diff --git a/core/week-2-old/workshop.html b/core/week-2-old/workshop.html index 8a86a51..44946cd 100644 --- a/core/week-2-old/workshop.html +++ b/core/week-2-old/workshop.html @@ -322,17 +322,17 @@

Workshop

ls -l
total 152
-drwxr-xr-x 2 runner docker  4096 Nov  6 09:47 data
-drwxr-xr-x 2 runner docker  4096 Nov  6 09:47 images
--rw-r--r-- 1 runner docker  1597 Nov  6 09:47 overview.qmd
--rw-r--r-- 1 runner docker 22717 Nov  6 09:52 study_after_workshop.html
--rw-r--r-- 1 runner docker   184 Nov  6 09:47 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  4807 Nov  6 09:47 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Nov  6 09:47 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 58063 Nov  6 09:47 workshop.html
--rw-r--r-- 1 runner docker  8550 Nov  6 09:47 workshop.qmd
--rw-r--r-- 1 runner docker  8577 Nov  6 09:52 workshop.rmarkdown
-drwxr-xr-x 3 runner docker  4096 Nov  6 09:47 workshop_files
+drwxr-xr-x 2 runner docker 4096 Nov 6 15:29 data +drwxr-xr-x 2 runner docker 4096 Nov 6 15:29 images +-rw-r--r-- 1 runner docker 1597 Nov 6 15:29 overview.qmd +-rw-r--r-- 1 runner docker 22717 Nov 6 15:34 study_after_workshop.html +-rw-r--r-- 1 runner docker 184 Nov 6 15:29 study_after_workshop.qmd +-rw-r--r-- 1 runner docker 4807 Nov 6 15:29 study_before_workshop.ipynb +-rw-r--r-- 1 runner docker 13029 Nov 6 15:29 study_before_workshop.qmd +-rw-r--r-- 1 runner docker 58063 Nov 6 15:29 workshop.html +-rw-r--r-- 1 runner docker 8550 Nov 6 15:29 workshop.qmd +-rw-r--r-- 1 runner docker 8577 Nov 6 15:34 workshop.rmarkdown +drwxr-xr-x 3 runner docker 4096 Nov 6 15:29 workshop_files

You can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:

@@ -340,17 +340,17 @@

Workshop

ls -hl
total 152K
-drwxr-xr-x 2 runner docker 4.0K Nov  6 09:47 data
-drwxr-xr-x 2 runner docker 4.0K Nov  6 09:47 images
--rw-r--r-- 1 runner docker 1.6K Nov  6 09:47 overview.qmd
--rw-r--r-- 1 runner docker  23K Nov  6 09:52 study_after_workshop.html
--rw-r--r-- 1 runner docker  184 Nov  6 09:47 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Nov  6 09:47 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Nov  6 09:47 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Nov  6 09:47 workshop.html
--rw-r--r-- 1 runner docker 8.4K Nov  6 09:47 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Nov  6 09:52 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Nov  6 09:47 workshop_files
+drwxr-xr-x 2 runner docker 4.0K Nov 6 15:29 data +drwxr-xr-x 2 runner docker 4.0K Nov 6 15:29 images +-rw-r--r-- 1 runner docker 1.6K Nov 6 15:29 overview.qmd +-rw-r--r-- 1 runner docker 23K Nov 6 15:34 study_after_workshop.html +-rw-r--r-- 1 runner docker 184 Nov 6 15:29 study_after_workshop.qmd +-rw-r--r-- 1 runner docker 4.7K Nov 6 15:29 study_before_workshop.ipynb +-rw-r--r-- 1 runner docker 13K Nov 6 15:29 study_before_workshop.qmd +-rw-r--r-- 1 runner docker 57K Nov 6 15:29 workshop.html +-rw-r--r-- 1 runner docker 8.4K Nov 6 15:29 workshop.qmd +-rw-r--r-- 1 runner docker 8.4K Nov 6 15:34 workshop.rmarkdown +drwxr-xr-x 3 runner docker 4.0K Nov 6 15:29 workshop_files

The -a option stands for “all” and shows us all the files, including hidden files.

