the sample projections according to the supposed effect: the batch information. +This can be done using the **Multivariate** {% icon tool %} tool. > Using Multivariate to get a coloured score plot from a PCA > @@ -449,7 +453,7 @@ This can be done using the **Multivariate** {% icon tool %} tool. > > > > > -> > Changing the `0.8` value to `0.4` makes the text size of labels on the score plot smaller. Since the plot box size by default is tiny, this enhances the readability of the plot. +> > Changing the `0.8` value to `0.4` makes the text size of labels on the score plot smaller. Since the plot box size by default is tiny, this enhances the readability of the plot. > {: .comment} > > > Comment to W4M users @@ -459,15 +463,15 @@ This can be done using the **Multivariate** {% icon tool %} tool. > {: .hands_on} -The output of **Multivariate** we will be interested in here is only the PDF file (Multivariate_figure.pdf). +The output of **Multivariate** we will be interested in here is only the PDF file (Multivariate_figure.pdf). Among the four plots displayed in the file, we can see at the bottom left corner that the first component clearly reveals two distinct groups. -These groups perfectly match the batch information we coloured the sample projections with. +These groups perfectly match the batch information we coloured the sample projections with. -This confirms that we indeed have at least a batch effect in the data. -To note, this comment is relevant thanks to the fact that supposedly we randomised the injection sequence. -This is essential to be able to efficiently separate any analytical effect from known biological variables when searching for effects. +This confirms that we indeed have at least a batch effect in the data. +To note, this comment is relevant thanks to the fact that supposedly we randomised the injection sequence. +This is essential to be able to efficiently separate any analytical effect from known biological variables when searching for effects. If you look at the sampleMetadata file we originally imported, you can notice that the biological group (*A* and *B*) are equally found in the two batches, -with alternation all through the injection order. +with alternation all through the injection order. ## Performing the correction process @@ -477,9 +481,9 @@ This is even more the case when dealing with batch effects and signal drifts. There is a strategy, described initially by Van Der Kloet in 2009 ({% cite VdK2009 %}), that has made its way to nowadays procedures ({% cite Dunn2011 %}). The idea is to model the signal drift and the batch effect level by using a reference that can be representative for every ions in the dataset. Indeed, signal drift and batch effects can have very different impacts accross ions in a same dataset, so it is crucial to have a reference that is reliable -for each ion independantly. +for each ion independantly. -Here the "universal" reference is obtained by using samples that are made by pooling together an extract of every samples in study. +Here the "universal" reference is obtained by using samples that are made by pooling together an extract of every samples in study. Thus, these Quality-control pooled samples ('pools') contain all the compounds that are originally found in the samples, being a reference for a very wide range of ions. By injecting these pools all through the injection sequence of the study samples, we obtain a reference for which the main variability observed is composed of the analytical effects we want to correct, since biologically they are supposed to be identical. @@ -492,12 +496,12 @@ the analytical effects we want to correct, since biologically they are supposed > > ![An example plot with the normalisation formula](../../images/lcms_BC_theo.png "How this works") > -> You can see a plot representing 6 sample measures (blue points) in a batch for a given extracted ion. +> You can see a plot representing 6 sample measures (blue points) in a batch for a given extracted ion. > The yellow line represents a model for the signal drift that can be used to normalise the data. -> This line is determined using the pools only (red squares). -> With the given formula, we can correct the signal drift. +> This line is determined using the pools only (red squares). +> With the given formula, we can correct the signal drift. > -> This work has to be done for each batch. +> This work has to be done for each batch. > Thus, if your sequence is divided into several batches, the idea is to obtain something similar to the following picture: > > ![A before/after plot showing an example of intensities before correction, with clear signal drift and batch effects, and after correction, where the effects have been erased thanks to the correction process](../../images/lcms_BC_theo2.png "Before/after picture") @@ -509,7 +513,7 @@ In this tutorial, we have all the information we need to perform the correction: - They are numerous enough in each batch for the regression to be reliable (well, at least we have enough of them to perform a linear modeling). - The dataset contains the mandatory information needed in the sampleMetadata file: the injection order, the batches of analysis and the sample type (pool or sample). -We can then use the **Batch correction** {% icon tool %} tool to perform the correction. +We can then use the **Batch correction** {% icon tool %} tool to perform the correction. > Using Batch correction to correct the data from signal drift and batch effet > @@ -545,8 +549,8 @@ another for the all_loess_pool/all_loess_sample (all_loess) ones. The main differences between the two strategies are the following: - one part allows regression type choice and applies the normalisation depending on internal quality metrics -- the other part offers the possibility to apply the correction without pool samples. -For more information, do not hesitate to read the help section provided with the Galaxy tool. +- the other part offers the possibility to apply the correction without pool samples. +For more information, do not hesitate to read the help section provided with the Galaxy tool. In this tutorial example, we used the *linear* option which is part of the 3L strategy. We could not use any of the other options because the other ones would need more pools per batch than what we have here. @@ -567,7 +571,7 @@ plus 3 additional pages at the end that display overall before/after indicators > > > > Compared to the batch effect that was highlighted as the main effect in the data before the correction process, > > we can see that after correction, the batch effect is no longer explaining the first PCA component. -> > This result is awaited since the reduction of the batch effect is one of the aim of the Batch correction step. +> > This result is awaited since the reduction of the batch effect is one of the aim of the Batch correction step. > > > {: .solution} > @@ -576,41 +580,41 @@ plus 3 additional pages at the end that display overall before/after indicators Now that we corrected the data from the signal drift and batch effect, we consider that differences in intensity between samples can be attributed mostly to differences in concentration of original compounds. However, we know that what we converted to intensity values in our table is initially signal measurements, thus we suspect that -intensities may be noisy at some point. +intensities may be noisy at some point. # Filtering signals of insufficient quality Similarly to many measuring devices, values that are generated by LC-MS devices are subject to noise. In the specific case of untargeted Metabolomics, the values are relative and can have, in a single dataset, a very large range of scales. It is difficult to quantify the noise, even so it is crucial to have a minimum confidence when searching for subtile differences between groups of individuals. -Thus, having a way to put appart variables (ions) that may be of insufficient quality is key to limit the risk of wrong conclusion while analysing the data. +Thus, having a way to put appart variables (ions) that may be of insufficient quality is key to limit the risk of wrong conclusion while analysing the data. Beyond the issue of noise, the quality of the variables in one's dataset is a key question. In particular, in untargeted Metabolomics the data has particularities that make the endpoint analyses complicated, such as the disproportion between sample size and variable number, the complex redundancy and the noise issue already mentioned. When quality indicators can be computed before any statistical analysis, it is a real advantage: it can improve the efficiency of later statistical analysis and also help to select good candidates in biomarker approaches. -One common and powerful way to assess measurements quality is the use of pools. +One common and powerful way to assess measurements quality is the use of pools. Indeed, now that the data is corrected for signal drift, we expect to have stable intensities within pools since there is no biological variability among them. -We can evaluate the remaining variability in pools for each ion, and consider it to be noise and/or analytical effects that we may not have managed to remove for specific ions. -This enables the use of quality thresholds to get rid of ions we consider not to be sufficiently reliable regarding intensity values. +We can evaluate the remaining variability in pools for each ion, and consider it to be noise and/or analytical effects that we may not have managed to remove for specific ions. +This enables the use of quality thresholds to get rid of ions we consider not to be sufficiently reliable regarding intensity values. -In this tutorial, we will illustrate the use of pools by computing coefficients of variation (CV). +In this tutorial, we will illustrate the use of pools by computing coefficients of variation (CV). This metric allows to evaluate the variability accross samples independantly of the unit scale. -This advantage enables the definition of a unique threshold value that can be applied to every ions whatever the scales. +This advantage enables the definition of a unique threshold value that can be applied to every ions whatever the scales. CV are computed for each ion in your dataset, so you can filter ions using the chosen threshold. Note: the greater the CV value, the greater the variability. -The first use of CV we will illustrate here is the computation of CVs for the pools only. The idea here is to grasp the pool variability. -It is expected that pools do not vary much since they correspond to the same biological content. -Thus, if your pools vary too much, you can suspect that the corresponding ion is not reliable enough. +The first use of CV we will illustrate here is the computation of CVs for the pools only. The idea here is to grasp the pool variability. +It is expected that pools do not vary much since they correspond to the same biological content. +Thus, if your pools vary too much, you can suspect that the corresponding ion is not reliable enough. The second use of CV we will use here is a comparison between pool CVs and sample CVs. Indeed, we expect sample CVs to be higher than pool CVs since they share the same noise and analytical variability but also carry biological variability. -The **Quality Metrics** {% icon tool %} tool provides different CV indicators depending on what is in your sample list. -In particular, in the present case-study, it computes pool CVs along with a ratio between pool CVs and sample CVs. -These two indicators are automatically calculated as long as the input datasets provide the needed information +The **Quality Metrics** {% icon tool %} tool provides different CV indicators depending on what is in your sample list. +In particular, in the present case-study, it computes pool CVs along with a ratio between pool CVs and sample CVs. +These two indicators are automatically calculated as long as the input datasets provide the needed information (a *sampleType* column in the sampleMetadata file with the information of *pool* and *sample*). Thus, for these two indicators the tool can be run without specific parameters to set. @@ -628,7 +632,7 @@ Thus, for these two indicators the tool can be run without specific parameters t > > > > You may have noticed that we already used this tool previously in the tutorial. > > Although CV columns were already available at that time, here you need to use this tool again since this time indicators will be computed on intensities -> > corrected from the signal drifts and batch effects. +> > corrected from the signal drifts and batch effects. > > Note that what we are going to use this time is the tabular output, but while you are at it you can always check the pdf file if you want. > {: .comment} > @@ -644,7 +648,7 @@ For now no filter has been applied on the dataset. To remove the ions of insuffi But first, you need to determine the thresholds you want to use. Here we have two indicators we want to use. One is the pool CVs, the other is the ratio between pool CVs and sample CVs. -This means that we will need to set two distinct thresholds, and to add two numerical filters in **Generic Filter** {% icon tool %}. +This means that we will need to set two distinct thresholds, and to add two numerical filters in **Generic Filter** {% icon tool %}. > Using Generic Filter to filter the dataset > @@ -673,8 +677,8 @@ This means that we will need to set two distinct thresholds, and to add two nume > > > > > -> > Here, we took the opportunity of this filter to remove the pools from the dataset. -> > Indeed, pools will be no longer used in this tutorial's steps, so we can remove them from the dataset. +> > Here, we took the opportunity of this filter to remove the pools from the dataset. +> > Indeed, pools will be no longer used in this tutorial's steps, so we can remove them from the dataset. > {: .comment} > > @@ -699,7 +703,7 @@ This means that we will need to set two distinct thresholds, and to add two nume > > > > > > 1. The *0.3* value corresponds to the maximum value kept in the dataset ('Interval of values to remove: *upper*') regarding the -> > *pool_CV* column in your *Variable metadata* file. +> > *pool_CV* column in your *Variable metadata* file. > > Thus, ions with pool CV values superior to 0.3 are excluded from the dataset. > > To note, pool CV values are commonly considered as reflecting unstable ions when superior to 0.3. > > 2. The *1.0* value corresponds to the maximum value kept in the dataset ('Interval of values to remove: *upper*') regarding the @@ -711,47 +715,47 @@ This means that we will need to set two distinct thresholds, and to add two nume > {: .question} -Presented threshold values here are common thresholds in Metabolomics studies. +Presented threshold values here are common thresholds in Metabolomics studies. Please note that thresholds should be chosen consistently regarding the LC-MS device caracteristics and the study objectives. -Thus you may need to be more strict in some cases and less strict in others. -However, being less strict than usual should always be appropriately justified. +Thus you may need to be more strict in some cases and less strict in others. +However, being less strict than usual should always be appropriately justified. # Study-specific data processing: example normalising data according to a non-analytical effect -The previous steps presented in this tutorial illustrated categories of data processing that need to be consider whatever the study in +The previous steps presented in this tutorial illustrated categories of data processing that need to be consider whatever the study in untargeted LC-MS Metabolomics projects. In some cases the decision may be not to take actions, but in all cases the issue has to be considered to apprehend the reliability of the data for further analyses. Nonetheless, each study is unique and specific issues can arise that would need some additional data processing steps that are very specific to the study. Thus, sticking to a standard data processing workflow may not be sufficient in some cases. -For example, one commonly considered data processing step in biomarker discovery studies is the reduction of redundancy, -which is a complex question that can be addressed using various strategies depending on the study objectives. +For example, one commonly considered data processing step in biomarker discovery studies is the reduction of redundancy, +which is a complex question that can be addressed using various strategies depending on the study objectives. In this section, we will illustrate an example of study-specific data processing that involves a normalisation of the dataset. This will follow the standard *Identify->Formalise->Handle* design that is common to any data processing approach. ## Identifying unwanted variability -First thing is of course to identify an issue in the data that needs to be handled. +First thing is of course to identify an issue in the data that needs to be handled. In the previous steps, this was the "easy" part since we already had knowledge about what needed to be handled. -We adressed well-known problems, for which solutions may not always be easy, but at least we know there is something. +We adressed well-known problems, for which solutions may not always be easy, but at least we know there is something. -In study-specific data processing, it may not be that simple. +In study-specific data processing, it may not be that simple. Usually, to see something you need to search for it. This means you have hypotheses prior to the data analysis. -However, sometimes unwanted variability is unexpected, making the search process difficult. +However, sometimes unwanted variability is unexpected, making the search process difficult. -Fortunately, whether you have hypotheses or not, there is a common starting point in Metabolomics that can help you see whether an issue seems to need special attention. +Fortunately, whether you have hypotheses or not, there is a common starting point in Metabolomics that can help you see whether an issue seems to need special attention. This is the use of PCA, that we already saw in previous steps to highlight awaited effects. In this tutorial, we constructed the dataset so we already know what is the variability to identify. In a real project it can also be the case, or at least we can have hypotheses about effects we would not be supprised to observe. -In this tutorial example, we considered samples as being urine samples. +In this tutorial example, we considered samples as being urine samples. It is known that urine samples can vary a lot in total solute concentration, potentially limiting the possibility to detect specific biological effects. -Thus, even if it may not be the case, we can wonder whether the variability of concentration may have a huge effect on the metabolomic dataset we have. +Thus, even if it may not be the case, we can wonder whether the variability of concentration may have a huge effect on the metabolomic dataset we have. This is why, while making a PCA, we may want to plot the first components and see whether the variability displayed seems to match the concentration. -In the sampleMetadata file provided in this tutorial, you can find a column named *Osmo* that is meant to correspond to measures of osmolality, -one way to represent the overall concentration of urine samples. +In the sampleMetadata file provided