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Bioinformatics learning resources for undergrads and grad students

Bioinformatics analysis skills are necessary across biological research fields right now. Generally, undergratuate curriculum does not introduce these skills. Graduate students need to learn thse skills. There are solutions! We have training opportunities, especially here at UC Davis! Undergradates who already have these skills will be in high demand in both graduate programs and jobs.

There's a trifecta of skills that bioinformaticians or researchers using bioinformatics skills to analyze nucleic acid sequencing data typically learn:

  • bash, commandline UNIX/Linux operating system file management/navigation and scripting
  • Python, programming language for scripting, visualizations and text wrangling
  • R, programming language for statistics and visualizations

Here are a list of resources to try on your own. I'm happy to provide help and answer questions if you run into any snags.

  1. Rosalind
    • Beginning Python
    • List of bioinformatics-related problems
    • Some of these take just a coffee-break period of time to solve. This might be a fun thing for the lab to do?
    • They give you an intro to the problem, a question and example of required output.
    • You have to program a solution to the problem, submit it, and it checks your script to see if it produces the "right" answer.
    • You can receive badges for problems solved correctly! (I've solved 32 problems, anyone want to challenge me?)
    • I see this as sortof like a journal club. Anyone want to get together and hack on some code? See if group can come up with the right answer, talk about process of coding an answer.
  2. ANGUS (Analysis of Next Generation Sequencing) workshop tutorials from 2-week summer course at UC Davis. These tutorials include SNP calling, genome/transcriptome assembly, using Jupyter notebooks, differential expression analysis, GWAS, etc.
  3. Commandline bootcamp: I see this as the first step for learning skills. If you can get through these 28 lessons, you have the beginning base of skills for how to navigate the commandline.
  4. R course at UCD, GGE course
  5. semester-long bioninfo course at UF
  6. Introduction to R, 1 week intro R course taught by Michael Koontz and Ryan Peek at DIBSI, 2017
  7. DIB training program at UCD