THE GENOME ACCESS COURSE

April 29 - 30, 2008
November 18 -19, 2008

(Register early - maximum attendance: 30 per class)

Trainers: 
Ben King, The Jackson Laboratory
Gareth Howell, The Jackson Laboratory
Laura Reinholdt, The Jackson Laboratory
Ravi Sachidanandam, Cold Spring harbor Laboratory

The Genome Access Course is an intensive two-day introduction to bioinformatics. 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.

A summary of the topics are listed below:

Sequence Resources and Databases
Extracting information from ENTREZ and other repositories
Sequence formats, including multiple sequence formats
Sequence conversion – using PISE
NCBI Entrez Gene, GenBank and other databases
NCBI RefSeq – Reference sequences
NCBI features such as LinkOut and BLink
NCBI TaxBrowser – Taxonomic information
Ensembl BioMart – bulk sequence and information retrieval
Model Organism Databases – e.g. Mouse Genome Informatics, Rat Genome Database, FlyBase
Expasy resources – SWISS-PROT
PANTHER
OMIM and human disease information
JCVI resources

Genome Browsers
Overview of major genome browsers: Ensembl, UCSC and NCBI Map Viewer browsers
Compare content of major browsers
Adding custom tracks

de novo Analysis of Sequences
Pairwise and Multiple Sequence Alignments
Methods: Dot Matrix Analysis; Dynamic Programming; k-tuple Methods
Comparing sequences directly using blast2sequences
Understanding BLAST and BLAT searches
Scoring Matrices: PAM, BLOSUM
Iterative profile and pattern searches: PSI-BLAST, PHI-BLAST
Multiple sequence alignment programs: CLUSTALW, T-Coffee
Visualizing & editing multiple alignments

Sequence Polymorphisms
SNPs – SNP Consortium
Genotyping
Haplotypes & HapMap
Haploview
Entrez dbSNP & Genome Browsers
HGVbase

Genome Analysis
Finding functionally important units in genome sequence by comparing genomes
Ortholog and paralog prediction at NCBI and Ensembl
Multicontigview in Ensembl
Comparison tracks in the UCSC Genome Browser
DCODE Resources: The ECR Genome Browser, zPicture and rVista
Jim Watson's Genome

Protein Function and Disease
Interrogating interlinked databases for protein function and associated disease-relevant information
Entrez at NCBI: Unigene and Homologene
Interpro at EBI
Organism-specific databases: OMIM (Human), MGI (Mouse), ZFIN (Zebrafish), FlyBase (Drosophila)
The Gene Ontology Consortium

Protein Structure
Protein Data Bank 3D structure database
DeepView structure viewer
NCBI Entrez Structure
Molecular Modeling Database - MMDB
Conserved Domain Database - CDD
Cn3D - NCBI structure viewer
Structure Comparison using VAST and DALI
Fold Classification with FSSP
Catalog of Membrane Protein Structures
Catalytic Site Atlas

Gene Set Enrichment and Pathways Analysis
Prioritize genes from microarray or proteomics experiments
Gene set enrichment analysis tools – GSEA and DAVID
Pathway resources – Reactome, HPRD NetPath, KEGG
Protein interaction resources –MIPS, MINT, BIND, DIP

The curriculum of The Genome Access Course has been developed in conjunction with staff at the Wellcome Trust Sanger Institute and the European Bioinformatics Institute (Hinxton, UK) who are teaching a parallel series of courses in the UK (see the Open Door Workshops).

The course will commence promptly at 9 am on the first day and end in the late afternoon on the second day. Applications are open to all on a first-come-first-served basis, subject to basic eligibility requirements. The course will be held at the CSHL campus. Each student will be provided with a PC laptop with wireless modem for the duration of the course. Lunch and coffee breaks will be provided as well as housing and an evening reception and dinner.

Pricing
Academic Package (one night housing) $655
Corporate Package (one night housing) $1150
Academic No-Housing Package $500
Corporate No-Housing Package $985

Extra nights @$175 per night

Regular packages are all inclusive and cover registration, food, housing, parking, reception & lobster banquet, etc. No Housing packages include all costs except housing. Full payment is due 3 weeks prior to the course.

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