@@ -358,19 +358,19 @@

Workshop

ls -alh
total 160K
-drwxr-xr-x 5 runner docker 4.0K Nov  6 09:52 .
-drwxr-xr-x 8 runner docker 4.0K Nov  6 09:52 ..
-drwxr-xr-x 2 runner docker 4.0K Nov  6 09:47 data
-drwxr-xr-x 2 runner docker 4.0K Nov  6 09:47 images
--rw-r--r-- 1 runner docker 1.6K Nov  6 09:47 overview.qmd
--rw-r--r-- 1 runner docker  23K Nov  6 09:52 study_after_workshop.html
--rw-r--r-- 1 runner docker  184 Nov  6 09:47 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Nov  6 09:47 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Nov  6 09:47 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Nov  6 09:47 workshop.html
--rw-r--r-- 1 runner docker 8.4K Nov  6 09:47 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Nov  6 09:52 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Nov  6 09:47 workshop_files
+drwxr-xr-x 5 runner docker 4.0K Nov 6 15:34 . +drwxr-xr-x 8 runner docker 4.0K Nov 6 15:34 .. +drwxr-xr-x 2 runner docker 4.0K Nov 6 15:29 data +drwxr-xr-x 2 runner docker 4.0K Nov 6 15:29 images +-rw-r--r-- 1 runner docker 1.6K Nov 6 15:29 overview.qmd +-rw-r--r-- 1 runner docker 23K Nov 6 15:34 study_after_workshop.html +-rw-r--r-- 1 runner docker 184 Nov 6 15:29 study_after_workshop.qmd +-rw-r--r-- 1 runner docker 4.7K Nov 6 15:29 study_before_workshop.ipynb +-rw-r--r-- 1 runner docker 13K Nov 6 15:29 study_before_workshop.qmd +-rw-r--r-- 1 runner docker 57K Nov 6 15:29 workshop.html +-rw-r--r-- 1 runner docker 8.4K Nov 6 15:29 workshop.qmd +-rw-r--r-- 1 runner docker 8.4K Nov 6 15:34 workshop.rmarkdown +drwxr-xr-x 3 runner docker 4.0K Nov 6 15:29 workshop_files

You can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:

diff --git a/core/week-6/workshop.html b/core/week-6/workshop.html index 4714407..9497fd1 100644 --- a/core/week-6/workshop.html +++ b/core/week-6/workshop.html @@ -264,7 +264,7 @@

On this page

  • Start date, last updated date, contact information
  • Description of Project organisation
  • Software requirements
    • -
  • Data provenance
    • +
  • Data description
  • Instructions for use
  • What should be in Supporting information
    • @@ -315,7 +315,7 @@

    Workshop

    Introduction

    Session overview

    -

    In this workshop

    +

    In this workshop we will consider how to document and curate reproducible data analyses. You will add a README to your project and start to populate it. This will include finding out how to find the software you are using.

    @@ -329,13 +329,19 @@

    Non-scr

    Non-scripted parts of the analysis such as manual data cleaning or using software that does not have a script to analyse data presented in the report should be documented. This includes the steps taken, parameter settings and the decisions made. It need not be written as a narrative - you can use bullet points and be concise.

    🎬 Go through any code you have written and edit your comments.

    🎬 Make a text file for each non-scripted part of the analysis and document the steps taken, parameter settings and decisions made. You likely will not be able to complete now where you will be analysing data in semester 2, but you can write down “place holders” where possible. For example, in using Fiji to analyse images:

    -
    ```
-Images were converted to:
-Manual cropping:
-Projection type used:
-etc
-
-```
    +
    +
    +
    + +
    +
    +image_processing_in_fiji.txt +
    +
    +
    +

    Images were converted to: Manual cropping: Projection type used: etc

    +
    +

    README files

    @@ -348,43 +354,44 @@

    What should be

  • Start date, last updated date, contact information

  • Description of Project organisation

  • Software requirements

    • -

  • Data provenance

    • +

  • Data description

  • Instructions for use

    • Project title and description

    +

    The title should be descriptive and concise. It does not have to match the title of the report but why give yourself more thinking!

    +

    The description should be a brief summary of the project. It should include the aim of the project and the methods used. It should be written in plain language so that someone who is not familiar with the field can understand it. It is likely to be similar to a report abstract but with less emphasis on introduction/background and discussion and more detail on the the methods.

