# Hands-on bioinformatics graduate courses at UC Davis

6/18/2023

The below courses and workshops should all be accessible to graduate students!

Contact Titus Brown at [e-mail] with additional information and updates ;).

## Graduate Courses

Alex Nord and Rishi Chaudhuri teach [NSC 219](https://catalog.ucdavis.edu/courses-subject-code/nsc/) (annual Winter) - think statistics, R programming, and basic bioinformatic concepts. More project focused/bring own data!

Titus Brown teaches [GGG 201b (Intro Genomics) lab](https://hackmd.io/5ue0x068SvezhwQgjhjx-A?view) - microbial genome mapping/variant calling, assembly, and RNAseq.

Titus Brown also teaches [GGG 298, Tools for data-intensive research](https://hackmd.io/Y3aIAoJsR_y-F-e2_UqZHw?view) - git/github, snakemake, conda, slurm, UNIX shell.

## Undergraduate Courses

BIS 15L? R and GitHub?

[STS 115: DATA SENSE & EXPLORATION – CRITICAL STORYTELLING WITH ANALYSIS (PART 1)](https://datalab.ucdavis.edu/2022/09/18/winter-2024-course-announcement-adventures/)

[STS 195: RESEARCH IN DATA STUDIES (PART 2)](https://datalab.ucdavis.edu/2022/09/18/winter-2024-course-announcement-adventures/)

Julin Maloof offers [BIS180L](http://jnmaloof.github.io/BIS180L_web/course_schedule/) (the capstone lab for the genomics part of the genetics and genomics undergraduate major).
* Julin estimates that 1/5 to 1/4 of the students are graduate students.

Joel Ledford offers B15L (intro programming for biologists) which has a large bioinformatics component.

Dan Runcie teaches an undergrad course ([BIT 150](https://www.coursicle.com/ucdavis/courses/BIT/150/)) that may be open to grad students.

Ian Korf teaches MCB182 - this has some theoretical bioinformatics content (alignment, blast, K-A stats, PWMs, prosite patterns, hmms).

Ian Korf also teaches MCB185 - this is a programming course with some programming examples from biology and bioinformatics.

Brenna Henn teaches ANT 157L: Advanced Human Genetics Lab. This is a computer lab course in human genetics and genomics that emphasizes hands-on engagement with human genetic/genomic data. Ancestry analysis, pedigrees, de novo Mendelian disease.

[ECS124: Theory & Practice of Bioinformatics](https://cs.ucdavis.edu/schedules-classes/ecs-124-theory-practice-bioinformatics) is a more computer science-focused bioinformatics course. Half bio-related major and half CS major undergrads in the class usually. This course mainly focuses on algorithm analysis (big o running time). It has topics such as Sequence alignment, Database Search, Machine Learning, Phylogenetics).There are major coding assignments using perl (C language background is prefered).

Justin Siegel teaches CHE 130B (offered Winter and Spring), computational drug design. The computer lab features protein structure and feature visualization, conservation analysis, molecule building, chemoinformatics, and protein-ligand binding predictions. Commonly attended by graduates and does not really require 130A despite what course catalog says (historical requirement)

## Workshops

The Genome Center Bioinformatics Core offers many workshops via [their training program](https://bioinformatics.ucdavis.edu/training). These are not free, however.

The DataLab offers many free workshops via [their training program](https://datalab.ucdavis.edu/workshops/). However, they are typically not focused on bioinformatics but more on data science.

## Appendix: lapsed and/or occasional workshops

Titus Brown taught [ANGUS, a two week workshop on NGS analysis](https://angus.readthedocs.io/en/2019/) for 10 years, but COVID killed it off. (It was not free, either.)

Titus Brown is trying out a new [Collaboratory workshop model](https://hackmd.io/ONG4bcrQSxi2kdR_ADTp2A?view) for students who already have successful analysis workflows and want to build on them/improve them. (June 2023)