Bioinformatics for biologist workshop

This workshop is a practical introduction to some basic bioinformatics tools for audience with little computational skills. The participants will have hands-on experience with simple, toy-example data. The following material was used in 2015 in two sections of the workshop in The University of Texas Health Science Center at San Antonio.

Each participant is expected to bring a laptop or have access to a computer during the workshop. They install Bio-Linux on their computes, which facilitates running simple analysis on toy-example data. To save time, each participant is provided with a USB flash drive that contains necessary files for installing Bio-Linux and also some example data.

1. Guidelines for installing BioLinux on Mac OS X or Windows using a virtual machine [ppt, pdf ].
2. The zipped folder for session 1, includes sample data, a script for installing Salmon on BioLinux, a cheat sheet, etc.
3. The main presentation in session 1:
   Part 1: BioLinux and Mapping RNASeq (Samlon) [ppt, pdf ]
   Part 2: R and Differential expression analysis (DESeq2) [ppt, pdf ]
   Part 3: Finding gene homologs (Ensembl Biomart) and Pathway and network analysis (GeneMANIA & InnateDB) [ppt, pdf ]
4. The zipped folder for session 1, includes sample protein MS data, a cheat sheet, etc.
5. The main presentation in session 2:
   Part 1: Pathway and functional analyses on protein MS results (String manipulation in R, InnateDB, MouseMine) [ppt, pdf ]
   Part 2: Sample size for RNA Seq experiments and DNA methylation (minfi) [ppt, pdf ]

Additional resources
Similar workshops and online courses are listed at “How to begin learning bioinformatics?”

- Salmon webpage. It is useful for mapping and analyzing RNAseq data.
- Titus Brown's tutorials, more advanced RNAseq analysis using Salmon on Amazon Web Services.
- A collection of useful tools for functional and pathway analysis.
- Stephen Turner's “List of Bioinformatics Workshops and Training Resources”.
- Evelien Bunnik had a workshop on multiomics data analysis in Spring 2020 in UTHSC-SA.
- Dhireesha Kudithipudi, the director of the Neuromorphic AI Lab, organized an AI Summit at UTSA in Nov 2019.

- The first session held on 20 Nov 2015 at the University of Texas Health Science Center - San Antonio.
- The second session held on 25 March 2016 at the University of Texas Health Science Center - San Antonio.