    Start date, last updated date, contact information

    -

    TODO

    -

    Ideally, a summary of changes with the date

    +

    We date our work so others know how old it is and when it was last updated. The very best READMEs are updated every time the project is updated so there is a “change log” at the top of the file. This is a list of changes made to the project with the date they were made. This especially useful in collaborative projects when you are not using a version control system. Sometimes, the change log is in a separate file called CHANGELOG.md. or similar.

    Description of Project organisation

    -

    TODO

    +

    Your aim is to organise your project and name files and files so that the organisation is clear to someone who has never seen it before. You are are aiming for “speaks for itself” organisation. However, you still need to give an overview of the organisation in the README. This should include the names of the folders and what is in them. You can also include a diagram of the project organisation if you like. Make sure it is easy for readers to distinguish between code, data, and outputs. Also explain your file naming convention along with any abbreviations or codes you have used.

    Software requirements

    -

    TODO

    -

    There are packages that give session information in R sessioninfo (Wickham et al. 2021) and Python (Ostblom, Joel 2019)

    -

    R:

    +

    You should list the software you used in your project. This should include the version of the software you used. This is important for reproducibility.

    +

    There are packages that give session information in R and Python

    +

    R: sessioninfo (Wickham et al. 2021)

    sessioninfo::session_info()

    -

    Python:

    +

    Python: session_info (Ostblom, Joel 2019)

    import session_info

    session_info.show()

    Fiji:

    Cite

    -
    -

    Data provenance

    -

    TODO

    +
    +

    Data description

    +

    You should describe all the data used in the project. This should include where the data came from, how it was collected, and any processing that was done to it. You may need to include links to the data sources. Include a “data dictionary” which describes the variables in the data and what they mean. This is especially important since most variable names are abbreviations or codes.

    Instructions for use

    -

    TODO

    +

    The last part of the README should be instructions for how to use it. You want to describe to reader what they need to do to recreate the results you present in your report. This should include:

      -

    • Instructions run the code, build reports, and reproduce the figures etc

      • -

    • Where to find the data, outputs

      • +

    • Brief description of the code structure especially if you have used a a mix of languages and scripts

      • +

    • Instructions to run the code and reproduce the figures or other outputs in the report

    • Any other information that needed to understand and recreate the work

    🎬 Write a README file for your project.

    @@ -395,7 +402,7 @@

    W

    All the inputs and outputs of the work

    • Original data or instructions/links to obtain the data. This includes all data in the report such as images, not just the numerical data

      • -

    • Code.

      • +

    • Code

    • Instructions for non-scripted parts of the analysis.

    • Anything generated from the code such as processed data and figures.

    • Anything generated from non-scripted parts of the analysis such as processed data and figures.

