Purpose:

I created this repository to share some of the materials and opinions I have generated over the years working as a bioinformatician in Pat Edger's lab and as an intern at Syngenta.

Descriptions:

Presentations:

• Best Practices for High-Quality Data Science
  • Purpose: This was created for the 2024 MSU Plant Genomics REU as a way to introduce fundamental concepts of reproducibility, data management, code anti-patterns, and version control. My brother was fundamental in introducing many topics such as version control, Makefiles, TeX, and much more; I wish I had learned or been aware of these topics much sooner in life as they have made my job a lot easier and more fulfilling, it is my hope that I can do the same for the REU students.
  • Audience: The audience is a mixed group of undergraduates with minimal research experience, and little to no knowledge of bioinformatics.

Templates:

• pull_request_pattern_form.md
  • This is just a small sample document that I like to use for pull-requests on GitHub/GitLab.
• regular_document.tex
  • I like to use this for generating small reports in LaTeX.
• template_python.py
  • This is a good starter template for bioinformatics work, it uses argparse and the logging module. Primary purpose is to provide this to beginner bioinformaticians as a skeleton.
• weekly_report.md
  • I originally created this to facilitate communication between an undergraduate I was mentoring while in Pat's lab. I feel like it is particularly useful when working on complex coding projects that have multiple moving parts. I also used this while at Syngenta to provide regular updates to my manager and team in lieu of meetings. The document is also good for keeping a track record of planned and completed work.