in this tutorial, you can find a column named *Osmo* that is meant to correspond to measures of osmolality, +one way to represent the overall concentration of urine samples. Let's try to colour the PCA score plots according to that variable. For this, we will use the **Multivariate** {% icon tool %} Galaxy module. > Using Multivariate to visualise the two first components of a PCA @@ -781,12 +785,12 @@ The PCA scores plot representing the projection of samples on the two first comp Taking into account that the PCA was computed on Unit-Variance-scaled data (see the **Multivariate** {% icon tool %} tool's help section for more details), this result confirms the impact of total concentration on our dataset. -Since this effect in data is independant of the question of interest that we suppose we investigate in the study (in the case of this tutorial), -we may want to get rid of this effect to prevent a power reduction in further statistical analysis. +Since this effect in data is independant of the question of interest that we suppose we investigate in the study (in the case of this tutorial), +we may want to get rid of this effect to prevent a power reduction in further statistical analysis. ## Formalising the information -This step is essential to be able to perform any data processing action. +This step is essential to be able to perform any data processing action. At this step we have already identified some unwanted variability, however to get rid of it we need to formalise the information in a way or another. As an example, in the *Removing "trash" signals* section, we acknowledged the fact that the LC-MS device could detect signals even in samples that are not supposed to contain @@ -795,7 +799,7 @@ The solution we chose then was to use blank samples to represent the uninformati Thus, the blank samples' intensities are the formalisation of the unwanted variability identified. In this section's example, the formalisation is already done: we have the *Osmo* column in our data, that furthermore enabled to identify the unwanted variability. -Thus, we can move to the next step already. However please remember that this part is still mandatory in the process, even if sometimes it is straightforward. +Thus, we can move to the next step already. However please remember that this part is still mandatory in the process, even if sometimes it is straightforward. ## Getting rid of the variability @@ -803,19 +807,19 @@ Now that the unwanted variability is identified and formalised, the next step is Here we have a quantitative effect linked to the *Osmo* variable. There are plenty of ways to handle this kind of effect, and a proper approach would be first to study the impact of this effect on data in details, -and then only to choose which data processing approach to use to efficiently correct this effect. +and then only to choose which data processing approach to use to efficiently correct this effect. -In this tutorial, we assume the *Osmo* effect is a multiplicative one. -This appears to be true in the dataset: the data was built especially for this tutorial so there is no surprise here. +In this tutorial, we assume the *Osmo* effect is a multiplicative one. +This appears to be true in the dataset: the data was built especially for this tutorial so there is no surprise here. Then we can use a normalisation approach to handle the question. Please remember that this is a fake dataset used to illustrate the importance and philosophy of data processing for LC-MS untargeted Metabolomics analyses. -For proper handling of urine concentration in one's study, it may require more in-depth procedures depending on the protocole. +For proper handling of urine concentration in one's study, it may require more in-depth procedures depending on the protocole. The **Normalization** {% icon tool %} Galaxy module enables to perform an adequate correction of this effect. The approach of this module is to apply the normalisation operation to each sample to make the data from all samples directly comparable with each other (to take into account variations of the overall concentrations of samples due to biological and technical reasons). -It provides different normalisation strategies, some of them particularly of interest for NMR-based metabolomic datasets. -In our example, what we are interested in is a normalisation based on the *Osmo* variable, which is one of the possibilities provided by the module. +It provides different normalisation strategies, some of them particularly of interest for NMR-based metabolomic datasets. +In our example, what we are interested in is a normalisation based on the *Osmo* variable, which is one of the possibilities provided by the module. > Using Normalization to handle the total concentration effect > @@ -834,18 +838,18 @@ In our example, what we are interested in is a normalisation based on the *Osmo* {: .hands_on} With the parameter choices made here, the module generates two outputs: a log file and a dataMatrix file. -The dataMatrix corresponds to the normalised intensities. This is what will be used in further analyses. +The dataMatrix corresponds to the normalised intensities. This is what will be used in further analyses. ## Checking the resulting data -Now that the normalisation process has been applied, one may want to check the effect on data. +Now that the normalisation process has been applied, one may want to check the effect on data. Has the effect been entirely removed from the data? Can we see a significant reduction of it in the data? Similarly to the checks we could make in the context of signal drift and batch effect correction with before/after plots, -it is wise to check the impact of any normalisation process on the dataset. -This check can be conducted trying to highlight the unwanted effect the same way it was highlighted in the initial step. +it is wise to check the impact of any normalisation process on the dataset. +This check can be conducted trying to highlight the unwanted effect the same way it was highlighted in the initial step. In our tutorial example we observed the *Osmo* effect on the two first components of a PCA. -Thus, we can compute a similar PCA using the normalised intensities and see whether the two first components still cary the unwanted variability. +Thus, we can compute a similar PCA using the normalised intensities and see whether the two first components still cary the unwanted variability. > Using Multivariate to visualise the two first components of a PCA > @@ -868,15 +872,15 @@ Thus, we can compute a similar PCA using the normalised intensities and see whet {: .hands_on} When looking at the Scores plot available in the PDF output, we can see that the previously observed link between the colouring scale -and the components' coordinates is no longer obvious. -We can then conclude that the *Osmo* effect has been notably reduced inside the dataset. +and the components' coordinates is no longer obvious. +We can then conclude that the *Osmo* effect has been notably reduced inside the dataset. It is even possible to see, on the first component, what seems to be a clear seperation of two groups of samples. -Theses groups do not correspond to an *Osmo* effect: we can see that high and low values of *Osmo* are found in each group with balance. +Theses groups do not correspond to an *Osmo* effect: we can see that high and low values of *Osmo* are found in each group with balance. We could be curious and wonder whether these groups would reflect a biological state. -In the sampleMetadata we have, there is a *Group* column, supposedly representing two biological groups A and B. -Let's see how theses groups are projected on the final PCA we have. +In the sampleMetadata we have, there is a *Group* column, supposedly representing two biological groups A and B. +Let's see how theses groups are projected on the final PCA we have. > Using Multivariate to visualise the two first components of a PCA > @@ -910,17 +914,17 @@ Let's see how theses groups are projected on the final PCA we have. > > > > > > We can see that the groups that seemed to be shown on the first PCA component match perfectly the biological categories available in the *Group* -> > column of the sampleMetadata file. -> > We could say that the normalisation process enabled to highlight a distinct effect of the biological groups. +> > column of the sampleMetadata file. +> > We could say that the normalisation process enabled to highlight a distinct effect of the biological groups. > > Note that it is possible that this effect would be already noticeable without the normalisation process, -> > however the perfect separation on the first component after normalisation is promising to be able to extract -> > clear information about the source of this separation. +> > however the perfect separation on the first component after normalisation is promising to be able to extract +> > clear information about the source of this separation. > > > {: .solution} > {: .question} -Now that the dataset seems to be processed adequately, with no identified remaining unwanted main effect +Now that the dataset seems to be processed adequately, with no identified remaining unwanted main effect (the principal effect being the groups of interest for the study), we can consider the data processing of this dataset completed. This does not mean that further data processing steps could not be considered depending on the study objectives, but we reached the end of the example used to illustrate the meaning and importance of untargeted LC-MS metabolomic data processing @@ -929,8 +933,8 @@ through this tutorial. # Conclusion -The question of data filtering and correction must be addressed in all projects, even thought in some cases it may lead to the decision of no action on data. -In particular, the removing of "trash" signals, the signal drift and batch effect correction and the filtering of signals of insufficient quality -are common aspects to consider when dealing with LC-MS data. -Remember that depending on your context (type of samples, protocol specificities...) specific filters/normalisations may be needed, independently of standards ones. +The question of data filtering and correction must be addressed in all projects, even thought in some cases it may lead to the decision of no action on data. +In particular, the removing of "trash" signals, the signal drift and batch effect correction and the filtering of signals of insufficient quality +are common aspects to consider when dealing with LC-MS data. +Remember that depending on your context (type of samples, protocol specificities...) specific filters/normalisations may be needed, independently of standards ones. Once you complete your customed processing procedure, your tables are ready for biologically-oriented exploration! diff --git a/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md b/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md index 71caf3b879e16f..d6f1f82f86264d 100644 --- a/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md +++ b/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md @@ -22,6 +22,15 @@ contributors: - lecorguille - workflow4metabolomics +contributions: + authorship: + - melpetera + - jfrancoismartin + - lecorguille + - workflow4metabolomics + editing: + funding: + - elixir-europe --- @@ -336,9 +345,9 @@ Once your sampleMetadata table is ready, you can proceed to the upload. In this > The class column > > Depending on further choices, the sampleMetadata file can be decisive. -> It can be used to colour some plots, but also for ion selection (see further in the tutorial). +> It can be used to colour some plots, but also for ion selection (see further in the tutorial). > Please note that the information needed for these steps **should be given as the second column of the sampleMetadata file**, -> the first one being the samples' identifiers. +> the first one being the samples' identifiers. {: .warning} diff --git a/topics/metabolomics/tutorials/lcms/tutorial.md b/topics/metabolomics/tutorials/lcms/tutorial.md index b094c8982aaa37..2f53eba9fa7265 100644 --- a/topics/metabolomics/tutorials/lcms/tutorial.md +++ b/topics/metabolomics/tutorials/lcms/tutorial.md @@ -15,12 +15,17 @@ key_points: - To process untargeted LC-MS metabolomic data, you need a large variety of steps and tools. - Although main steps are standard, various ways to combined tools exist, depending on your data. - Resources are available in Galaxy, but do not forget that you need appropriate knowledge to perform a relevant analysis. -contributors: -- melpetera -- lecorguille -- jfrancoismartin -- yguitton -- workflow4metabolomics + +contributions: + authorship: + - melpetera + - lecorguille + - jfrancoismartin + - yguitton + - workflow4metabolomics + editing: + funding: + - elixir-europe --- diff --git a/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.md b/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.md index f4f9d1bd0d6009..45c7f8a12c39cf 100644 --- a/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.md +++ b/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.md @@ -9,9 +9,9 @@ questions: - In which compartments of the chilli are the measured VOCs located? - In which compartment of the chilli is the capsaicin located? objectives: -- Plot average mass spectra and overlaid mass spectra of single spectra. -- Filter MSI data for a specific m/z range. -- Automatic generation of many m/z images. +- Plot average mass spectra and overlaid mass spectra of single spectra. +- Filter MSI data for a specific m/z range. +- Automatic generation of many m/z images. - Overlay the distribution of several m/z in one image. time_estimation: 1H key_points: @@ -19,17 +19,22 @@ key_points: - MSI data can be filtered for m/z ranges of interest to speed up analysis time. - Distribution images for many analytes can be automatically generated with the MSI m/z image tool. - The MSI m/z image tools allow overlaying the distribution images for several analytes. -contributors: -- foellmelanie -- MarenStillger +contributions: + authorship: + - foellmelanie + - MarenStillger + editing: + funding: + - elixir-europe + - uni-freiburg --- -Mass spectrometry imaging (MSI) is applied to measure the spatial distribution of hundreds of biomolecules in a sample. A mass spectrometer scans over the entire sample and collects a mass spectrum every 5-200 µm. This results in thousands of spots (or pixels) for each of which a mass spectrum is acquired. Each mass spectrum consists of hundreds of analytes that are measured by their mass-to-charge (m/z) ratio. For each analyte the peak intensity in the mass spectra of every pixel is known and can be set together to map the spatial distribution of the analyte in the sample. +Mass spectrometry imaging (MSI) is applied to measure the spatial distribution of hundreds of biomolecules in a sample. A mass spectrometer scans over the entire sample and collects a mass spectrum every 5-200 µm. This results in thousands of spots (or pixels) for each of which a mass spectrum is acquired. Each mass spectrum consists of hundreds of analytes that are measured by their mass-to-charge (m/z) ratio. For each analyte the peak intensity in the mass spectra of every pixel is known and can be set together to map the spatial distribution of the analyte in the sample. -The technique has a broad range of applications as it is able to measure many different kinds of analytes such as peptides, proteins, metabolites or chemical compounds in a large variety of samples such as cells, tissues and liquid biopsies. Application areas include pharmacokinetic studies, biomarker discovery, molecular pathology, forensic studies, plant research and material sciences. The strength of MSI is the simultaneous analysis of hundreds of analytes in an unbiased, untargeted, label-free, fast and affordable measurement while maintaining morphological information. +The technique has a broad range of applications as it is able to measure many different kinds of analytes such as peptides, proteins, metabolites or chemical compounds in a large variety of samples such as cells, tissues and liquid biopsies. Application areas include pharmacokinetic studies, biomarker discovery, molecular pathology, forensic studies, plant research and material sciences. The strength of MSI is the simultaneous analysis of hundreds of analytes in an unbiased, untargeted, label-free, fast and affordable measurement while maintaining morphological information. Depending on the analyte of interest and the application, different mass spectrometers are used. A mass spectrometer measures the analytes by ionizing, evaporating and sorting them by their mass-to-charge (m/z) ratio. Put simply, a mass spectrometer consists basically of three parts: an ionization source, a mass analyzer and a detector. The most common ionization sources for MSI are MALDI (Matrix Assisted Laser Desorption/Ionization), DESI (Desorption Electrospray Ionization) and SIMS (Secondary Ion Mass Spectrometry). @@ -37,9 +42,9 @@ Depending on the analyte of interest and the application, different mass spectro One common type of mass spectrometer for MSI is a MALDI Time-Of-Flight (MALDI-TOF) device. During MALDI ionization, a laser is fired onto the sample, which has been covered with a special matrix that absorbs the laser energy and transfers it to the analytes. This process vaporizes and ionizes the analytes. As they are now charged, they can be accelerated in an electric field towards the TOF tube. The time of flight through the tube to the detector is measured, which allows calculation of the mass over charge (m/z) of the analyte, as both mass and charge are correlated with time of flight. During measurement, complete mass spectra with hundreds of m/z - intensity pairs are acquired in thousands of sample plots, leading to large and complex datasets. Each mass spectrum is annotated with coordinates (x,y) that define its location in the sample. This allows visualization of the intensity distribution of each m/z feature in the sample as a heatmap. -Depending on the analyte of interest, the sample type and the mass spectrometer, the sample preparation steps as well as the properties of the acquired data vary. Apart from these differences, the preparation and measurement of the sample is normally straightforward, while the analysis of the large and complex dataset is the main bottleneck of a MSI experiment. +Depending on the analyte of interest, the sample type and the mass spectrometer, the sample preparation steps as well as the properties of the acquired data vary. Apart from these differences, the preparation and measurement of the sample is normally straightforward, while the analysis of the large and complex dataset is the main bottleneck of a MSI experiment. -In this tutorial we will determine analytes with a localized distribution in a chilli cross section. The data analysis steps can be transferred to any other application in which the morphological distribution of an analyte in a sample is analyzed. A common application is studying the distribution of a drug and its metabolites in an animal model to better understand pharmacokinetic properties of the drug. +In this tutorial we will determine analytes with a localized distribution in a chilli cross section. The data analysis steps can be transferred to any other application in which the morphological distribution of an analyte in a sample is