      • diff --git a/search.json b/search.json index 63f55d7..81fcd64 100644 --- a/search.json +++ b/search.json @@ -335,7 +335,7 @@ "href": "core/week-6/workshop.html", "title": "Workshop", "section": "", - "text": "In this workshop", + "text": "In this workshop we will consider how to document and curate reproducible data analyses. You will add a README to your project and start to populate it. This will include finding out how to find the software you are using.", "crumbs": [ "Core Supporting Info", "Week 6: Supporting Information 2", @@ -347,7 +347,7 @@ "href": "core/week-6/workshop.html#session-overview", "title": "Workshop", "section": "", - "text": "In this workshop", + "text": "In this workshop we will consider how to document and curate reproducible data analyses. You will add a README to your project and start to populate it. This will include finding out how to find the software you are using.", "crumbs": [ "Core Supporting Info", "Week 6: Supporting Information 2", @@ -371,7 +371,7 @@ "href": "core/week-6/workshop.html#non-scripted-parts-of-the-analysis", "title": "Workshop", "section": "Non-scripted parts of the analysis", - "text": "Non-scripted parts of the analysis\nNon-scripted parts of the analysis such as manual data cleaning or using software that does not have a script to analyse data presented in the report should be documented. This includes the steps taken, parameter settings and the decisions made. It need not be written as a narrative - you can use bullet points and be concise.\n🎬 Go through any code you have written and edit your comments.\n🎬 Make a text file for each non-scripted part of the analysis and document the steps taken, parameter settings and decisions made. You likely will not be able to complete now where you will be analysing data in semester 2, but you can write down “place holders” where possible. For example, in using Fiji to analyse images:\n```\nImages were converted to:\nManual cropping:\nProjection type used:\netc\n\n```", + "text": "Non-scripted parts of the analysis\nNon-scripted parts of the analysis such as manual data cleaning or using software that does not have a script to analyse data presented in the report should be documented. This includes the steps taken, parameter settings and the decisions made. It need not be written as a narrative - you can use bullet points and be concise.\n🎬 Go through any code you have written and edit your comments.\n🎬 Make a text file for each non-scripted part of the analysis and document the steps taken, parameter settings and decisions made. You likely will not be able to complete now where you will be analysing data in semester 2, but you can write down “place holders” where possible. For example, in using Fiji to analyse images:\n\n\n\n\n\n\nimage_processing_in_fiji.txt\n\n\n\nImages were converted to: Manual cropping: Projection type used: etc", "crumbs": [ "Core Supporting Info", "Week 6: Supporting Information 2", @@ -395,7 +395,7 @@ "href": "core/week-6/workshop.html#what-should-be-in-a-readme", "title": "Workshop", "section": "What should be in a README?", - "text": "What should be in a README?\n\nProject title and description\nStart date, last updated date, contact information\nDescription of Project organisation\nSoftware requirements\nData provenance\nInstructions for use\n\n\nProject title and description\n\n\nStart date, last updated date, contact information\nTODO\nIdeally, a summary of changes with the date\n\n\nDescription of Project organisation\nTODO\n\n\nSoftware requirements\nTODO\nThere are packages that give session information in R sessioninfo (Wickham et al. 2021) and Python (Ostblom, Joel 2019)\nR:\nsessioninfo::session_info()\nPython:\nimport session_info\nsession_info.show()\nFiji:\nCite\n\n\nData provenance\nTODO\n\n\nInstructions for use\nTODO\n\nInstructions run the code, build reports, and reproduce the figures etc\nWhere to find the data, outputs\nAny other information that needed to understand and recreate the work\n\n🎬 Write a README file for your project.", + "text": "What should be in a README?\n\nProject title and description\nStart date, last updated date, contact information\nDescription of Project organisation\nSoftware requirements\nData description\nInstructions for use\n\n\nProject title and description\nThe title should be descriptive and concise. It does not have to match the title of the report but why give yourself more thinking!\nThe description should be a brief summary of the project. It should include the aim of the project and the methods used. It should be written in plain language so that someone who is not familiar with the field can understand it. It is likely to be similar to a report abstract but with less emphasis on introduction/background and discussion and more detail on the the methods.\n\n\nStart date, last updated date, contact information\nWe date our work so others know how old it is and when it was last updated. The very best READMEs are updated every time the project is updated so there is a “change log” at the top of the file. This is a list of changes made to the project with the date they were made. This especially useful in collaborative projects when you are not using a version control system. Sometimes, the change log is in a separate file called CHANGELOG.md. or similar.\n\n\nDescription of Project organisation\nYour aim is to organise your project and name files and files so that the organisation is clear to someone who has never seen it before. You are are aiming for “speaks for itself” organisation. However, you still need to give an overview of the organisation in the README. This should include the names of the folders and what is in them. You can also include a diagram of the project organisation if you like. Make sure it is easy for readers to distinguish between code, data, and outputs. Also explain your file naming convention along with any abbreviations or codes you have used.