The Genome Access Course (TGAC)

The Genome Access Course is an intensive two-day introduction to bioinformatics. Participants are expected to arrive by 6 p.m. on the first day (Monday March 26) with the course running two full days until 5 p.m. on the third day (Wednesday March 28).

The course is broken into modules that are each designed to give a broad overview of a given topic, with ample time for examples chosen by the instructors. Each module features a brief lecture describing the theory, methods and tools followed by a set of worked examples that students complete. Students are encouraged to engage instructors during the course with specific tasks or problems that pertain to their own research.

The core of the course is the analysis of sequence information framed in the context of completed genome sequences. Featured resources and examples primarily come from mammalian species, but concepts can be applied to any species. The course also features methods to assist the analysis and prioritization of gene lists from large scale microarray gene expression and proteomics experiments. Summaries of the topics are listed below.

 NCBI Sequence, Gene, and Protein Resources

 Model Organism Databases: Mouse Genome Informatics, Rat Genome Database, ZFIN, FlyBase

 Protein Sequence and Domain Resources: UniProt, PDB, InterPro

 Proteomics Resources: IPI, ExPaSY, PRIDE

 microRNA Resources: miRBase, microCosm Targets, TargetScan, PicTar

 Repositories of High-Throughput Sequence Data

 Repositories of Gene Expression Data: GEO, ArrayExpress

 Gene Expression Profiling Resources

 Gene Ontology

 Genome Sequencing and Assembly

 Gene Annotation

 Overview and Comparison of Major Genome Browsers: Ensembl, UCSC, NCBI Map Viewer

 Adding custom tracks

 Bulk genome retrieval tools: BioMart, UCSC Table Browser

 Local, Global, Pairwise, and Multiple Sequence Alignments

 BLAST and BLAT Algorithms

 Scoring Matrices: PAM, BLOSUM

 Iterative Profile and Pattern Searches

 Multiple Sequence Alignment Programs

 Visualizing & Editing Multiple Alignments

 Types of Sequence and Structural Variation

 SNP Resources: dbSNP

 Structural Variation Resources: dbVar, DGVa, HGVbase

 Finding Putative Regulatory Elements in Genome Sequence by Comparing Genomes

 Ortholog and Paralog Resources

 Multicontigview in Ensembl

 Comparative Tracks in the UCSC Genome Browser

 DCODE and ENCODE Resources

 Common File Formats: FASTQ, SAM, BAM

 Quality Control and Diagnostic Analyses

 Mapping Reads To a Reference Sequence

 Finding Putative Mutations and Polymorphisms

 RNA-Seq Data Analysis

 ChIP-Seq Data Analysis

 de novo Assembly

 Galaxy Resources

 Prioritizing Genes from Microarray and Proteomics Experiments

 Gene Set Enrichment Analysis Tools: GSEA, DAVID

 Pathway Resources: Reactome, HPRD NetPath, KEGG

 Protein Interaction Resources: MIPS, MINT, BIND, DIP

Each student will be provided with a laptop (if needed) and internet access for the duration of the course. You can also bring your own laptop to the course provided it meets the following requirements: 1) a standard browser (Internet Explorer, Firefox, etc.) that is up-to-date with security patches and bug fixes, 2) wireless internet capacity, and 3) the ability to view and modify plain text files and spreadsheets (e.g., Microsoft Word and Excel). Both PCs and Macs are acceptable as long as they're updated with all security patches and bug fixes.

The Genome Access Course is open to all on a first-come, first-served registration system. It is most beneficial for bench scientists transitioning into projects that require intensive analysis or integration of large data sets. The course will introduce you to publicly available resources, and it will also help you develop a vocabulary that can be used to collaborate with computational scientists. If you already have significant programming or data analysis experience, this course is not appropriate for you.