analyzed. A common application is studying the distribution of a drug and its metabolites in an animal model to better understand pharmacokinetic properties of the drug. > @@ -53,11 +58,11 @@ In this tutorial we will determine analytes with a localized distribution in a c # Chilli dataset -In this tutorial we will use the chilli dataset generated in the lab of Robert Winkler at the CINVESTAV institute in Irapuato (Mexico) and deposited at [Zenodo](https://zenodo.org/record/484496). The data was acquired to demonstrate their self-made low-cost 'plug and play' MSI system as well as their open source R scripts and to show they allow the direct spatially resolved detection of volatile organic compounds (VOCs) from plant tissue ({% cite Maldonado_Torres_2014 %} and {% cite Gamboa_Becerra_2015 %}). +In this tutorial we will use the chilli dataset generated in the lab of Robert Winkler at the CINVESTAV institute in Irapuato (Mexico) and deposited at [Zenodo](https://zenodo.org/record/484496). The data was acquired to demonstrate their self-made low-cost 'plug and play' MSI system as well as their open source R scripts and to show they allow the direct spatially resolved detection of volatile organic compounds (VOCs) from plant tissue ({% cite Maldonado_Torres_2014 %} and {% cite Gamboa_Becerra_2015 %}). -The mass spectrometer consisted of a low-temperature plasma (LTP) ionization source coupled to a quadrupole mass analyzer. This ionization source allows measurement of semi-volatile organic compunds directly from fresh material under ambient conditions without destruction of the sample. To get an idea how this set up and the chilli looks, have a look at their [video](https://www.youtube.com/watch?v=NbZ1QqTZvXM) and [website](http://lababi.bioprocess.org/). The chilli (*Capsicum annuum*) was purchased from a local market in Irapuato, Mexico and longitudinally cut into a slice of 80 x 35 mm and 4 mm thickness and laid onto a glass slide. Mass spectra were acquired with a spatial resolution of 1 mm and in a mass range from 15 – 2000 m/z to measure semi-volatile and volatile organic compounds (VOCs). +The mass spectrometer consisted of a low-temperature plasma (LTP) ionization source coupled to a quadrupole mass analyzer. This ionization source allows measurement of semi-volatile organic compunds directly from fresh material under ambient conditions without destruction of the sample. To get an idea how this set up and the chilli looks, have a look at their [video](https://www.youtube.com/watch?v=NbZ1QqTZvXM) and [website](http://lababi.bioprocess.org/). The chilli (*Capsicum annuum*) was purchased from a local market in Irapuato, Mexico and longitudinally cut into a slice of 80 x 35 mm and 4 mm thickness and laid onto a glass slide. Mass spectra were acquired with a spatial resolution of 1 mm and in a mass range from 15 – 2000 m/z to measure semi-volatile and volatile organic compounds (VOCs). -We will check the properties of the dataset and then perform a similar analysis to that described by {% cite Gamboa_Becerra_2015 %}: plotting an average mass spectrum, filtering the dataset for the relevant m/z range, automatical generation of m/z images to find analytes that correspond to morphological features and generating an image that overlays three different analytes. +We will check the properties of the dataset and then perform a similar analysis to that described by {% cite Gamboa_Becerra_2015 %}: plotting an average mass spectrum, filtering the dataset for the relevant m/z range, automatical generation of m/z images to find analytes that correspond to morphological features and generating an image that overlays three different analytes. ![Chilli](../../images/msi_distribution_chilli.png "Cross section of a chilli in a similar orientation as in the publication by Gamboa-Becerra") @@ -131,7 +136,7 @@ Before starting any analysis it is important to check the characteristics and qu > - Press **Run Tool** > > > Properties of the imzML file -> > To set the parameters for the mass spectrometry imaging tools correctly the following three parameters should be known about the dataset: 1) is the imzML file type processed or continuous, 2) are the spectra in profile or centroided mode and 3) the accuracy of the mass spectrometer. For the chilli dataset the publication states that it is a processed imzML type in centroided mode. This information can also be extracted by opening the local imzML component of the file in a text editor or web browser. Line 10 and 11 state: +> > To set the parameters for the mass spectrometry imaging tools correctly the following three parameters should be known about the dataset: 1) is the imzML file type processed or continuous, 2) are the spectra in profile or centroided mode and 3) the accuracy of the mass spectrometer. For the chilli dataset the publication states that it is a processed imzML type in centroided mode. This information can also be extracted by opening the local imzML component of the file in a text editor or web browser. Line 10 and 11 state: > > > > > > @@ -150,9 +155,9 @@ Before starting any analysis it is important to check the characteristics and qu > > > > > > -> > This means that the file consists of 4166 spectra (count="4166") and that the imzML type is 'processed' as the first spectrum (scan="1") has 11127 m/z values (defaultArrayLength="11127) while the following spectra (not shown here) have different numbers of m/z values. In processed imzML files each spectrum has an individual m/z axis, in contrast to the continuous imzML type, where all spectra have the same m/z axis. In many software tools processed imzML files are not or only partly supported. The MSI tools in Galaxy are based on [Cardinal](http://cardinalmsi.org/) and therefore support imzML files, but require a binning of the m/z values while reading the file. The bin size should be chosen according to the m/z accuracy of the mass spectrometer. For the chilli dataset we therefore use 0.1 m/z, as this results in m/z bins of 0.2 m/z which corresponds to the m/z step size that was used in the publication. +> > This means that the file consists of 4166 spectra (count="4166") and that the imzML type is 'processed' as the first spectrum (scan="1") has 11127 m/z values (defaultArrayLength="11127) while the following spectra (not shown here) have different numbers of m/z values. In processed imzML files each spectrum has an individual m/z axis, in contrast to the continuous imzML type, where all spectra have the same m/z axis. In many software tools processed imzML files are not or only partly supported. The MSI tools in Galaxy are based on [Cardinal](http://cardinalmsi.org/) and therefore support imzML files, but require a binning of the m/z values while reading the file. The bin size should be chosen according to the m/z accuracy of the mass spectrometer. For the chilli dataset we therefore use 0.1 m/z, as this results in m/z bins of 0.2 m/z which corresponds to the m/z step size that was used in the publication. > > -> > Regarding the spectra, line 10 states that the spectra are in profile mode while the 'run' section defines spectrum 1 as a centroided spectrum. As the 'run' section is directly linked to the spectra in the ibd file, this is the information to trust. Furthermore, the 'dataProcessingList' element gives a hint that peak picking was performed, which is confirmed in the publication. +> > Regarding the spectra, line 10 states that the spectra are in profile mode while the 'run' section defines spectrum 1 as a centroided spectrum. As the 'run' section is directly linked to the spectra in the ibd file, this is the information to trust. Furthermore, the 'dataProcessingList' element gives a hint that peak picking was performed, which is confirmed in the publication. > {: .comment} > {: .hands_on} @@ -168,26 +173,26 @@ Before starting any analysis it is important to check the characteristics and qu > > > > 1. The measured m/z range was m/z 15 - 2000. > > 2. 4166 spectra were measured. -> > 3. The rough shape of the chilli section is visible in the "Number of peaks per spectrum"; "Total Ion Current" and "PCA result" images. +> > 3. The rough shape of the chilli section is visible in the "Number of peaks per spectrum"; "Total Ion Current" and "PCA result" images. > > > {: .solution} > {: .question} -Open the quality report with the eye button and check the summary table on the first page to answer question 1 and 2. The shape of the chilli can roughly be seen in the images showing the number of peaks per spectrum and the total ion current, with higher values in the middle part of the fruit that roughly corresponds to the placenta. In the PCA image the complete chilli, except for the lowest part of the fruit, is visible in light colours compared to the dark background. +Open the quality report with the eye button and check the summary table on the first page to answer question 1 and 2. The shape of the chilli can roughly be seen in the images showing the number of peaks per spectrum and the total ion current, with higher values in the middle part of the fruit that roughly corresponds to the placenta. In the PCA image the complete chilli, except for the lowest part of the fruit, is visible in light colours compared to the dark background. -To further investigate mass spectra of different chilli compartments we select one pixel for each tissue area (pericarp, placenta and seeds) from the total ion current image. Knowing the exact shape of the chilli tissue from Figure 4 of the publication helps to find the corresponding areas. This are the pixels we have chosen for the tutorial: +To further investigate mass spectra of different chilli compartments we select one pixel for each tissue area (pericarp, placenta and seeds) from the total ion current image. Knowing the exact shape of the chilli tissue from Figure 4 of the publication helps to find the corresponding areas. This are the pixels we have chosen for the tutorial: seeds: x=39 y=53, placenta: x=50 y=44, pericarp: x=25 y=60 -The relevant m/z range for VOCs was not known before the measurement and therefore chosen quite liberally. The average mass spectra plots give a hint about the relevant m/z range of the sample with most peaks below 750 m/z and no distinct peaks above 750 m/z. +The relevant m/z range for VOCs was not known before the measurement and therefore chosen quite liberally. The average mass spectra plots give a hint about the relevant m/z range of the sample with most peaks below 750 m/z and no distinct peaks above 750 m/z. ![quality report](../../images/msi_distribution_qc.png "Example plots from the quality report") ## Plotting average mass spectra -We will follow up on the average mass spectra plots from the quality control report as well as on the differences between mass spectra from different chilli compartments. First, we generate more zoomed in mass spectra plots to get an idea about the m/z range that is relevant for VOCs. Next, we will plot and compare mass spectra that derive from different regions of the chilli. +We will follow up on the average mass spectra plots from the quality control report as well as on the differences between mass spectra from different chilli compartments. First, we generate more zoomed in mass spectra plots to get an idea about the m/z range that is relevant for VOCs. Next, we will plot and compare mass spectra that derive from different regions of the chilli. > Average mass spectra > @@ -224,19 +229,19 @@ We will follow up on the average mass spectra plots from the quality control rep > > -> 1. What is the approximate m/z of the heaviest peak visible in the average spectra plot of the complete m/z range? +> 1. What is the approximate m/z of the heaviest peak visible in the average spectra plot of the complete m/z range? > 2. What is the approximate m/z of the peak with the highest average intensity? > > > > > > > 1. There is a tiny peak at m/z ~760. -> > 2. The highest peak is at ~80 m/z, which can best be seen in the mass spectrum between 15 and 200 m/z. +> > 2. The highest peak is at ~80 m/z, which can best be seen in the mass spectrum between 15 and 200 m/z. > > > {: .solution} > {: .question} -In the average spectrum of the complete m/z range there are no visible peaks above 800 m/z. Most of the high intensity peaks are below 300 Th, which corresponds to the typical masses of VOCs. Even in the zoomed mass spectra between 1500 and 2000 m/z only a few distinct peaks can be identified in the noise. In accordance with {% cite Gamboa_Becerra_2015 %}, we will restrict further analysis to the m/z range between 15 and 1000. +In the average spectrum of the complete m/z range there are no visible peaks above 800 m/z. Most of the high intensity peaks are below 300 Th, which corresponds to the typical masses of VOCs. Even in the zoomed mass spectra between 1500 and 2000 m/z only a few distinct peaks can be identified in the noise. In accordance with {% cite Gamboa_Becerra_2015 %}, we will restrict further analysis to the m/z range between 15 and 1000. ![Average plots](../../images/msi_distribution_average_spectra.png "Complete and zoomed in average mass spectra") @@ -276,12 +281,12 @@ We will rerun the MSI plot spectra tool and add annotation to the pixels that co > > -> 1. Which compartment does the highest intensity peak belong to? +> 1. Which compartment does the highest intensity peak belong to? > 2. Which compartment does the third-highest intensity peak belong to? > > > > > -> > 1. The highest intensity peak at around 80 m/z belongs to the spectrum that is located in the pericarp of the chilli. +> > 1. The highest intensity peak at around 80 m/z belongs to the spectrum that is located in the pericarp of the chilli. > > 2. The peak at around 60 m/z belongs to the spectrum that is located in the seeds. > {: .solution} > @@ -314,20 +319,20 @@ The single spectra that derive from different chilli compartments show some majo > > > > > -> > 1. After filtering 4926 m/z features are left. +> > 1. After filtering 4926 m/z features are left. > > 2. The dataset originally had 9926 m/z features; after filtering 4926 are left, which means that 5000 were removed. > > > {: .solution} > {: .question} -The MSI tools are only able to write outputs as continuous imzML format; therefore, from now on the dataset is in continuous imzML format and "processed imzML file" can be set to 'no' in the following tools. +The MSI tools are only able to write outputs as continuous imzML format; therefore, from now on the dataset is in continuous imzML format and "processed imzML file" can be set to 'no' in the following tools. # Multiple and overlayed analyte images ## Automatic generation of analyte images -The main question for the chilli dataset is which m/z features have a localized distribution in the fruit. This question can be addressed by automatically generating distribution images for all analytes (m/z features) and then visually identifying which features are localized in specific compartments of the fruit. {% cite Gamboa_Becerra_2015 %} scan the m/z range with a step size of 0.2 m/z and a tolerance of 0.4 Th, which resulted in more than 2000 images which they visually explored for localized features. In this training we will only generate images for the two mass ranges where we have already seen high intensity peaks in the spectra plots: around 60 and 80 m/z. +The main question for the chilli dataset is which m/z features have a localized distribution in the fruit. This question can be addressed by automatically generating distribution images for all analytes (m/z features) and then visually identifying which features are localized in specific compartments of the fruit. {% cite Gamboa_Becerra_2015 %} scan the m/z range with a step size of 0.2 m/z and a tolerance of 0.4 Th, which resulted in more than 2000 images which they visually explored for localized features. In this training we will only generate images for the two mass ranges where we have already seen high intensity peaks in the spectra plots: around 60 and 80 m/z. This requires three steps. Firstly, all m/z features of the dataset with the MSI data exporter are extracted. Secondly, all m/z features are filtered in the m/z ranges that we are interested in: between 55 and 65 Th, as well as between 75 and 85 m/z (this step can be skipped to obtain distribution images for all features). Thirdly, the MSI m/z image tool is used to automatically generate distribution images for each of the m/z from the second step. As the data is already binned to 0.2 Th, only the m/z tolerance of 0.4 m/z has to be specified. The large tolerance was chosen to obtain images from overlapping m/z ranges to make the signal intensity more robust against small m/z inaccuracies in individual mass spectra. @@ -357,7 +362,7 @@ This requires three steps. Firstly, all m/z features of the dataset with the MSI > > > 1. Which are the two analyte images that show the most localized distribution? -> 2. Which compartments are the two features localized in? +> 2. Which compartments are the two features localized in? > > > > > @@ -381,7 +386,7 @@ After m/z features with a localized distribution have been found, it is interest ## Overlay image for three analyte features -To get an idea about the distribution of capsaicin in the chilli we will plot its distribution in an overlay image with the two unknown but localized features 62.2 m/z and 84.2 m/z. +To get an idea about the distribution of capsaicin in the chilli we will plot its distribution in an overlay image with the two unknown but localized features 62.2 m/z and 84.2 m/z. > Overlay image for several m/z features > @@ -422,11 +427,11 @@ To get an idea about the distribution of capsaicin in the chilli we will plot it > > -> 1. Which compartment is capsaicin located in? +> 1. Which compartment is capsaicin located in? > > > > > -> > 1. Capsaicin is located in the middle of the placenta, as well as partly in the seeds. +> > 1. Capsaicin is located in the middle of the placenta, as well as partly in the seeds. > > > {: .solution} > @@ -436,7 +441,7 @@ To get an idea about the distribution of capsaicin in the chilli we will plot it # Conclusion -This tutorial covered the steps to explore the properties of a dataset and visualize the morphological distribution of molecules. +This tutorial covered the steps to explore the properties of a dataset and visualize the morphological distribution of molecules. ![workflow](../../images/msi_distribution_workflow.png "Workflow that was used during this tutorial.") From f74b887817c7390df158503823af8eca93dc278e Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:14:03 +0200 Subject: [PATCH 204/262] add shortname --- ORGANISATIONS.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml index a177399511dfde..7a55f6b3e7d229 100644 --- a/ORGANISATIONS.yaml +++ b/ORGANISATIONS.yaml @@ -76,6 +76,7 @@ elixir-europe: ror: "044rwnt51" elixir-goblet-ttt: + short_name: Goblet name: ELIXIR Goblet Train the Trainers joined: 2022-09 github: false From a13a51ee41d2f89f37b7f1516217c44d38ad53cc Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:15:18 +0200 Subject: [PATCH 205/262] link to hall of fame pages in logo soup --- _layouts/home.html | 38 +++++++++----------------------------- 1 file changed, 9 insertions(+), 29 deletions(-) diff --git a/_layouts/home.html b/_layouts/home.html index df63956062c66c..70452694caa617 100644 --- a/_layouts/home.html +++ b/_layouts/home.html @@ -304,47 +304,27 @@

