Create list of resources for dissemination

[sjspielman]

As part of this workshop, we would like to provide links to useful resources on reproducibility topics. This could take a variety of formats, including a stand-alone "cheatsheet" or an actual page on the workshop website.

Some resources we have already identified as useful here include:

• Reproducibility 4 Everyone
  • Great collection of resources including slides for a core course that we can reuse.
  • Slides are CC-BY: 26-10-2021_template_main-slides_full
• ITCR course on reproducibility by our friend Candace Savonen (with our earlier input)
  • Note extensive references: https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/references.html
  • Advanced reproducibility
• Nature collections on reproducibility: https://www.nature.com/collections/prbfkwmwvz
• Bioinformatics Data Skills, Vince Buffalo (this is a bit more advanced)
• The Turing Way Guide to Reproducible Research
• Carpentries modules:
  • Shell for genomics
  • Project organization for genomics
  • Git
  • Shell (software carpentries version)
• Good enough practices in scientific computing, Wilson et al.
• PLOS Ten Simple Rules of varying usefulness
  • Ten Simple Rules for Reproducible Computational Research
  • Ten simple rules for writing Dockerfiles for reproducible data science
  • Ten Simple Rules for Taking Advantage of Git and GitHub
  • Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
  • Ten simple rules for quick and dirty scientific programming
• Leaning bioinformatics at Home, compiled by Harvard Informatics, specifically: Git and version control links
• Introductions to UNIX
  • Bootcamp
  • UNIX Tutorial for Beginners
  • https://rafalab.github.io/dsbook/unix.html Unix Chapter
  • Big Book of R compiled by Oscar Baruffa (contains good links to reproducible skills practices)
• Let’s not forget experimentalists: https://www.protocols.io/
• https://codeocean.com/
• Reproducibility standards for machine learning in the life sciences

[jaclyn-taroni]

This is next sprint or the one after that IMO, will label it as such.

[jaclyn-taroni]

@Jen-OMalley I am going to assign you to this issue. For the most part, you'll need to turn the list of resources above into a markdown document in docs/ per #6

[Jen-OMalley]

This list now exists in /docs. Going to close the issue.