Bioinformatics

From LA Biohackers

We will be offering seminars on bioinformatics and how it can be used in DIYbio. Our current project lies in using GEO as a source for raw gene expression data and utilizing Amazon's cloud to do analysis on an as needed basis.

Contents 1 Tutorials 1.1 General 1.2 R/BioConductor 1.3 Clustering for R/BioConductor 2 Information and Data Resources 2.1 General 2.2 Coursework 2.3 NCBI 2.4 Cloud 3 Current Projects

Tutorials

General

• Computational Biology Primers
• More Computational Biology Primers
• 1000 Genomes Project Tutorial Videos

R/BioConductor

• Basic Introduction to R and BioConductor (pdf)
• Tutorial: analysing Microarray data using BioConductor (pdf)

Clustering for R/BioConductor

• affyPara - Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Information and Data Resources

General

• Wikipedia Bioinformatics entry
• UCSC Genome Browser
• Bioconductor
• BioPerl
• NGS edition of Bioinformatics Journal
• List of NGS software
• Imputation and Association Protocols

Coursework

• Course listing for UCSC Biomolecular Engineering Dept. Most course pages have problem sets and guidelines for the course material.

NCBI

• PubMed
• GEO - Gene Expression Omnibus
• eUtils
• NCBI API Keys

Cloud

• Cloud BioLinux

Current Projects

• GEO Mining