Objectives
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.

Design

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.
usb_workshop.jpg

Slides and material

  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”.

Date and location

- 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.