\n\n\nSoftware requirements\nYou should list the software you used in your project. This should include the version of the software you used. This is important for reproducibility.\nThere are packages that give session information in R and Python\nR: sessioninfo (Wickham et al. 2021)\nsessioninfo::session_info()\nPython: session_info (Ostblom, Joel 2019)\nimport session_info\nsession_info.show()\nFiji:\nCite\n\n\nData description\nYou should describe all the data used in the project. This should include where the data came from, how it was collected, and any processing that was done to it. You may need to include links to the data sources. Include a “data dictionary” which describes the variables in the data and what they mean. This is especially important since most variable names are abbreviations or codes.\n\n\nInstructions for use\nThe last part of the README should be instructions for how to use it. You want to describe to reader what they need to do to recreate the results you present in your report. This should include:\n\nBrief description of the code structure especially if you have used a a mix of languages and scripts\nInstructions to run the code and reproduce the figures or other outputs in the report\nAny other information that needed to understand and recreate the work\n\n🎬 Write a README file for your project.", "crumbs": [ "Core Supporting Info", "Week 6: Supporting Information 2", @@ -407,7 +407,7 @@ "href": "core/week-6/workshop.html#what-should-be-in-supporting-information", "title": "Workshop", "section": "What should be in Supporting information", - "text": "What should be in Supporting information\nAll the inputs and outputs of the work\n\nOriginal data or instructions/links to obtain the data. This includes all data in the report such as images, not just the numerical data\nCode.\nInstructions for non-scripted parts of the analysis.\nAnything generated from the code such as processed data and figures.\nAnything generated from non-scripted parts of the analysis such as processed data and figures.\nA copy of the report it supports.\na README file", + "text": "What should be in Supporting information\nAll the inputs and outputs of the work\n\nOriginal data or instructions/links to obtain the data. This includes all data in the report such as images, not just the numerical data\nCode\nInstructions for non-scripted parts of the analysis.\nAnything generated from the code such as processed data and figures.\nAnything generated from non-scripted parts of the analysis such as processed data and figures.\nA copy of the report it supports.\na README file", "crumbs": [ "Core Supporting Info", "Week 6: Supporting Information 2", @@ -2513,7 +2513,7 @@ "href": "core/week-2-old/workshop.html#rstudio-terminal", "title": "Workshop", "section": "RStudio terminal", - "text": "RStudio terminal\nThe RStudio terminal is a convenient interface to the shell without leaving RStudio. It is useful for running commands that are not available in R. For example, you can use it to run other programs like fasqc, git, ftp, ssh\nNavigating your file system\nSeveral commands are frequently used to create, inspect, rename, and delete files and directories.\n$\nThe dollar sign is the prompt (like > on the R console), which shows us that the shell is waiting for input.\nYou can find out where you are using the pwd command, which stands for “print working directory”.\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old\n\n\nYou can find out what you can see with ls which stands for “list”.\n\nls\n\ndata\nimages\noverview.qmd\nstudy_after_workshop.html\nstudy_after_workshop.qmd\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.html\nworkshop.qmd\nworkshop.rmarkdown\nworkshop_files\n\n\nYou might have noticed that unlike R, the commands do not have brackets after them. Instead, options (or switches) are given after the command. For example, we can modify the ls command to give us more information with the -l option, which stands for “long”.\n\nls -l\n\ntotal 152\ndrwxr-xr-x 2 runner docker 4096 Nov 6 09:47 data\ndrwxr-xr-x 2 runner docker 4096 Nov 6 09:47 images\n-rw-r--r-- 1 runner docker 1597 Nov 6 09:47 overview.qmd\n-rw-r--r-- 1 runner docker 22717 Nov 6 09:52 study_after_workshop.html\n-rw-r--r-- 1 runner docker 184 Nov 6 09:47 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4807 Nov 6 09:47 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Nov 6 09:47 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 58063 Nov 6 09:47 workshop.html\n-rw-r--r-- 1 runner docker 8550 Nov 6 09:47 workshop.qmd\n-rw-r--r-- 1 runner docker 8577 Nov 6 09:52 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4096 Nov 6 09:47 workshop_files\n\n\nYou can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:\n\nls -hl\n\ntotal 152K\ndrwxr-xr-x 2 runner docker 4.0K Nov 6 09:47 data\ndrwxr-xr-x 2 runner docker 4.0K Nov 6 09:47 images\n-rw-r--r-- 1 runner docker 1.6K Nov 6 09:47 overview.qmd\n-rw-r--r-- 1 runner docker 23K Nov 6 09:52 study_after_workshop.html\n-rw-r--r-- 1 runner docker 184 Nov 6 09:47 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Nov 6 09:47 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Nov 6 09:47 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 57K Nov 6 09:47 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Nov 6 09:47 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Nov 6 09:52 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Nov 6 09:47 workshop_files\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 160K\ndrwxr-xr-x 5 runner docker 4.0K Nov 6 09:52 .