    Acknowledgment and Funding

    - {% for entity in site.data['funders'] %} + {% for entity in site.data['grants'] %}
    - {% if entity[1].url %} - - {% else %} - - {% endif %} +
    - {% if entity[1].url %} - + {{ entity[1].short_name | default: entity[1].name }} - {% else %} - {{ entity[1].short_name | default: entity[1].name }} - {% endif %}
    {% endfor %} {% for entity in site.data['organisations'] %}
    - {% if entity[1].url %} - - {% else %} - - {% endif %} +
    - {% if entity[1].url %} - + {{ entity[1].short_name | default: entity[1].name }} - {% else %} - {{ entity[1].short_name | default: entity[1].name }} - {% endif %}
    {% endfor %} From c73c15d6dab7c5378d4c6e57c4d03070732f7ed8 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:15:38 +0200 Subject: [PATCH 206/262] reorder hof page for orgs --- _layouts/contributor_index.html | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html index 14dba6728c5f7d..f2e185c12ddad4 100644 --- a/_layouts/contributor_index.html +++ b/_layouts/contributor_index.html @@ -25,6 +25,8 @@

    {% if entity.funder%}

    The activities listed below were partially funded by this project.

    +

    {{ entity.funding_statement | markdownify }}

    + {% endif %} @@ -78,12 +80,9 @@

    Former Members

    Contributions

    - {% if entity.funder %} - {{ entity.funding_statement | markdownify }} - {% endif %}

    - The following list includes only slides and tutorials where the individual has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post. + The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post. {% unless entity.github == false %}

    From ce8a784bdb4509aaf2100c5465db0634150581f1 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:21:28 +0200 Subject: [PATCH 207/262] rename funders to grants --- _plugins/gtn/metrics.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_plugins/gtn/metrics.rb b/_plugins/gtn/metrics.rb index 73e252eb1be78c..64bc679083d7a4 100644 --- a/_plugins/gtn/metrics.rb +++ b/_plugins/gtn/metrics.rb @@ -109,8 +109,8 @@ def self.collect_metrics(site) type: 'counter' }, 'gtn_funders_total' => { - value: segment(site.data['funders'].values.reject { |x| x['halloffame'] == 'no' }, 'orcid'), - help: 'Total number of funders', + value: segment(site.data['grants'].values.reject { |x| x['halloffame'] == 'no' }, 'orcid'), + help: 'Total number of grants', type: 'counter' }, 'gtn_tutorials_total' => { From 6a55c197946a045259dd308132b70cb47a43bb0b Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:26:32 +0200 Subject: [PATCH 208/262] rename funders to grants --- _plugins/api.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_plugins/api.rb b/_plugins/api.rb index d94ac92034f8ba..c211813341dd8b 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -164,7 +164,7 @@ def generate(site) # Contributors Jekyll.logger.debug '[GTN/API] Contributors, Funders, Organisations' - %w[contributors funders organisations].each do |type| + %w[contributors grants organisations].each do |type| page2 = PageWithoutAFile.new(site, '', 'api/', "#{type}.json") page2.content = JSON.pretty_generate(site.data[type].map { |c, _| mapContributor(site, c) }) page2.data['layout'] = nil From 60caf451aa203d08b05c40c6d3c2e7f70a69f881 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:47:21 +0200 Subject: [PATCH 209/262] add empty lists for placeholder contribution keys --- topics/epigenetics/tutorials/ewas-suite/tutorial.md | 4 ++-- topics/epigenetics/tutorials/hicexplorer/tutorial.md | 4 ++-- topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md | 2 +- topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md | 2 +- topics/metabolomics/tutorials/lcms/tutorial.md | 2 +- .../tutorials/msi-analyte-distribution/tutorial.md | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/topics/epigenetics/tutorials/ewas-suite/tutorial.md b/topics/epigenetics/tutorials/ewas-suite/tutorial.md index ca03203c1734dd..387843ccf08b82 100644 --- a/topics/epigenetics/tutorials/ewas-suite/tutorial.md +++ b/topics/epigenetics/tutorials/ewas-suite/tutorial.md @@ -18,8 +18,8 @@ contributions: - kkamieniecka - khaled196 - poterlowicz-lab - editing: - testing: + editing: [] + testing: [] funding: - elixir-europe --- diff --git a/topics/epigenetics/tutorials/hicexplorer/tutorial.md b/topics/epigenetics/tutorials/hicexplorer/tutorial.md index 8d5698671590e7..96e06462b25aab 100644 --- a/topics/epigenetics/tutorials/hicexplorer/tutorial.md +++ b/topics/epigenetics/tutorials/hicexplorer/tutorial.md @@ -18,8 +18,8 @@ contributions: - fidelram - vivekbhr - polkhe - editing: - testing: + editing: [] + testing: [] funding: - elixir-europe - deNBI diff --git a/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md b/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md index b15ee612543c2d..ac312cf9f55fc0 100644 --- a/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md +++ b/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.md @@ -21,7 +21,7 @@ contributions: authorship: - melpetera - workflow4metabolomics - editing: + editing: [] funding: - elixir-europe --- diff --git a/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md b/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md index d6f1f82f86264d..431a8215984e7a 100644 --- a/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md +++ b/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md @@ -28,7 +28,7 @@ contributions: - jfrancoismartin - lecorguille - workflow4metabolomics - editing: + editing: [] funding: - elixir-europe --- diff --git a/topics/metabolomics/tutorials/lcms/tutorial.md b/topics/metabolomics/tutorials/lcms/tutorial.md index 2f53eba9fa7265..5729e20598d044 100644 --- a/topics/metabolomics/tutorials/lcms/tutorial.md +++ b/topics/metabolomics/tutorials/lcms/tutorial.md @@ -23,7 +23,7 @@ contributions: - jfrancoismartin - yguitton - workflow4metabolomics - editing: + editing: [] funding: - elixir-europe diff --git a/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.md b/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.md index 45c7f8a12c39cf..488f98c158ddeb 100644 --- a/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.md +++ b/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.md @@ -24,7 +24,7 @@ contributions: authorship: - foellmelanie - MarenStillger - editing: + editing: [] funding: - elixir-europe - uni-freiburg From 49420458001b6fdb83b5972cffcac0096c70ed02 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:48:03 +0200 Subject: [PATCH 210/262] add a bit more debugging info --- _plugins/api.rb | 1 + 1 file changed, 1 insertion(+) diff --git a/_plugins/api.rb b/_plugins/api.rb index c211813341dd8b..c6fdb5943eda77 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -209,6 +209,7 @@ def generate(site) out = site.data[topic].dup out['materials'] = TopicFilter.topic_filter(site, topic).map do |x| q = x.dup + puts q['url'] q['contributors'] = Gtn::Contributors.get_contributors(q).dup.map do |c| mapContributor(site, c) end From 60c758328bb9eb6ac2a737f19d8ee1f51e0b5a32 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:51:22 +0200 Subject: [PATCH 211/262] rephrase --- _layouts/contributor_index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html index f2e185c12ddad4..0245cb1b591500 100644 --- a/_layouts/contributor_index.html +++ b/_layouts/contributor_index.html @@ -24,7 +24,7 @@

    {{ entity.name | default: page.contributor }}

    {% if entity.funder%} -

    The activities listed below were partially funded by this project.

