UCSC Summer Short Course in Bioinformatics and Programming resource repository
This free course is an initiative of the UCSC Genomics Institute Committee on Diversity, Equity, and Inclusion, and was created in order to reduce barriers to learning foundational skills in computational biology. Our goal is to make bioinformatics more accessible and inclusive, and to increase access for under-represented and under-resourced communities.
Here you’ll find slides, code, and all the other material we are using to explore the world of bioinformatics.
Contact: Roman Reggiardo | rreggiar AT ucsc.edu |
Vikas Peddu | vpeddu AT ucsc.edu | 2023 Lead Instructor |
Daniel Arriaza | dwarriaz AT ucsc.edu | 2023 Co-instructor |
Here is the course material in HTML and/or PDF slide format. If you need to go from HTML (website-like interaction) please print to PDF from your browser. Recommended to open these in a new tab: ctrl- or cmd- click
Protected: Summer 2023 Lecture Recordings
Lecture 00a: UCSC ITS Virtual Machine access and intro guide
Lecture 00b: Bioinformatics, Biology, and Data
Lecture 01a: File explorer to command line
Lecture 01b: Command line to Bash
Lecture 01c: Scripting for Automation
- process_lab_data.sh
Project 01: Making a command line tool – Iterative Variant Calling
- call_variant.sh
Lecture 03: Conditionals and Branching - Download: ipynb
Lecture 05: ORF Finder
- Download: ipnyb
- New Fasta download
Lecture 06: ORF Finder Continued
- Download: ipnyb