\ndrwxr-xr-x 8 runner docker 4.0K Nov 6 09:52 ..\ndrwxr-xr-x 2 runner docker 4.0K Nov 6 09:47 data\ndrwxr-xr-x 2 runner docker 4.0K Nov 6 09:47 images\n-rw-r--r-- 1 runner docker 1.6K Nov 6 09:47 overview.qmd\n-rw-r--r-- 1 runner docker 23K Nov 6 09:52 study_after_workshop.html\n-rw-r--r-- 1 runner docker 184 Nov 6 09:47 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Nov 6 09:47 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Nov 6 09:47 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 57K Nov 6 09:47 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Nov 6 09:47 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Nov 6 09:52 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Nov 6 09:47 workshop_files\n\n\nYou can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:\n\ncd data\npwd\ncd ..\npwd\ncd data\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old/data\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old/data\n\n\nhead 1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nhead -20 data/1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nSOURCE 3 ORGANISM_COMMON: SPERM WHALE; \nSOURCE 4 ORGANISM_TAXID: 9755; \nSOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \nSOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; \nSOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; \nSOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15A \nKEYWDS HELICAL, GLOBULAR, ALL-HYDROGEN CONTAINING STRUCTURE, OXYGEN STORAGE- \nKEYWDS 2 TRANSPORT COMPLEX \nEXPDTA NEUTRON DIFFRACTION \nAUTHOR F.SHU,V.RAMAKRISHNAN,B.P.SCHOENBORN \nless 1cq2.pdb\nless is a program that displays the contents of a file, one page at a time. It is useful for viewing large files because it does not load the whole file into memory before displaying it. Instead, it reads and displays a few lines at a time. You can navigate forward through the file with the spacebar, and backwards with the b key. Press q to quit.\nA wildcard is a character that can be used as a substitute for any of a class of characters in a search, The most common wildcard characters are the asterisk (*) and the question mark (?).\nls *.csv\ncp stands for “copy”. You can copy a file from one directory to another by giving cp the path to the file you want to copy and the path to the destination directory.\ncp 1cq2.pdb copy_of_1cq2.pdb\ncp 1cq2.pdb ../copy_of_1cq2.pdb\ncp 1cq2.pdb ../bob.txt\nTo delete a file use the rm command, which stands for “remove”.\nrm ../bob.txt\nbut be careful because the file will be gone forever. There is no “are you sure?” or undo.\nTo move a file from one directory to another, use the mv command. mv works like cp except that it also deletes the original file.\nmv ../copy_of_1cq2.pdb .\nMake a directory\nmkdir mynewdir" + "text": "RStudio terminal\nThe RStudio terminal is a convenient interface to the shell without leaving RStudio. It is useful for running commands that are not available in R. For example, you can use it to run other programs like fasqc, git, ftp, ssh\nNavigating your file system\nSeveral commands are frequently used to create, inspect, rename, and delete files and directories.\n$\nThe dollar sign is the prompt (like > on the R console), which shows us that the shell is waiting for input.\nYou can find out where you are using the pwd command, which stands for “print working directory”.\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old\n\n\nYou can find out what you can see with ls which stands for “list”.\n\nls\n\ndata\nimages\noverview.qmd\nstudy_after_workshop.html\nstudy_after_workshop.qmd\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.html\nworkshop.qmd\nworkshop.rmarkdown\nworkshop_files\n\n\nYou might have noticed that unlike R, the commands do not have brackets after them. Instead, options (or switches) are given after the command. For example, we can modify the ls command to give us more information with the -l option, which stands for “long”.\n\nls -l\n\ntotal 152\ndrwxr-xr-x 2 runner docker 4096 Nov 6 15:29 data\ndrwxr-xr-x 2 runner docker 4096 Nov 6 15:29 images\n-rw-r--r-- 1 runner docker 1597 Nov 6 15:29 overview.qmd\n-rw-r--r-- 1 runner docker 22717 Nov 6 15:34 study_after_workshop.html\n-rw-r--r-- 1 runner docker 184 Nov 6 15:29 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4807 Nov 6 15:29 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Nov 6 15:29 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 58063 Nov 6 15:29 workshop.html\n-rw-r--r-- 1 runner docker 8550 Nov 6 15:29 workshop.qmd\n-rw-r--r-- 1 runner docker 8577 Nov 6 15:34 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4096 Nov 6 15:29 workshop_files\n\n\nYou can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:\n\nls -hl\n\ntotal 152K\ndrwxr-xr-x 2 runner docker 4.0K Nov 6 15:29 data\ndrwxr-xr-x 2 runner docker 4.0K Nov 6 15:29 images\n-rw-r--r-- 1 runner docker 1.6K Nov 6 15:29 overview.qmd\n-rw-r--r-- 1 runner docker 23K Nov 6 15:34 study_after_workshop.html\n-rw-r--r-- 1 runner docker 184 Nov 6 15:29 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Nov 6 15:29 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Nov 6 15:29 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 57K Nov 6 15:29 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Nov 6 15:29 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Nov 6 15:34 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Nov 6 15:29 workshop_files\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 160K\ndrwxr-xr-x 5 runner docker 4.0K Nov 6 15:34 .