UCSC Summer Short Course in Bioinformatics and Programming resource repository

View the Project on GitHub rreggiar/ucsc_scbc_2022

Welcome to the 2023 UCSC Summer Short Course in Bioinformatics and Coding

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 LinkedIn
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

Background and Setup resources

Lecture 00a: UCSC ITS Virtual Machine access and intro guide

Lecture 00b: Bioinformatics, Biology, and Data

Command Line and Bash

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 02: Intro to Python

Lecture 03: Conditionals and Branching - Download: ipynb

Lecture 04: Functions

Lecture 05: ORF Finder
- Download: ipnyb
- New Fasta download

Lecture 06: ORF Finder Continued
- Download: ipnyb

Other Resources

UCSC Genome Browser

More Bioinformatics challenges: Rosalind