Develop getting started documentation/materials

[korikuzma]

Submitter Name

Alex Wagner (@ahwagner)

Submitter Affiliation

Nationwide Children's Hospital

Requested By

biocommons community

Additional Submitter Details

No response

Lead(s)

LEAD NEEDED

biocommons Repo

general

Project Details

The goal for this project is to update or develop documentation that support new users. The exact goals will be decided by those who participate in this project based on the skills available and specific outcomes that they identify. A few suggestions:

• Install seqrepo, uta, hgvs, and anyvar from scratch. Collect documentation errors, gaps, and ambiguities as issues, and consider addressing those issues.
• Update and/or write new jupyter notebooks that demonstrate each component.
• Reconsider documentation organization within and across projects.

It would be nice to have something good for non technical folks and people just getting started with a biocommons project. Maybe hands on tutorials similar to the notebooks in vrs-python?

@ahwagner :
It would be nice if the biocommons utils had pages similar to phenopackets.org (links to vision, people involved, readthedocs etc). Maybe could have this as pages on biocommons.org.

Can we parallel hgvs documentation on readthedocs for the other tools? Quick start is amazing!

Skill Level

Newcomer

Required Skills

Python, Jupyter Notebooks, Read the Docs

[korikuzma]

There is a nice figure on the biocommons website that show the majority of biocommons projects and how they interact with each other (see here). It would be nice to include more text on this.

[ccaitlingo]

hgvs has several helpful walk-throughs here. creating-a-variant, hgvs-poster, and using-hgvs look especially good, although they might still need more context.

[marisolcontreras1]

Interested in learning

[katiestahl]

interested in helping with this since I remember having a lot of issues when I was getting started, and I used different instructions from the Readme. Additionally, I recall running into environmental issues that were unique to users setting up biocommons projects (uta, seqrepo come to mind) using a Mac with Apple M1 chips.

Would also be interested in leading/co-leading this issue