Here I am accumulating a list of links to help students or others interested in developing some skills in computational biology. I’ve divided the list into two sections. Move on to the advanced when you’ve completed the basic section. Skills you should get, and resources to help you get them:


Basic Resources

1. Git and GitHub

GitHub is the center of development in our group. Git can feel overwhelming, but it is best to just dive in and it will be worth your time.

2. Markdown

Markdown is an easy-to-read, easy-to-write plain text format, which converts to HTML for web viewing.

3. R

R is unparalleled for statistical packages and powerful data visualization and analysis projects.

4. Bioconductor

5. Unix command line

6. Python

8. High-performance computing and SLURM


Advanced Resources

1. Git and GitHub

2. Markdown

3. R

4. Bioconductor

5. Unix command line

6. Python

7. Programming concepts

8. High-performance computing and SLURM

SLURM (the Simple Linux Utility for Resource Management) is the cluster workload manager used by Rivanna at UVA and at many high-performance clusters elsewhere. If you need to submit jobs to a cluster, learn SLURM.

9. Writing

10. Python Sphinx

Sphinx is a documentation generator. It is useful because it allows you to easily produce a really nice, web-linked documentation system from in-code comments, which saves from you having to document code twice. The cost is: you must write your comments in a sphinx-compatible formats, which requires some initial investment and ongoing discipline. In the long run, this investment will pay off, as it will become easy to generate nice documentation for your software.

Because easy-to-use documentation is vital for sharing code, we will be using Sphinx to document python packages we produce, so please invest a few minutes in understanding the system so you can navigate and contribute to documentation.

You’ll have to install it, and the theme we use http://www.sphinx-doc.org/en/stable/install.html

sudo apt-get install python-sphinx
sudo apt-get install python-pip
pip install --user sphinx_rtd_theme

11. Writing R/Bioconductor packages

Other bioinformatics resources from Stephen Turner, and for workshops on these topics, check out bioconnector at UVA.