    +

    The materials and activities listed below were funded (to some degree) by this project.

    {{ entity.funding_statement | markdownify }}

    {% endif %} From d29f38e8aca158355a5acd31eb94ea85bdab67ad Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:57:27 +0200 Subject: [PATCH 212/262] add citations for linter --- topics/epigenetics/tutorials/hicexplorer/tutorial.bib | 0 topics/epigenetics/tutorials/hicexplorer/tutorial.md | 4 ++-- 2 files changed, 2 insertions(+), 2 deletions(-) create mode 100644 topics/epigenetics/tutorials/hicexplorer/tutorial.bib diff --git a/topics/epigenetics/tutorials/hicexplorer/tutorial.bib b/topics/epigenetics/tutorials/hicexplorer/tutorial.bib new file mode 100644 index 00000000000000..e69de29bb2d1d6 diff --git a/topics/epigenetics/tutorials/hicexplorer/tutorial.md b/topics/epigenetics/tutorials/hicexplorer/tutorial.md index 96e06462b25aab..1371ef7cf9907c 100644 --- a/topics/epigenetics/tutorials/hicexplorer/tutorial.md +++ b/topics/epigenetics/tutorials/hicexplorer/tutorial.md @@ -246,7 +246,7 @@ The steps so far would have led to long run times if real data would have been u # TAD calling -“The partitioning of chromosomes into topologically associating domains (TADs) is an emerging concept that is reshaping our understanding of gene regulation in the context of physical organization of the genome” [Ramirez et al. 2017](https://doi.org/10.1101/115063). +“The partitioning of chromosomes into topologically associating domains (TADs) is an emerging concept that is reshaping our understanding of gene regulation in the context of physical organization of the genome” ({% cite Ramrez2017 %}). TAD calling works in two steps: First HiCExplorer computes a TAD-separation score based on a z-score matrix for all bins. Then those bins having a local minimum of the TAD-separation score are evaluated with respect to the surrounding bins to assign a p-value. Then a cutoff is applied to select the bins more likely to be TAD boundaries. @@ -383,7 +383,7 @@ The resulting image should look like this one: # Loop detection -In Hi-C data, the term `loop` refers to a 3D structure which represents enhancer-promoter, gene, architectural or polycomb-mediated interactions. These interactions have the characteristics to be enriched in a single region compared to the local background. These loops are also called long-range interactions with an expected maximum distance of 2 MB (see [Rao et al. 2014](https://doi.org/10.1016/j.cell.2014.11.021)). +In Hi-C data, the term `loop` refers to a 3D structure which represents enhancer-promoter, gene, architectural or polycomb-mediated interactions. These interactions have the characteristics to be enriched in a single region compared to the local background. These loops are also called long-range interactions with an expected maximum distance of 2 MB (see {% cite Rao2014 %}). ![Loops visualization](../../images/loops_bonev_cavalli.png) From c850e75123959b1c2fba4b821ddfd9bd05d3f017 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 17:59:32 +0200 Subject: [PATCH 213/262] adjust heading level for linter --- topics/epigenetics/tutorials/hicexplorer/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/epigenetics/tutorials/hicexplorer/tutorial.md b/topics/epigenetics/tutorials/hicexplorer/tutorial.md index 1371ef7cf9907c..f53a4f2d3ca766 100644 --- a/topics/epigenetics/tutorials/hicexplorer/tutorial.md +++ b/topics/epigenetics/tutorials/hicexplorer/tutorial.md @@ -225,7 +225,7 @@ This is often caused by bins of low counts. Use a more stringent filtering of bi This can be solved by a more stringent z-score values for the filter threshold or by a look at the plotted matrix. For example, chromosomes with 0 reads in its bins can be excluded from the correction by not defining it for the set of chromosomes that should be corrected (parameter 'Include chromosomes'). -### Plotting the corrected Hi-C matrix +## Plotting the corrected Hi-C matrix We can now plot chromosome 2L with the corrected matrix. @@ -240,7 +240,7 @@ We can now plot chromosome 2L with the corrected matrix. {: .hands_on} -### Load new data +## Load new data The steps so far would have led to long run times if real data would have been used. We therefore prepared a new matrix for you, `corrected contact matrix dm3 large`. Please load it into your history. From dfbbfd56f034b4b4d901ce319e4a25833afb0dca Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:01:27 +0200 Subject: [PATCH 214/262] fix links for linter --- .../genome-annotation/tutorials/genome-annotation/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/genome-annotation/tutorials/genome-annotation/tutorial.md b/topics/genome-annotation/tutorials/genome-annotation/tutorial.md index a19eac923b1597..c4ace35a8fda0d 100644 --- a/topics/genome-annotation/tutorials/genome-annotation/tutorial.md +++ b/topics/genome-annotation/tutorials/genome-annotation/tutorial.md @@ -117,7 +117,7 @@ At first you need to identify those structures of the genome which code for prot > Aragorn in depth > -> read more about **Aragorn** [here](https://nar.oxfordjournals.org/content/32/1/11.full.pdf+html). +> read more about **Aragorn** [in this publication](https://nar.oxfordjournals.org/content/32/1/11.full.pdf+html). {: .details} # Functional Annotation @@ -209,7 +209,7 @@ This file will be the input for more detailed analysis: > `vsearch` in depth > -> Documentation for vsearch see [here](https://github.com/torognes/vsearch). +> Documentation for vsearch available via their [GitHub repository](https://github.com/torognes/vsearch). {: .details} * **Diamond**: Diamond is a high-throughput program for aligning a file of short reads against a protein reference database such as NR, at 20,000 times the speed of Blastx, with high sensitivity. From 1063c66a35395a48549cac72a50210fb7861e236 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:03:27 +0200 Subject: [PATCH 215/262] fix heading levels --- topics/metabolomics/tutorials/lcms/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/metabolomics/tutorials/lcms/tutorial.md b/topics/metabolomics/tutorials/lcms/tutorial.md index 5729e20598d044..56bba435749ffa 100644 --- a/topics/metabolomics/tutorials/lcms/tutorial.md +++ b/topics/metabolomics/tutorials/lcms/tutorial.md @@ -214,7 +214,7 @@ Note that you can either: {: .tip} -#### Prepare your sampleMetadata file +### Prepare your sampleMetadata file The sampleMetadata file is a tab-separated table, in text format. This table has to be filled by the user. You can use any software you find appropriate to construct your table, as long as you save your file in a compatible format. For example, you can @@ -287,7 +287,7 @@ Once your sampleMetadata table is ready, you can proceed to the upload. In this {: .tip} -#### Upload the sampleMetada file with 'Get data' +### Upload the sampleMetada file with 'Get data' > Upload the sampleMetada > From f3b82b93442ae9a3e6a9e84ff448bdd50bdfb842 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:17:14 +0200 Subject: [PATCH 216/262] fix linting errors --- .../tutorials/multiplex-tissue-imaging-TMA/tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md b/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md index 6d72adafef7d53..3887310e446adc 100644 --- a/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md +++ b/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.md @@ -33,7 +33,7 @@ Find a full [example history](https://cancer.usegalaxy.org/u/watsocam/h/gtnexemp ![Aviator screenshot, described in figure caption](../../images/multiplex-tissue-imaging-TMA/ex2_combined_avivator.png "Fully registered image of the MCMICRO Exemplar-002 Tissue microarray. Exemplar-002 consists of four cores, each with a distinct tissue organization and expression of biomarkers. In the image, there are six biomarkers shown: DNA (white), CD163 (yellow), CD3D (blue), CD31 (red), VDAC1 (green), and Keratin (orange). This image is being viewed using Avivator, an interactive tool that allows the user to selectively view channels and adjust channel intensities.") -> ### Agenda +> > > In this tutorial, we will cover: > @@ -233,7 +233,7 @@ The quantification step will produce a CSV cell feature table for every image in {: .hands_on} -# **Convert McMicro Output to Anndata** +# Convert McMicro Output to Anndata Anndata ({% cite Virshup2021 %}) is a Python package and file format schema for working with annotated data matrices that has gained popularity in the single-cell analysis community. Many downstream analysis tools, including Scimap from MCMICRO, Scanpy ({% cite Wolf2018 %}), and Squidpy ({% cite Palla2022 %}) are built around anndata format files (h5ad). This tool splits the marker intensity data into a separate dataframe (`X`), and places all observational data (spatial coordinates, morphological features, etc.) in the cell feature table into a separate dataframe (`obs`) that shares the same indices as `X`. In downstream analyses, new categorical variables, such as phenotype assignments for each cell, are stored in the `obs` dataframe. @@ -256,7 +256,7 @@ Learn more about this file format at the [anndata documentation](https://anndata {: .hands_on} -# Scimap: **Single Cell Phenotyping** +# Scimap: Single Cell Phenotyping There are several ways to classify cells available in Galaxy-ME. Unsupervised approaches, such as Leiden clustering, can be performed on all cells and phenotypes can be manually annotated based on marker expression patterns observed by the user. This approach is time consuming, so here we will demonstrate automated phenotyping based on thresholds of specific lineage markers using MCMICRO's Scimap. Scimap phenotyping can either be provided a table of manual gate values for each marker of interest (which can be determined using the **GateFinder** tool in Galaxy-ME), or by default, Scimap will fit a Gaussian Mixture Model (GMM) to the `log(intensity)` data for each marker to determine positive and negative populations for that marker. The marker intensity values are rescaled between (0,1) with 0.5 being the cut-off between negative and positive populations. Scimap uses a 'Phenotype workflow' to guide the classification of cells (Figure 5.). For more on how to construct a Scimap workflow, see the [Scimap documentation](https://scimap-doc.readthedocs.io/en/latest/tutorials/scimap-tutorial-cell-phenotyping/). @@ -303,7 +303,7 @@ UNetCoreograph outputs each individual core image in `tiff` format. Interactive {: .hands_on} -## **Rename OME-TIFF Channels** +## Rename OME-TIFF Channels Some tools can cause the channel names in an OME-TIFF image to be lost. To fix this, or to change the channel names to whatever the user prefers, the **Rename OME-TIFF Channels** tool can be invoked using a markers file similar to the one used in previous steps. From e5ad7b4d0cba3651c6a07202a3609a8a0dd6f4de Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:25:04 +0200 Subject: [PATCH 217/262] add citations --- .../tutorials/hicexplorer/tutorial.bib | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/topics/epigenetics/tutorials/hicexplorer/tutorial.bib b/topics/epigenetics/tutorials/hicexplorer/tutorial.bib index e69de29bb2d1d6..a16dd6263efa33 100644 --- a/topics/epigenetics/tutorials/hicexplorer/tutorial.bib +++ b/topics/epigenetics/tutorials/hicexplorer/tutorial.bib @@ -0,0 +1,24 @@ +@article{Ramrez2017, + title = {High-resolution TADs reveal DNA sequences underlying genome organization in flies}, + url = {http://dx.doi.org/10.1101/115063}, + DOI = {10.1101/115063}, + publisher = {Cold Spring Harbor Laboratory}, + author = {Ramírez, Fidel and Bhardwaj, Vivek and Villaveces, José and Arrigoni, Laura and Gr\"{u}ning, Bj\"{o}rn A. and Lam, Kin Chung and Habermann, Bianca and Akhtar, Asifa and Manke, Thomas}, + year = {2017}, + month = mar +} + +@article{Rao2014, + title = {A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping}, + volume = {159}, + ISSN = {0092-8674}, + url = {http://dx.doi.org/10.1016/j.cell.2014.11.021}, + DOI = {10.1016/j.cell.2014.11.021}, + number = {7}, + journal = {Cell}, + publisher = {Elsevier BV}, + author = {Rao, Suhas S.P. and Huntley, Miriam H. and Durand, Neva C. and Stamenova, Elena K. and Bochkov, Ivan D. and Robinson, James T. and Sanborn, Adrian L. and Machol, Ido and Omer, Arina D. and Lander, Eric S. and Aiden, Erez Lieberman}, + year = {2014}, + month = dec, + pages = {1665–1680} +} From 4b0d213999dc3f364a9409d554e9ffe22c519edd Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:26:47 +0200 Subject: [PATCH 218/262] fix link text --- topics/metabolomics/tutorials/lcms/tutorial.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/topics/metabolomics/tutorials/lcms/tutorial.md b/topics/metabolomics/tutorials/lcms/tutorial.md index 56bba435749ffa..73aae3621737a5 100644 --- a/topics/metabolomics/tutorials/lcms/tutorial.md +++ b/topics/metabolomics/tutorials/lcms/tutorial.md @@ -994,8 +994,7 @@ dataset size) and your study design. You should think carefully about what is ap In this tutorial, we will take the example of univariate analysis, using the `bmi` column of the **sampleMetadata file** as the study's biological factor investigated (body mass index). Since this variable is quantitative, we will chose in this example to measure the link between the BMI and the measured ions using a **statistical correlation calculation**. For more examples of -statistical analysis performed on LC-MS data, you can take a few minutes to watch the [usemetabo.org](https://usemetabo.org) open course video -[here](https://usemetabo.org/courses/w4mlc-ms-statistical-analysis). +statistical analysis performed on LC-MS data, you can take a few minutes to watch the [usemetabo.org](https://usemetabo.org) open [course video](https://usemetabo.org/courses/w4mlc-ms-statistical-analysis). ## Computation of statistical indices From dc19239bdc6a333320672c9ba814b3e47d859358 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:28:00 +0200 Subject: [PATCH 219/262] fix headings --- topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md b/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md index 431a8215984e7a..c56d7c5c6a03d8 100644 --- a/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md +++ b/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.md @@ -260,7 +260,7 @@ Note that you can either: {: .tip} -#### Prepare your sampleMetadata file +### Prepare your sampleMetadata file The sampleMetadata file is a tab-separated table, in text format. This table has to be filled by the user. You can use any software you find appropriate to construct your table, as long as you save your file in a compatible format. For example, you can @@ -351,7 +351,7 @@ Once your sampleMetadata table is ready, you can proceed to the upload. In this {: .warning} -#### Upload the sampleMetada file with 'Get data' +### Upload the sampleMetada file with 'Get data' > Upload the sampleMetada > From d550510eda389d49c33b023ac8b62a63d845a72c Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:32:50 +0200 Subject: [PATCH 220/262] linter fixes --- .../tutorials/genome-annotation/tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/genome-annotation/tutorials/genome-annotation/tutorial.md b/topics/genome-annotation/tutorials/genome-annotation/tutorial.md index c4ace35a8fda0d..97df870a527ad6 100644 --- a/topics/genome-annotation/tutorials/genome-annotation/tutorial.md +++ b/topics/genome-annotation/tutorials/genome-annotation/tutorial.md @@ -39,19 +39,19 @@ It consists of three main steps: # Introduction into File Formats -**FASTA** +## FASTA DNA and protein sequences are written in FASTA format where you have in the first line a ">" followed by the description. In the second line the sequence starts. ![FASTA file](../../images/fasta_format.png) -**GFF3** +## GFF3 The general feature format (gene-finding format, generic feature format, GFF) is a file format used for describing genes and other features of DNA, RNA and protein sequences. GFF3 overview -**GENBANK** +## GENBANK The genbank sequence format is a rich format for storing sequences and associated annotations. From 4e24deee2f2aaa484dd4fa0ed26c68ebc0c22174 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:32:54 +0200 Subject: [PATCH 221/262] linter fixes --- topics/metabolomics/tutorials/lcms/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/metabolomics/tutorials/lcms/tutorial.md b/topics/metabolomics/tutorials/lcms/tutorial.md index 73aae3621737a5..29d6f2b6e62425 100644 --- a/topics/metabolomics/tutorials/lcms/tutorial.md +++ b/topics/metabolomics/tutorials/lcms/tutorial.md @@ -874,7 +874,7 @@ to get rid of it. > {: .hands_on} -**What transformation has this tool done to the ions' intensities?