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:
- Python virtual environments
- Virtual machines such as VirtualBox
- singularity for deploying things to HPC systems.
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.