New series on scientific computing skills.

I’ll be starting a new blog series on topics related to scientific computing skills.

I teach part of a graduate course called “Advanced Bioinformatics”. My part of the course is really more about how to go about “reproducible research” for computational biology.

I will use these posts as a place to collect my thoughts. The plan is that I’ll assign these posts as readings in the next iterations of the class. Eventually, I will aggregate them into an open-source “book” that will live online.

I will be addressing the following topics:

• The importance of environment isolation.
• Different tools for isolating your working environments:
  • conda
  • Python virtual environments
  • packrat
  • Virtual machines such as VirtualBox
  • Docker
  • distrobox
  • singularity for deploying things to HPC systems.
  • etc.

I’ll try to address the pros and cons of various methods. The goal is to give students a flavor of what is possible and to let them find their own way to work productively.