** +### What transformation has this tool done to the ions' intensities? For each ion independently, the normalisation process works as described in the following picture: From 28919663fcb2a2bc482efa9927f099e2c2ed7b92 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:44:08 +0200 Subject: [PATCH 222/262] add some more funding contributors as suggested by @bgruening in #4913 --- .../tutorials/galaxy-intro-101/tutorial.md | 25 +++++++++++++------ .../tutorials/galaxy-intro-short/tutorial.md | 5 +++- .../galaxy-intro-strands/tutorial.md | 12 ++++++--- 3 files changed, 30 insertions(+), 12 deletions(-) diff --git a/topics/introduction/tutorials/galaxy-intro-101/tutorial.md b/topics/introduction/tutorials/galaxy-intro-101/tutorial.md index c9c7cabfe74f5b..3304938a00c0c5 100644 --- a/topics/introduction/tutorials/galaxy-intro-101/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-101/tutorial.md @@ -23,14 +23,23 @@ key_points: - Galaxy provides ways to share your results and methods with others subtopic: core priority: 2 -contributors: -- shiltemann -- nsoranzo -- blankclemens -- nekrut -- bgruening -- pajanne -- hexylena + +contributions: + authorship: + - shiltemann + - nsoranzo + - blankclemens + - nekrut + - bgruening + - pajanne + - hexylena + funding: + - psu + - erasmusmc + - elixir-europe + - uni-freiburg + - deNBI + recordings: - captioners: - shiltemann diff --git a/topics/introduction/tutorials/galaxy-intro-short/tutorial.md b/topics/introduction/tutorials/galaxy-intro-short/tutorial.md index a03e585d165b97..113b490a1dfa55 100644 --- a/topics/introduction/tutorials/galaxy-intro-short/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-short/tutorial.md @@ -36,7 +36,10 @@ contributions: editing: - bebatut - ahmedhamidawan - + funding: + - AustralianBioCommons + - elixir-europe + - uni-freiburg --- # Overview diff --git a/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md b/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md index c2f91b857becb0..99b116e83eeb27 100644 --- a/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-strands/tutorial.md @@ -17,9 +17,15 @@ key_points: - "Galaxy can connect to external sources for data import and visualization purposes" - "Galaxy provides ways to share your results and methods with others" subtopic: next-steps -contributors: - - tnabtaf - - gallardoalba + +contributions: + authorship: + - tnabtaf + - gallardoalba + funding: + - elixir-europe + - deNBI + - uni-freiburg recordings: - youtube_id: P1mEWZ_tAgQ From 35b604128455b461895bfbbacda4ad1014242800 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 18:47:46 +0200 Subject: [PATCH 223/262] fix indent error --- .../introduction/tutorials/galaxy-intro-short/tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/introduction/tutorials/galaxy-intro-short/tutorial.md b/topics/introduction/tutorials/galaxy-intro-short/tutorial.md index 113b490a1dfa55..e866e4285ea8b5 100644 --- a/topics/introduction/tutorials/galaxy-intro-short/tutorial.md +++ b/topics/introduction/tutorials/galaxy-intro-short/tutorial.md @@ -36,10 +36,10 @@ contributions: editing: - bebatut - ahmedhamidawan - funding: - - AustralianBioCommons - - elixir-europe - - uni-freiburg + funding: + - AustralianBioCommons + - elixir-europe + - uni-freiburg --- # Overview From 4aeca3d9f7a19247a08a3ee14032a3ecca9b2ad2 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 19:25:32 +0200 Subject: [PATCH 224/262] add gallantries as funding type contributor --- .../tutorials/flye-assembly/tutorial.md | 16 ++++++----- .../tutorials/cli-advanced/tutorial.md | 6 +++-- .../tutorials/cli-bashcrawl/tutorial.md | 8 +++--- .../tutorials/cli-basics/tutorial.md | 6 +++-- .../python-advanced-np-pd/tutorial.md | 4 ++- .../tutorials/python-basics/tutorial.md | 4 ++- .../tutorials/python-plotting/tutorial.md | 4 ++- .../tutorials/r-advanced/tutorial.md | 4 ++- .../tutorials/r-dplyr/tutorial.md | 10 ++++--- .../tutorials/rstudio/tutorial.md | 4 ++- .../tutorials/apollo/slides.html | 4 ++- .../tutorials/mapping/slides.html | 5 +++- .../tutorials/quality-control/slides.html | 4 ++- .../tutorials/quality-control/tutorial.md | 27 ++++++++++--------- .../tutorials/intro-to-ml-with-r/tutorial.md | 4 ++- .../rna-seq-counts-to-viz-in-r/tutorial.md | 5 +++- .../tutorials/circos/slides.html | 4 ++- .../tutorials/circos/tutorial.md | 5 +++- .../tutorials/jbrowse/tutorial.md | 4 ++- 19 files changed, 85 insertions(+), 43 deletions(-) diff --git a/topics/assembly/tutorials/flye-assembly/tutorial.md b/topics/assembly/tutorials/flye-assembly/tutorial.md index a4d1d67dbe48a2..d42407a3c530d7 100644 --- a/topics/assembly/tutorials/flye-assembly/tutorial.md +++ b/topics/assembly/tutorials/flye-assembly/tutorial.md @@ -17,13 +17,15 @@ level: Intermediate key_points: - PacBio data allows to perform good quality genome assembly - Quast and BUSCO make it easy to compare the quality of assemblies -contributors: -- abretaud -- alexcorm -- r1corre -- lleroi -- stephanierobin -- gallantries +contributions: + authorship: + - abretaud + - alexcorm + - r1corre + - lleroi + - stephanierobin + funding: + - gallantries follow_up_training: - type: internal diff --git a/topics/data-science/tutorials/cli-advanced/tutorial.md b/topics/data-science/tutorials/cli-advanced/tutorial.md index 1bf456fd3da03a..fd1ff3576e3375 100644 --- a/topics/data-science/tutorials/cli-advanced/tutorial.md +++ b/topics/data-science/tutorials/cli-advanced/tutorial.md @@ -63,12 +63,14 @@ key_points: notebook: language: bash subtopic: bash -contributors: +contributions: + authorship: - carpentries - hexylena - bazante1 - - gallantries - avans-atgm + funding: + - gallantries tags: - bash --- diff --git a/topics/data-science/tutorials/cli-bashcrawl/tutorial.md b/topics/data-science/tutorials/cli-bashcrawl/tutorial.md index bee6c2d6c1e949..5e79c18c1e566a 100644 --- a/topics/data-science/tutorials/cli-bashcrawl/tutorial.md +++ b/topics/data-science/tutorials/cli-bashcrawl/tutorial.md @@ -27,9 +27,11 @@ key_points: notebook: language: bash subtopic: bash -contributors: -- hexylena -- gallantries +contributions: + authorship: + - hexylena + funding: + - gallantries tags: - game - bash diff --git a/topics/data-science/tutorials/cli-basics/tutorial.md b/topics/data-science/tutorials/cli-basics/tutorial.md index 83325326dae464..4ff0f09bd755a5 100644 --- a/topics/data-science/tutorials/cli-basics/tutorial.md +++ b/topics/data-science/tutorials/cli-basics/tutorial.md @@ -63,12 +63,14 @@ key_points: notebook: language: bash subtopic: bash -contributors: +contributions: + authorship: - carpentries - hexylena - bazante1 - - gallantries - avans-atgm + funding: + - gallantries tags: - bash --- diff --git a/topics/data-science/tutorials/python-advanced-np-pd/tutorial.md b/topics/data-science/tutorials/python-advanced-np-pd/tutorial.md index b70729b78dced0..58e25b7f9dadda 100644 --- a/topics/data-science/tutorials/python-advanced-np-pd/tutorial.md +++ b/topics/data-science/tutorials/python-advanced-np-pd/tutorial.md @@ -24,10 +24,12 @@ key_points: - Python has many libraries offering a variety of capabilities, which makes it popular for beginners, as well as, more experienced users - You can use scientific libraries like Numpy and Pandas to perform data analysis. subtopic: python -contributors: +contributions: + authorship: - mcmaniou - fpsom - carpentries + funding: - gallantries priority: 2 diff --git a/topics/data-science/tutorials/python-basics/tutorial.md b/topics/data-science/tutorials/python-basics/tutorial.md index 64b2d0b565daca..6d1a65a0c382e4 100644 --- a/topics/data-science/tutorials/python-basics/tutorial.md +++ b/topics/data-science/tutorials/python-basics/tutorial.md @@ -23,10 +23,12 @@ key_points: - Python is a fairly easy programming language to learn and use, but be mindful of the indexing. - Python has many libraries offering a variety of capabilities, which makes it popular for beginners, as well as, more experienced users subtopic: python -contributors: +contributions: + authorship: - mcmaniou - fpsom - carpentries + funding: - gallantries priority: 1 diff --git a/topics/data-science/tutorials/python-plotting/tutorial.md b/topics/data-science/tutorials/python-plotting/tutorial.md index fa101387c0a786..0070e9a7f7649c 100644 --- a/topics/data-science/tutorials/python-plotting/tutorial.md +++ b/topics/data-science/tutorials/python-plotting/tutorial.md @@ -23,10 +23,12 @@ key_points: - Python has many libraries offering a variety of capabilities, which makes it popular for beginners, as well as, more experienced users - You can use scientific libraries like Matplotlib to perform exploratory data analysis. subtopic: python -contributors: +contributions: + authorship: - mcmaniou - fpsom - carpentries + funding: - gallantries priority: 3 diff --git a/topics/data-science/tutorials/r-advanced/tutorial.md b/topics/data-science/tutorials/r-advanced/tutorial.md index 03cb724322b940..033df963a80bb7 100644 --- a/topics/data-science/tutorials/r-advanced/tutorial.md +++ b/topics/data-science/tutorials/r-advanced/tutorial.md @@ -40,11 +40,13 @@ key_points: - Pipes can be used to combine simple operations into complex procedures. subtopic: r priority: 2 -contributors: +contributions: + authorship: - carpentries - bebatut - fpsom - tobyhodges + funding: - gallantries tags: - R diff --git a/topics/data-science/tutorials/r-dplyr/tutorial.md b/topics/data-science/tutorials/r-dplyr/tutorial.md index 29cfd9e26ce5ab..be0400ee66755c 100644 --- a/topics/data-science/tutorials/r-dplyr/tutorial.md +++ b/topics/data-science/tutorials/r-dplyr/tutorial.md @@ -22,10 +22,12 @@ time_estimation: 1H key_points: - Dplyr and tidyverse make it a lot easier to process data - The functions for selecting data are a lot easier to understand than R's built in alternatives. -contributors: -- hexylena -- gallantries -- avans-atgm +contributions: + authorship: + - hexylena + - avans-atgm + funding: + - gallantries subtopic: r notebook: language: r diff --git a/topics/galaxy-interface/tutorials/rstudio/tutorial.md b/topics/galaxy-interface/tutorials/rstudio/tutorial.md index d6ad9bcca1df0a..4ba154ccf1baba 100644 --- a/topics/galaxy-interface/tutorials/rstudio/tutorial.md +++ b/topics/galaxy-interface/tutorials/rstudio/tutorial.md @@ -20,10 +20,12 @@ tags: - interactive-tools key_points: - Why it's helpful to be able to work with R interactively within Galaxy -contributors: +contributions: + authorship: - bebatut - fpsom - tobyhodges + funding: - gallantries subtopic: analyse --- diff --git a/topics/genome-annotation/tutorials/apollo/slides.html b/topics/genome-annotation/tutorials/apollo/slides.html index 46d577f0839522..135b26d3854480 100644 --- a/topics/genome-annotation/tutorials/apollo/slides.html +++ b/topics/genome-annotation/tutorials/apollo/slides.html @@ -24,11 +24,13 @@ - Apollo allows a group to view and manually refine predicted genome annotations - Use Apollo to edit annotations within your group. - Export manual annotations as GFF3. -contributors: +contributions: + authorship: - abretaud - hexylena - nathandunn - mboudet + funding: - gallantries recordings: diff --git a/topics/sequence-analysis/tutorials/mapping/slides.html b/topics/sequence-analysis/tutorials/mapping/slides.html index cff4630af32b3c..5ddc4ed246a630 100644 --- a/topics/sequence-analysis/tutorials/mapping/slides.html +++ b/topics/sequence-analysis/tutorials/mapping/slides.html @@ -19,12 +19,15 @@ - Choice of mapper can affect downstream results - Know your data! - Genome browsers can be used to view aligned reads -contributors: +contributions: + authorship: - joachimwolff - shiltemann - EngyNasr - gallardoalba + funding: - gallantries + - elixir-europe recordings: - captioners: diff --git a/topics/sequence-analysis/tutorials/quality-control/slides.html b/topics/sequence-analysis/tutorials/quality-control/slides.html index 2559bd2c76ea02..84daf4aa3b0a31 100644 --- a/topics/sequence-analysis/tutorials/quality-control/slides.html +++ b/topics/sequence-analysis/tutorials/quality-control/slides.html @@ -20,13 +20,15 @@ - Run quality control on every sequencing dataset before any other analyses - Choose QC parameters carefully - Re-run FastQC to check the impact of the quality control -contributors: +contributions: + authorship: - bebatut - abretaud - alexcorm - lleroi - r1corre - stephanierobin + funding: - gallantries diff --git a/topics/sequence-analysis/tutorials/quality-control/tutorial.md b/topics/sequence-analysis/tutorials/quality-control/tutorial.md index 51d8629eac4fef..ab9e599a8da411 100644 --- a/topics/sequence-analysis/tutorials/quality-control/tutorial.md +++ b/topics/sequence-analysis/tutorials/quality-control/tutorial.md @@ -26,16 +26,19 @@ key_points: - Check the impact of the quality control - Different tools are available to provide additional quality metrics - For paired-end reads analyze the forward and reverse reads together -contributors: -- bebatut -- mblue9 -- alexcorm -- abretaud -- lleroi -- r1corre -- stephanierobin -- gallantries -- neoformit +contributions: + authorship: + - bebatut + - mblue9 + - alexcorm + - abretaud + - lleroi + - r1corre + - stephanierobin + - neoformit + funding: + - gallantries + recordings: - youtube_id: coaMGvZazoc length: 50M @@ -58,9 +61,9 @@ recordings: length: 51M galaxy_version: 24.1.2.dev0 date: '2024-09-30' - speakers: + speakers: - dianichj - captioners: + captioners: - dianichj bot-timestamp: 1727710795 diff --git a/topics/statistics/tutorials/intro-to-ml-with-r/tutorial.md b/topics/statistics/tutorials/intro-to-ml-with-r/tutorial.md index 7e19d39ea08f3e..03714aea110f33 100644 --- a/topics/statistics/tutorials/intro-to-ml-with-r/tutorial.md +++ b/topics/statistics/tutorials/intro-to-ml-with-r/tutorial.md @@ -41,8 +41,10 @@ tags: - interactive-tools key_points: - To be added -contributors: +contributions: + authorship: - fpsom + funding: - gallantries recordings: diff --git a/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.md b/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.md index a4edc1c4f9fecf..5a3ae2a853970f 100644 --- a/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.md +++ b/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.md @@ -33,10 +33,13 @@ tags: - interactive-tools key_points: - When creating plots with `ggplot2`, think about the graphics in layers (aesthetics, geometry, statistics, scale transformation, and grouping). -contributors: + +contributions: + authorship: - bebatut - fpsom - tobyhodges + funding: - gallantries recordings: diff --git a/topics/visualisation/tutorials/circos/slides.html b/topics/visualisation/tutorials/circos/slides.html index 7b1456b8c9c8d6..7825557f921aa2 100644 --- a/topics/visualisation/tutorials/circos/slides.html +++ b/topics/visualisation/tutorials/circos/slides.html @@ -12,9 +12,11 @@ - Circos is very powerful, but also very complex - Creating plots is an iterative process - The full configuration directory can be downloaded from Galaxy to be further tweaked locally -contributors: +contributions: + authorship: - hexylena - shiltemann + funding: - gallantries recordings: diff --git a/topics/visualisation/tutorials/circos/tutorial.md b/topics/visualisation/tutorials/circos/tutorial.md index f3259d8e0c08a0..f2f1adf7ea5a3d 100644 --- a/topics/visualisation/tutorials/circos/tutorial.md +++ b/topics/visualisation/tutorials/circos/tutorial.md @@ -13,10 +13,13 @@ time_estimation: "2h" key_points: - "Circos is an effective tool to make circular visualisation of high-dimensional datasets" - "Circos is often used for genomics, but can also be used for other types of data" -contributors: +contributions: + authorship: - shiltemann - hexylena - gallardoalba + funding: + - gallantries level: Intermediate recordings: diff --git a/topics/visualisation/tutorials/jbrowse/tutorial.md b/topics/visualisation/tutorials/jbrowse/tutorial.md index 6d7216388010d7..ada2ccc97d323d 100644 --- a/topics/visualisation/tutorials/jbrowse/tutorial.md +++ b/topics/visualisation/tutorials/jbrowse/tutorial.md @@ -18,9 +18,11 @@ level: Intermediate tags: - gmod - jbrowse1 -contributors: +contributions: + authorship: - hexylena - shiltemann + funding: - gallantries --- From d5243980ba7e70273ce241bff0771b3f50861081 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Tue, 8 Oct 2024 19:26:18 +0200 Subject: [PATCH 225/262] only show funder section if defined in metadata --- _layouts/tutorial_hands_on.html | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/_layouts/tutorial_hands_on.html b/_layouts/tutorial_hands_on.html index bc89cc0c770fc1..5611b51b40ca5e 100644 --- a/_layouts/tutorial_hands_on.html +++ b/_layouts/tutorial_hands_on.html @@ -291,7 +291,7 @@

