From 95f215b14671720739d8fe7eda18fbe55fd6c0f0 Mon Sep 17 00:00:00 2001 From: Emma Rand <7593411+3mmaRand@users.noreply.github.com> Date: Wed, 18 May 2022 09:00:01 +0100 Subject: [PATCH 1/3] Update index.md --- index.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/index.md b/index.md index c50dd68..10e35ba 100644 --- a/index.md +++ b/index.md @@ -4,7 +4,9 @@ [Cloud-SPAN](https://cloud-span.york.ac.uk) is a project run by the Department of Biology at the University of York with the aim to training researchers in the experimental design and analysis of 'omics data using cloud-based High Performance Computing (HPC) resources. -This course teaches how to create and manage your own Cloud-SPAN Amazon Web Services (AWS) **instance**, which is a Linux virtual machine configured with 'omics data and software analysis tools. The instance you will create is the same instance that is used in the Cloud-SPAN courses [Prenomics](https://cloud-span.github.io/prenomics00-intro/) and [Genomics](https://cloud-span.github.io/00genomics). As such it is an excellent vehicle for those who want to self-study those courses or have taken them and now want to practice further or with other materials in their own time. +This course teaches how to create and manage your own Cloud-SPAN Amazon Web Services (AWS) **instance**, which is a Linux virtual machine configured with 'omics data and software analysis tools. The instance you will create is the same instance that is used in the Cloud-SPAN courses [Prenomics](https://cloud-span.github.io/prenomics00-intro/) and [Genomics](https://cloud-span.github.io/00genomics). + +If you attend tutor-led editions of Cloud-SPAN's [Prenomics](https://cloud-span.github.io/prenomics00-intro/) and [Genomics](https://cloud-span.github.io/00genomics) courses you do not need to create your own instance. We will do that for you! But if would like to practice afterwards, or study the courses in your own time, you will need to create an instance first. You will learn (1) how to open and configure your AWS account, which will enable you to use any AWS service; (2) how to create and manage (start, stop and terminate) your instance; and (3) the cost of using your instance. @@ -46,10 +48,10 @@ The largest cloud providers at the time of writing in terms of market share are If you need some help to complete this course, or would like to discuss further some of its topics, you can join our weekly drop-in sessions held on Thursdays at 3pm. Please follow this link to our Blackboard [Drop-in Sessions](something). ## Where to go from here +Once you have created your instance you will will be able to follow Cloud-SPAN's [Prenomics](https://cloud-span.github.io/prenomics00-intro/) and [Genomics](https://cloud-span.github.io/00genomics) modules. -| Resource | Description | +| Module | Description | | -------------------------- | ---------| -| [Installing Git Bash](https://cloud-span.github.io/prenomics00-intro/setup.html)| Only Windows users need these instructions to install the Git Bash program which is needed to login to their instance. (Linux and MacOs users should use the `terminal` program to login to their instance.)| -| [Logging to your instance](https://cloud-span.github.io/prenomics01-file-directories/02-logging-onto-cloud/) | Instructions to login to your instance (a lesson from the Cloud-SPAN Prenomics course).| -| [Using the Shell](https://cloud-span.github.io/prenomics02-command-line/) | Instructions for you to use your instance through the command line interface, also known as the Shell (a lesson from the Cloud-SPAN Prenomics course).| -| [Running 'omics applications](https://cloud-span.github.io/00genomics/)| Examples of using 'omics data and applications (the foundation Cloud-SPAN Genomics course). | +| [Prenomics](https://cloud-span.github.io/prenomics00-intro/)| Prenomics is a 4 - 6 hour module that teaches the basics of command-line programming, including: (1) file directory structure, (2) use of command-line utilities to connect to and use cloud computing and storage resources and (3) basic shell commands for file navigation and basic script writing. It is designed to prepare people for [Genomics](https://cloud-span.github.io/00genomics) but, depending on previous experience, you may not need it. There is short (~5 minutes) [Self-assessment Quiz](https://shiny.york.ac.uk/er13/prenomics-quiz/#section-why) to help you decide if you would benefit from attending Prenomics before the Genomics.| +| [Genomics](https://cloud-span.github.io/00genomics/) | Genomics is a 8 - 12 hour module that teaches data management and analysis for genomics research including: (1) best practices for organization of bioinformatics projects and data, (2) use of command-line utilities to connect to and use cloud computing and storage resources, (3) use of command-line tools for data preparation, (4) use of command-line tools to analyze sequence quality and perform and automate variant calling. | + From a946e4e81ce272b19a0ed34614d3788914fd5c1d Mon Sep 17 00:00:00 2001 From: Emma Rand <7593411+3mmaRand@users.noreply.github.com> Date: Wed, 18 May 2022 09:01:52 +0100 Subject: [PATCH 2/3] Update index.md --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index 10e35ba..6f29e10 100644 --- a/index.md +++ b/index.md @@ -20,7 +20,7 @@ The course is designed for 2-3 hours of self-study. > > Tablets and mobile phones are not suitable for taking the course, as the screenshots that are shown through the course were taken from desktop screens. > -> Please note that this course does **not** cover **using your instance**: tasks such as managing the data in your instance or running genomics analyses are covered in the [Prenomics](https://cloud-span.github.io/prenomics00-intro/) and [Genomics](https://cloud-span.github.io/genomics01-intro) courses. The relevant sections of these courses are below under the heading **Where to go from here.** +> Please note that this course does **not** cover **using your instance**: tasks such as managing the data in your instance or running genomics analyses are covered in the [Prenomics](https://cloud-span.github.io/prenomics00-intro/) and [Genomics](https://cloud-span.github.io/genomics01-intro). {: .prereq} ## Background From 4ac0479db2749e96b3e510cfc761c01d67923947 Mon Sep 17 00:00:00 2001 From: Emma Rand <7593411+3mmaRand@users.noreply.github.com> Date: Fri, 20 May 2022 08:02:06 +0100 Subject: [PATCH 3/3] Update index.md --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index 6f29e10..3c7e3e8 100644 --- a/index.md +++ b/index.md @@ -40,7 +40,7 @@ The largest cloud providers at the time of writing in terms of market share are | Lesson | Overview | | -------------------------- | ---------| | [Open your AWS account](https://cloud-span.github.io/create-aws-instance-1-open-account/) | Learn how to open and configure your AWS account, which enables you to use AWS services.| -| [Create and manage your AWS instance](https://cloud-span.github.io/create-aws-instance-2-manage-instance/)| Learn how to create, start, stop, and terminate your instance using the AWS Console, and how to login to your instance. See section below `Where to go from here` for related resources. | +| [Create and manage your AWS instance](https://cloud-span.github.io/create-aws-instance-2-manage-instance/)| Learn how to create, start, stop, and terminate your instance using the AWS Console, and how to login to your instance. | | [AWS Costs Explained](https://cloud-span.github.io/create-aws-instance-3-costs-explained/) | Learn about the costs of using your Cloud-SPAN AWS instance, the AWS Free Tier and Research Credits available.| ## Help and Support