\ndrwxr-xr-x 8 runner docker 4.0K Nov 6 15:34 ..\ndrwxr-xr-x 2 runner docker 4.0K Nov 6 15:29 data\ndrwxr-xr-x 2 runner docker 4.0K Nov 6 15:29 images\n-rw-r--r-- 1 runner docker 1.6K Nov 6 15:29 overview.qmd\n-rw-r--r-- 1 runner docker 23K Nov 6 15:34 study_after_workshop.html\n-rw-r--r-- 1 runner docker 184 Nov 6 15:29 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Nov 6 15:29 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13K Nov 6 15:29 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 57K Nov 6 15:29 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Nov 6 15:29 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Nov 6 15:34 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Nov 6 15:29 workshop_files\n\n\nYou can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:\n\ncd data\npwd\ncd ..\npwd\ncd data\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old/data\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old/data\n\n\nhead 1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nhead -20 data/1cq2.pdb\nHEADER OXYGEN STORAGE/TRANSPORT 04-AUG-99 1CQ2 \nTITLE NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 \nTITLE 2 ANGSTROM \nCOMPND MOL_ID: 1; \nCOMPND 2 MOLECULE: MYOGLOBIN; \nCOMPND 3 CHAIN: A; \nCOMPND 4 ENGINEERED: YES; \nCOMPND 5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED \nSOURCE MOL_ID: 1; \nSOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; \nSOURCE 3 ORGANISM_COMMON: SPERM WHALE; \nSOURCE 4 ORGANISM_TAXID: 9755; \nSOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \nSOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; \nSOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; \nSOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15A \nKEYWDS HELICAL, GLOBULAR, ALL-HYDROGEN CONTAINING STRUCTURE, OXYGEN STORAGE- \nKEYWDS 2 TRANSPORT COMPLEX \nEXPDTA NEUTRON DIFFRACTION \nAUTHOR F.SHU,V.RAMAKRISHNAN,B.P.SCHOENBORN \nless 1cq2.pdb\nless is a program that displays the contents of a file, one page at a time. It is useful for viewing large files because it does not load the whole file into memory before displaying it. Instead, it reads and displays a few lines at a time. You can navigate forward through the file with the spacebar, and backwards with the b key. Press q to quit.\nA wildcard is a character that can be used as a substitute for any of a class of characters in a search, The most common wildcard characters are the asterisk (*) and the question mark (?).\nls *.csv\ncp stands for “copy”. You can copy a file from one directory to another by giving cp the path to the file you want to copy and the path to the destination directory.\ncp 1cq2.pdb copy_of_1cq2.pdb\ncp 1cq2.pdb ../copy_of_1cq2.pdb\ncp 1cq2.pdb ../bob.txt\nTo delete a file use the rm command, which stands for “remove”.\nrm ../bob.txt\nbut be careful because the file will be gone forever. There is no “are you sure?” or undo.\nTo move a file from one directory to another, use the mv command. mv works like cp except that it also deletes the original file.\nmv ../copy_of_1cq2.pdb .\nMake a directory\nmkdir mynewdir" }, { "objectID": "core/week-2-old/workshop.html#differences-between-r-and-python", diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-73-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-73-1.png index aaf187f..062336f 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-73-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-73-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-74-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-74-1.png index bf6c276..2285f98 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-74-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-74-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-80-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-80-1.png index ccead38..7c4395b 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-80-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-80-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-81-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-81-1.png index 9af2c38..3beaf83 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-81-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-81-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-87-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-87-1.png index 831a3fc..b444480 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-87-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-87-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-88-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-88-1.png index cedbc00..3fd76f7 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-88-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-88-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-89-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-89-1.png index eb1a756..db4e97d 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-89-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-89-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-95-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-95-1.png index 13768d0..f70dd02 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-95-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-95-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-96-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-96-1.png index 28e57a2..c48c826 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-96-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-96-1.png differ