    You've Finished the Tutorial

    function tutorial_finish() { if(typeof plausible !== 'undefined'){ // Plausible may be undefined (script blocked) - // or it may be defined, but opted-out (select box/DNT), + // or it may be defined, but opted-out (select box/DNT), // which means `plausible()` will work but not send data, *nor* execute the callback. plausible('TutorialComplete', {props: {path: document.location.pathname}}) } @@ -427,11 +427,12 @@

    {{locale['citing-tutorial'] | default: "Citing this Tutorial"}}

    + {% if page.contributions and page.contributions.funding %}

    {{locale['references']| default: "Funding" }}

    These individuals or organisations provided funding support for the development of this resource

    - {% if page.contributions %} + {% include _includes/funding-statement.md funders=page.contributions.funding %} - {% endif %} + {% endif %} + + +

    Stats for materials contributed to by {{ entity.name | default: page.contributor }}

    + From b410f32e245c1e357a1cd9a172211288064a79ab Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 15 Oct 2024 17:43:41 +0200 Subject: [PATCH 253/262] fix missing affils --- CONTRIBUTORS.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 10ab150f87ef43..66dde8fce93e54 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -939,9 +939,9 @@ hexylena: joined: 2017-09 elixir_node: nl affiliations: + - erasmusmc - gallantries - by-covid - - erasmusmc - elixir-europe - elixir-converge former_affiliations: @@ -1421,6 +1421,7 @@ mjostaszewski: orcid: 0000-0003-1473-370X affiliations: - elixir-europe + - by-covid MariaTsayo: name: Maria Tsagiopoulou @@ -1501,6 +1502,7 @@ MattiHoch: orcid: 0000-0002-2486-0246 affiliations: - elixir-europe + - by-covid maximskorik: name: Maxim Skoryk From 23017b0a882f1c32c4d08f5a9cbb9282dfefc044 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 15 Oct 2024 17:44:13 +0200 Subject: [PATCH 254/262] missing explanation of ordering --- _layouts/contributor_index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html index 5ad0b3aacb3629..bb8ce747e034cb 100644 --- a/_layouts/contributor_index.html +++ b/_layouts/contributor_index.html @@ -65,7 +65,7 @@

    Former Affiliations

    {% assign member_count = entity.members | size %} {% if member_count > 0 %}

    Members

    -

    These individuals have noted that they are affiliated in some way with this organisation. This list is non-exhaustive.

    +

    These individuals have noted that they are affiliated in some way with this organisation. This list is non-exhaustive, and randomly ordered.

