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The Genome Access Course (TGAC)

  December 29, 2017  

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
March 26 - 28, 2018

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.

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

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.

Target Audience
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. 
Organized by: Instructors: Delphine Fagegaltier, Benjamin King, Emily Hodges, Steven Munger
Invited Speakers: TBA
Deadline for Abstracts: First-come, first-serve registration
Registration: Apply here 
E-mail: morrow@cshl.edu
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