November 7 - 9, 2016
Cold Spring Harbor Laboratory, New York

Benjamin King,
Mount Desert Island Biological Laboratory
Gareth Howell, The Jackson Laboratory
Assaf Gordon,
The New York Genome Center
Emily Hodges, Vanderbilt University School of Medicine
Jeremy Ward,
Middlebury College

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 (November 7) with the course running two full days until 5 p.m. on the third day (November 9).

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. 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.

Major support provided by the Helmsley Charitable Trust. Limited financial aid is available; please apply in writing to the course registrar describing your need for financial support.


 Academic Package (two nights of housing) $1,030
 Corporate Package (two nights of housing) $1,715
 Academic No-Housing Package $725
 Corporate No-Housing Package $1,295
 Extra nights at $245 per night

All packages cover registration, food, coffee breaks, and a reception. Transportation to and from Cold Spring Harbor is not included. Full payment is due three weeks prior to the course.