    {% include _includes/contributor-list.html contributors=entity.members badge=true shuffle=true %}
    From 97b8913ef0d6306a655560cb745b2b18ce070b17 Mon Sep 17 00:00:00 2001 From: Anna Syme Date: Wed, 16 Oct 2024 11:17:25 +1100 Subject: [PATCH 255/262] Update Helixer tutorial.md - gffread inputs In the tutorial, for the tool gffread, for `select fasta outputs`, I think the wrong item is specified. I have changed it from `fasta file with spliced exons` to `protein fasta file`, because the next step in the tutorial (using Busco) needs this protein fasta file. --- topics/genome-annotation/tutorials/helixer/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/genome-annotation/tutorials/helixer/tutorial.md b/topics/genome-annotation/tutorials/helixer/tutorial.md index 468730c7d242ef..011250ee4adee2 100644 --- a/topics/genome-annotation/tutorials/helixer/tutorial.md +++ b/topics/genome-annotation/tutorials/helixer/tutorial.md @@ -170,7 +170,7 @@ We want to run BUSCO on the protein sequences predicted from gene sequences of t > - {% icon param-file %} *"Input GFF3 or GTF feature file"*: output of {% tool [Helixer](toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1)) %} > - In *"Reference Genome"* select: `From your history` (Input dataset) > - *"Genome Reference Fasta"*: `masked genome` (Input dataset) -> - In *"Select fasta outputs"* select: `fasta file with spliced exons for each GFF transcript (-y)` +> - In *"Select fasta outputs"* select: `protein fasta file with the translation of CDS for each record (-y)` > - *"full GFF attribute preservation (all attributes are shown)"*: `Yes` > - *"decode url encoded characters within attributes"*: `Yes` > - *"warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records"*: `Yes` From e5bfa7ac47384ab0f98c094d6af80c65c49f2a56 Mon Sep 17 00:00:00 2001 From: Felicitas Kindel <123303803+felicitas215@users.noreply.github.com> Date: Thu, 17 Oct 2024 10:31:52 +0200 Subject: [PATCH 256/262] Update tutorial.md Clarify Helixer's behavior when using a soft-masked or hard-masked genome --- topics/genome-annotation/tutorials/helixer/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/genome-annotation/tutorials/helixer/tutorial.md b/topics/genome-annotation/tutorials/helixer/tutorial.md index 011250ee4adee2..b48ab35d853462 100644 --- a/topics/genome-annotation/tutorials/helixer/tutorial.md +++ b/topics/genome-annotation/tutorials/helixer/tutorial.md @@ -67,7 +67,7 @@ In this tutorial, you'll learn how to perform a structural annotation of the gen To annotate our genome using Helixer, we will use the following files: -- The **genome sequence** in fasta format. For best results, the sequence should be soft-masked beforehand. You can learn how to do it by following the [RepeatMasker tutorial]({% link topics/genome-annotation/tutorials/repeatmasker/tutorial.md %}). For this tutorial, we will try to annotate the genome assembled in the [Flye assembly tutorial]({% link topics/assembly/tutorials/flye-assembly/tutorial.md %}) and already masked for you using RepeatMasker. +- The **genome sequence** in fasta format. For this tutorial, we will try to annotate the genome assembled in the [Flye assembly tutorial]({% link topics/assembly/tutorials/flye-assembly/tutorial.md %}). (Note: Helixer will ignore soft-masking. Hard-masking is not recommnded for Helixer either, as it does not ignore the hard-masked regions, but will get less information from them, which could influence your predictions in a negative way.) > Data upload > From 1fee12919900d6f76b86868175fa983ebd53ed55 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 17 Oct 2024 10:43:59 +0200 Subject: [PATCH 257/262] remove stray conflict line --- CONTRIBUTORS.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 315ab832fa2dd9..75f94bee0b8bc4 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -2582,7 +2582,6 @@ ThibaudGlinez: - pndb - elixir-europe -<<<<<<< HEAD sonjafiliposka: name: Sonja Filiposka joined: 2024-07 From 2234941f3d4eeecac20a79fa5eeeed98b89b21ad Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 17 Oct 2024 10:47:16 +0200 Subject: [PATCH 258/262] set to draft --- .../tutorials/fair-by-design/tutorial.md | 65 ++++++++++--------- 1 file changed, 33 insertions(+), 32 deletions(-) diff --git a/topics/contributing/tutorials/fair-by-design/tutorial.md b/topics/contributing/tutorials/fair-by-design/tutorial.md index 714eb379b6529b..668b1fdc2a384a 100644 --- a/topics/contributing/tutorials/fair-by-design/tutorial.md +++ b/topics/contributing/tutorials/fair-by-design/tutorial.md @@ -1,6 +1,7 @@ --- layout: tutorial_hands_on title: FAIR-by-Design methodology +draft: true abbreviations: FAIR: Findable, Accessible, Interoperable, Reusable OER: Open Educational Repositories @@ -137,7 +138,7 @@ May all your materials be FAIR! > More details on the FAIR principles > [Follow the FAIR in a nutshell tutorial available on GTN]( {% link topics/fair/tutorials/fair-intro/tutorial.md %} ) -> +> > [Follow the FAIR Galaxy Training Material tutorial available on GTN]( {% link topics/fair/tutorials/fair-gtn/tutorial.md %} ) {: .details} @@ -260,7 +261,7 @@ More on the RDA minimal metadata schema here {% cite hoebelheinrich_2022 %} > >Use Blooms Taxonomy > >Formulate the objectives as actionable verb + observable knowledge, skill, attitude, behavior or ability. > {: .tip} -> +> > [Read more](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects_cont/#defining-learning-objectives) {: .question } @@ -280,28 +281,28 @@ Reusable materials can be found anywhere. These are just some examples: **GTN** -- [GTN learning resources](https://training.galaxyproject.org) +- [GTN learning resources](https://training.galaxyproject.org) - [TeSS Catalogue by Elixir](https://tess.elixir-europe.org) **OER** -- [DOAB](https://directory.doabooks.org/) -- [MERLOT](https://www.merlot.org/merlot/index.htm) -- [OASIS](https://oasis.geneseo.edu/index.php) -- [OER Commons](https://www.oercommons.org/) -- [OERTX CORA](https://www.projectcora.org/) -- [GALILEO](https://oer.galileo.usg.edu/) +- [DOAB](https://directory.doabooks.org/) +- [MERLOT](https://www.merlot.org/merlot/index.htm) +- [OASIS](https://oasis.geneseo.edu/index.php) +- [OER Commons](https://www.oercommons.org/) +- [OERTX CORA](https://www.projectcora.org/) +- [GALILEO](https://oer.galileo.usg.edu/) - [FORRT](https://forrt.org/) **EOSC** -- [EOSC Training catalogue on the EOSC Marketplace](https://search.marketplace.eosc-portal.eu/search/training?q=*) +- [EOSC Training catalogue on the EOSC Marketplace](https://search.marketplace.eosc-portal.eu/search/training?q=*) - Most EOSC projects have their own training catalogues and/or platforms. **General** -- [Creative Commons Search](https://search.creativecommons.org/) - content provided under a CC license -- [Zenodo](https://zenodo.org/) - a multi-disciplinary open repository +- [Creative Commons Search](https://search.creativecommons.org/) - content provided under a CC license +- [Zenodo](https://zenodo.org/) - a multi-disciplinary open repository - [OSF](https://osf.io/) - a free, open research platform ### Potential for reuse @@ -357,13 +358,13 @@ Each MVS profile defines a list of technical and soft skills required for the pr >How to organise the files > > GTN defines a specific hierarchical structure that needs to be followed when developing learning materials. -> +> > > Check out the following tutorials > > [How to create a skeleton for a new learning topic]( {% link topics/contributing/tutorials/create-new-topic/tutorial.md#creating-a-new-topic-with-its-own-materials %} ) -> > +> > > > [How to create the skeleton of a new tutorial]( {% link topics/contributing/tutorials/create-new-tutorial/tutorial.md %} ) > {: .details} -> +> {: .hands-on} >Syllabus is ready @@ -372,33 +373,33 @@ Each MVS profile defines a list of technical and soft skills required for the pr >Available feedback form > GTN provides a readily available feedback form that is automatically added at the end of each tutorial. The feedback form is used to gather quantitative and qualitative feedback. -> +> > > Learn more about feedback in training > > [Follow the Assessment and feedback in training and teachings tutorial available on GTN]( {% link topics/teaching/tutorials/assessment/tutorial.md#dealing-with-feedback %} ) > {: .details} -> +> {: .tip} >Facilitation guide kit > A facilitation guide should help prepare for the actual training. -> +> > The facilitation guide kit includes documentation of the process of organising and running a training. What different people need to have, know and do so that everything runs smoothly. -> +> > > Learn more about facilitation > > [Follow the Organizing a workshop tutorial available on GTN]( {% link topics/teaching/tutorials/organize-workshop/tutorial.md %} ) -> > +> > > > [Follow the Running a workshop as instructor tutorial available on GTN]( {% link topics/teaching/tutorials/running-workshop/tutorial.md %} ) > {: .details} -> +> > Another option is to use something like the [TRIPLE project TRAINING TOOLKIT](https://project.gotriple.eu/project-deliverables/triple-training-toolkit/). -> +> {: .tip} >What about instructor notes? > They need to be detailed enough so that anyone can reuse the learning content, especially slides properly. -> +> > Any specific information relevant for instructors that would like to organise a training based on your GTN tutorial content should be added in Details box. -> +> > This practice significantly increases the reuse potential of the material. {: .question} @@ -516,13 +517,13 @@ Each MVS profile defines a list of technical and soft skills required for the pr > Collaborative environment for team work > Choose an environment for producing the learning material that will enable multiple people to work on the same material at one. -> +> > - GitHub is one of the most popular options at the moment (find out more here) > - GTN is also based on GitHub and defines [specific procedures on how one can contribute and collaborate](https://github.com/galaxyproject/training-material/blob/main/CONTRIBUTING.md) using GitHub -> +> > > GTN: collaboration using GitHub > > [Follow the Contributing with GitHub via its interface tutorial available on GTN]( {% link topics/contributing/tutorials/github-interface-contribution/tutorial.md %} ) -> > +> > > > [Follow the Contributing with GitHub via command-line tutorial available on GTN]( {% link topics/contributing/tutorials/github-command-line-contribution/tutorial.md %} ) > {: .details} {: .tip} @@ -571,7 +572,7 @@ The existing materials you are reusing are available under a [CC license](https: >I want to reuse a small part of it > No problem, you can reuse any existing CC licensed material in your learning materials as long as the reused portion is used as a showcase or to make a specific point and it is not the core of your work. -> +> > Remember that if the work is licensed with ND, you can not modify it while reusing. {: .details} @@ -620,7 +621,7 @@ You should also be able to remove attribution upon request. > Read more about how to attribute > [{% icon point-right %} Attribution and Citing](https://fair-by-design-methodology.github.io/FAIR-by-Design_ToT/latest/Stage%201%20%E2%80%93%20Prepare/02-Preparing%20FAIR%20Learning%20Objects/02-Preparing%20FAIR%20Learning%20Objects/#attribution-and-citing) -> +> > [{% icon point-right %} How to handle attribution?](https://courses.lumenlearning.com/suny-oerguide/chapter/how-to-handle-attribution/) {: .details} @@ -629,7 +630,7 @@ You should also be able to remove attribution upon request. The developed learning materials should cover the widest range of learner variability including the ones that use or do not use assistive technology. -![Universal access logo](../../images/universal-access-6602642_640.png) +![Universal access logo](../../images/universal-access-6602642_640.png) "Universal Access Human" by J S from Pixabay @@ -648,7 +649,7 @@ PDF document accessibility is measured with a separate technical specification < >GTN Accessibility > GTN has developed an accessibility mission aiming for WCAG 2.0 AA compliance by implementing a number of accessibility features. -> +> {: .tip} @@ -704,7 +705,7 @@ PDF document accessibility is measured with a separate technical specification < > Having FAIR learning materials does not always mean that the materials are open to everyone and there are no costs or access rules attached. In this case the bundle that is going to be published in an open repository such as Zenodo should contain the following: > 1. Syllabus, that contains all metadata that describe the materials. Metadata should always be open. > 2. Accompanying information (optional) to augment the description of the materials and describe the details when it comes to accessing and using the materials from a trainer perspective. -> +> > The complete learning materials package itself should be published in a closed repository where the corresponding access rules (and costs) can be implemented. {: .warning} From f7e28bf60163f53dc985a78764faea0e32e5b720 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 17 Oct 2024 10:52:02 +0200 Subject: [PATCH 259/262] update metadata --- GRANTS.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/GRANTS.yaml b/GRANTS.yaml index d4be030b72e2b0..e7a73e90b46121 100644 --- a/GRANTS.yaml +++ b/GRANTS.yaml @@ -227,9 +227,8 @@ skills4eosc: name: Skills for European Open Science Cloud short_name: "Skills4SEOSC" joined: 2024-07 - funder: true funding_id: "10040140" - funding_system: cordis + funding_database: cordis funder_name: Horizon Europe url: https://www.skills4eosc.eu/ github: false From 38616bb9b0eb0be97888c9b15f58d3c61f939fd8 Mon Sep 17 00:00:00 2001 From: Felicitas Kindel <123303803+felicitas215@users.noreply.github.com> Date: Thu, 17 Oct 2024 13:56:33 +0200 Subject: [PATCH 260/262] Update CONTRIBUTORS.yaml --- CONTRIBUTORS.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 75f94bee0b8bc4..da3b8062ebc27b 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -778,6 +778,13 @@ cumbof: orcid: 0000-0003-2920-5838 joined: 2018-02 +felicitas215: + name: Felicitas Kindel + email: f.kindel@fz-juelich.de + orcid: 0009-0000-6149-0224 + joined: 2024-10 + affiliations: + - forschungszentrum-juelich fidelram: name: Fidel Ramirez From 0046b2ebd13187f7a2a5d64928dbeb4b8e60e7a3 Mon Sep 17 00:00:00 2001 From: Felicitas Kindel <123303803+felicitas215@users.noreply.github.com> Date: Thu, 17 Oct 2024 15:20:18 +0200 Subject: [PATCH 261/262] Update ORGANISATIONS.yaml Added the Forschungszentrum Juelich --- ORGANISATIONS.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml index 7a55f6b3e7d229..441a292e995435 100644 --- a/ORGANISATIONS.yaml +++ b/ORGANISATIONS.yaml @@ -114,6 +114,12 @@ find: github: false ror: "05tcsqz68" +forschungszentrum-juelich: + short_name: FZJ + name: Forschungszentrum Jülich GmbH + url: https://www.fz-juelich.de/de + github: false + ifb: short_name: IFB name: Institut Français de Bioinformatique From 1fd5f43a32cf16c69fe71b3f8d1cb9e0cc197a96 Mon Sep 17 00:00:00 2001 From: Felicitas Kindel <123303803+felicitas215@users.noreply.github.com> Date: Fri, 18 Oct 2024 08:06:01 +0200 Subject: [PATCH 262/262] add felicitas215 to the tutorial's editing list --- topics/genome-annotation/tutorials/helixer/tutorial.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/topics/genome-annotation/tutorials/helixer/tutorial.md b/topics/genome-annotation/tutorials/helixer/tutorial.md index b48ab35d853462..d99a9ecde5f3d1 100644 --- a/topics/genome-annotation/tutorials/helixer/tutorial.md +++ b/topics/genome-annotation/tutorials/helixer/tutorial.md @@ -30,6 +30,8 @@ contributions: authorship: - rlibouba - abretaud + editing: + - felicitas215 funding: - eurosciencegateway abbreviations: