THE GENOME ACCESS COURSE
Cold Spring Harbor Laboratory's Genome Research Center

November 29 - 30, 2006

(Register early - maximum attendance: 30 per class)

Trainers: 
Ben King, The Jackson Laboratory
Gareth Howell, The Jackson Laboratory
Tristan Fiedler, Cold Spring Harbor Laboratory

The Genome Access Course is an intensive two-day introduction to bioinformatics and will address the following topics:

Sequence Resources and Databases
Extracting information from ENTREZ and other repositories
Sequence formats, including multiple sequence formats
Sequence conversion – using PISE
RefSeq – Reference sequences
OMIM and Human Disease Information
TaxBrowser – Taxonomic Information
Organismal Databases – e.g. FlyBase
Other Entrez Databases
NCBI features such as LinkOut and BLink
TIGR resources
Reactome and other pathway databases such as PANTHER

Sequence Comparisons
Pairwise and Multiple Sequence Alignments
Methods: Dot Matrix Analysis; Dynamic Programming; k-tuple Methods
Comparing sequences directly using blast2sequences
Understanding BLAST searches
Scoring Matrices: PAM, BLOSUM
Profile and pattern searches: PSI-BLAST, PHI-BLAST
Multiple Alignment Methods: Dynamic Programming; Progressive; Iterative (Genetic Algorithm, HMM)
Programs: CLUSTALW, T-Coffee
Visualizing & editing multiple alignments

Gene Prediction
Gene structure – prokaryotic vs. eukaryotic
Understanding the genome annotation pipeline
Entrez Gene
Genome Browser gene tracks
Gene prediction programs such as Twinscan

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

Genome Analysis
Paralogy vs. orthology
Ortholog prediction in Ensembl
Comparative genome analysis (PipMaker, VISTA)
Resources: ENSEMBL; NCBI; UCSC; TIGR

Protein Analysis & Proteomics
Protein Structure Review
Protein Sequence Databases
Secondary Structure Prediction
Inferring protein function
3D Structure Databases (PDB) and Resources (Chime, Cn3D)
2D-PAGE resources
Kinetic Modeling: Gepasi, Virtual Cell
Pathway Databases: WIT, KEGG, BioCyc, etc.

Phylogenetic Analysis
Relation to Multiple sequence alignment
Understanding hylogenetic trees
Using PISE to create trees via PHYLIP
Methods: Maximum Parsimony, Distance Methods (Fitch & Margoliash, Neighbor-Joining, Unweighted Pair Group)
Complications of phylogenetic analysis

The course is broken into modules designed to give a broad overview of a given topic, with ample time for examples chosen by the instructors (see detailed curriculum at the bottom of this page). Each module will be in three parts, consisting of a discussion of theory and methods, coverage of software and web resources, and use of selected tools with examples (including those supplied by the students). The modular design allows the instructors to tailor the presentation to the interests of the students. 

The core of the course will cover the manipulation and analysis of sequence information. Students are encouraged to supply problem sets and sequences of interest to the trainers for possible incorporation as examples in the modules. Materials will be available on the web and students can continue to ask questions of the trainers as they apply what they have learned in their individual endeavors.

The curriculum of The Genome Access Course has been developed in conjunction with staff at the Wellcome Trust Sanger Centre and the European Bioinformatics Institute (Hinxton, UK) who separately 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 of the course and end in the late afternoon on the second day. Applications to the course are open to all on a first-come-first-served basis, subject to basic eligibility requirements. The course will be held at the Laboratory's newly opened Genome Research Center at Woodbury located seven miles south of the main Laboratory 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 at the Genome Research Center, while housing and an evening reception and dinner will be provided at the main laboratory. Ample parking is available at the Genome Research Center, and transportation will be provided between the two campuses at set times. 

Pricing
Academic Package (one night housing) $630
Corporate Package (one night housing) $1100
Academic No-Housing Package $485
Corporate No-Housing Package $945

Extra nights @$150 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.

Currency converter