Building a Cloud-SPAN community of practice

[evelyngreeves]

Project Lead: @evelyngreeves Mentor: @annefou

Welcome to OLS-5! This issue will be used to track your project and progress during the program. Please use this checklist over the next few weeks as you start Open Life Science program :tada:.

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Week 1 (week starting 28 February 2022): Meet your mentor!

• [x] Meet mentor for 30 minutes

• [x] Create an account on GitHub

• [x] Check if you have access to the HackMD notes set up for your meetings with your mentor

• [ ] Prepare to meet your mentor(s) by completing a short homework provided in your shared notes

• [x] Complete your own copy of the open leadership self-assessment and share it to your mentor If you're a group, each teammate should complete this assessment individually. This is here to help you set your own personal goals during the program. No need to share your results, but be ready to share your thoughts with your mentor.

• [x] Make sure you know when and how you'll be meeting with your mentor.

Before Week 2 (week starting 7 March 2022): Cohort Call (Welcome to Open Life Science!)

• [ ] Attend call or catch up via YouTube
• [x] Create an issue on the OLS-5 GitHub repository for your OLS work and share the link to your mentor.
• [x] Draft a brief vision statement using your goals This lesson from the Open Leadership Training Series (OLTS) might be helpful
• [x] Leave a comment on this issue with your draft vision statement & be ready to share this on the call
• [x] Check the Syllabus for notes and connection info for all the cohort calls.

Before Week 3 (week starting 14 March 2022): Meet your mentor!

• [x] Meet mentor
• [ ] Look up two other projects and comment on their issues with feedback on their vision statement
• [ ] Complete this compare and contrast assignment about current and desired community interactions and value exchanges
• [x] Complete your Open Canvas (instructions, canvas)
• [x] Share a link to your Open Canvas in your GitHub issue
• [ ] Start your Roadmap
• [ ] Comment on your issue with your draft Roadmap
• [x] Suggest a cohort name at the bottom of the shared notes and vote on your favorite with a +1

Before Week 4: Cohort Call (Tooling and roadmapping for Open projects)

• [x] Attend call or catch up via YouTube
• [ ] Look up two other projects and comment on their issues with feedback on their open canvas.

Week 5 and later

• [ ] Meet mentor
• [x] Create a GitHub repository for your project
• [x] Add the link to your repository in your issue My wider project already has multiple repositories but this repository is specifically built with our community in mind (a major aspect of my OLS project).
• [x] Use your canvas to start writing a README.md file, or landing page, for your project
• [ ] Link to your README in a comment on this issue
• [x] Add an open license to your repository as a file called LICENSE.md
• [x] Add a Code of Conduct to your repository as a file called CODE_OF_CONDUCT.md
• [ ] Invite new contributors to into your work!

This issue is here to help you keep track of work as you start Open Life Science program. Please refer to the OLS-5 Syllabus for more detailed weekly notes and assignments past week 4.

Week 6

• [ ] Attend call or catch up via YouTube

Week 7

• [ ] Meet mentor

Week 8

• [ ] Attend call or catch up via YouTube

Week 9

• [ ] Meet mentor

Week 10

• [ ] Attend call or catch up via YouTube

Week 11

• [ ] Meet mentor

Week 12

• [ ] Attend call or catch up via YouTube

Week 13

• [ ] Meet mentor

Week 14

• [ ] Attend call or catch up via YouTube

Week 15

• [ ] Meet mentor

[evelyngreeves]

Vision statement (first draft!): I’m working with the Cloud-SPAN team and environmental biotechnology community to develop training resources and build a community of practice to help early career researchers access the HPC resources needed for big data 'omics.

[AleCandian]

Hi @evelyngreeves, nice statement! I have a (maybe naïve) question: what is 'omics? :) Also I am curious: in my experience the access to HPC resources is granted through (often) competitive applications. Do you plan to create training for Early Career Researchers on how to write these proposals? Or are you focusing on training them on how to use HPC and optimising their software for this specific architecture?

[evelyngreeves]

Thanks @AleCandian, and good question! In this case "omics" is usually referring to "genomics" (aka studying/mapping DNA) but within biology it's also possible to study proteomics (proteins), transcriptomics (RNA), metabolomics (metabolites) etc. All of the "omics" involve large datasets and some similar analysis techniques, which is why they are often grouped together. They can also be linked! So a researcher might analyse multiple omics datasets to understand their subject better.

At the moment the focus is on using HPC and optimising software. We're using cloud-based containerised instances via Amazon Web Services, so the application process is less relevant. Lots of our target audience will only need to perform a discrete set of analyses using HPC (as part of a much wider data analysis workflow), so the cloud is a good option for them. We are hoping to extend our training to include institutional/regional HPC clusters too, so writing proposals is a very good point to consider - thank you 😄 Although, it's worth noting that many institutions in the UK have their own HPC cluster (or share one with other institutions locally) which have a minimal application process for their own researchers and are generally large enough for basic analyses.

Thank you for your feedback! I'll check yours out soon.

[evelyngreeves]

Here's a link to my open canvas for the project: https://docs.google.com/presentation/d/1o7i8A8vGHuhCyfM_I9xKuYh5b8nHk6ZlCZuidMMm8uI/edit?usp=sharing

Would love to hear others' feedback on it!