Sara's writing samples

Described below:

• Gen3 platform documentation update
• VA Data Commons documentation
• Nextflow in BRH workspaces
• Example files uploaded to this repo

Some examples online

In general, all of these documents were created as Markdown files using VS Code, then Material for MkDocs was used to build documentation from the Markdown files. The static site is hosted in GitHub Pages. All of these online documentations are from 2023-2025.

Gen3 platform documentation update

The new documentation was created by converting the old documentation from Hugo or Docusaurus files to Markdown, then they were reorganized and built into MkDocs documentation. The Helm documentation was integrated into the Gen3 Platform documentation, and sections were prioritized for updating. This process took about 5 months with 2 people working on it part-time.

• Old Gen3 platform docs site (in Hugo): https://gen3.org/resources/
• Old Gen3 Helm docs site (in Docusaurus): https://old.docs.gen3.org/
• New Gen3 platform docs site (in MkDocs, with Helm integrated): https://docs.gen3.org/
• I had the most impact on the Helm section of the Gen3 documentation: https://docs.gen3.org/gen3-resources/operator-guide/helm/, and particularly these two guides:
  • the guide to minimum local Gen3 deployment with Helm
  • the guide to configuration for Gen3 Helm

VA Data Commons documentation

The new documentation was created by converting the old Sphynx documentation to MkDocs, adding additional tool context and general instructions for logging in, and expanding the instructions and updating the screenshots for several of the apps. I am the only person who updated the documentation from the old content.

• I updated from these old VADC docs (in Sphynx): https://va.data-commons.org/dashboard/Public/documentation/index.html
• Here are the new VADC docs I created (in MkDocs): https://uc-cdis.github.io/vadc-mkdocs/

Nextflow in BRH workspaces

I helped to convert all of the BRH documentation to MkDocs and expand several sections. However, the section on which I had the most significant impact was the documentation for our beta-testers to use for testing our Nextflow execution in the workspace. With the exception of the first page, I created these documents de novo after working through the process myself.

• I created these docs to help beta-testers understand how to use Nextflow and create security-compliant containers for use in BRH Workspaces (note this link is the first of several pages): https://uc-cdis.github.io/BRH-documentation/nextflow-getting-started/

Example files uploaded to this repo

(listed from most recent to oldest)

• 2024-install-in-local-virtual-envt.md: This file was created in 2024 to help colleagues understand how and why to use a virtual environment when installing software. I created this entirely myself.
• 2017-ACCESS-grant-proposal.pdf: This is a funded grant proposal that I helped to write with several colleagues. I did not write the first draft, but I helped with revisions and editing.
• 2012-selected-bridges-grant-pieces: This folder holds several grant pieces from a funded grant proposal. I wrote the initial draft based on my own program vision, and revised based on comments from several readers.
• 2008-idiots-guide-to-BEAST.pdf: This is internal documentation I created to help members of my postdoc lab after I taught myself how to use the BEAST suite of software. I created this myself, except for sections that indicate they were taken from the BEAST manual.
• 2008-cub-scout-pizzazz.pdf: This is a training document I created to help other Scout volunteers to understand how to approach the Cub Scouts program in an engaging way for the kids. I wrote this all de novo (except the skits and songs and things -- I did not invent those).