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Register for TGAC

THE GENOME ACCESS COURSE (TGAC)
April 21 - 23, 2013
July 18 - 20, 2013
November 17 - 19, 2013

The November course will be held in New York City in conjunction with the New York Genome Center.
Click here for more details.

Instructors: 
Ben King, Mount Desert Island Biological Laboratory
Jeremy Ward, Middlebury College
Charla Lambert, Cold Spring Harbor Laboratory

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 (April 21, July 18, or November 17) with the course running two full days through late afternoon on the third day (April 23, July 20, or November 19).

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.

Sequence, Gene, and Protein Resources
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 Browsers
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

de novo Analysis of Sequences
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

Sequence Variation
Types of Sequence and Structural Variation
SNP Resources: dbSNP
Structural Variation Resources: dbVar, DGVa, HGVbase

Comparative Genome Analysis and Functional Genomic Elements
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

Analysis of High-Throughput Sequence Data
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

Gene Set Enrichment and Pathway Analysis
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

Target Audience: The Genome Access Course 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. For more detailed curriculum on methods used in computational biology, please see the Computational & Comparative Genomics course. Students interested in the practical aspects of software development are encouraged to apply to the course on Programming for Biology. Students who would like in-depth training in the analysis of next-generation sequencing data (e.g., genome assembly and annotation, SNP calling, and the detection of structural variants) may be interested in the course on Advanced Sequencing Technologies & Applications. Finally, please see the course on Statistical Methods for Functional Genomics if you would like training in the statistical analysis of high-throughput genomics data.

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 teach a parallel series of courses in the UK; see the Open Door Workshops for more information.

Pricing
Academic Package (two nights of housing) $995
Corporate Package (two nights of housing) $1655
Academic No-Housing Package $700
Corporate No-Housing Package $1250

Extra nights @$235 per night

Regular packages are all-inclusive and cover registration, food, coffee breaks, housing, parking, and a reception. No-Housing packages cover all costs except housing. Full payment is due 3 weeks prior to the course.

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Cold Spring Harbor Laboratory
Meetings & Courses Program
PO Box 100, 1 Bungtown Road
Cold Spring Harbor, NY 11724-2213
Phone (516) 367-8346
Fax: (516) 367-8845

meetings@cshl.edu