Open Door Workshop, Montevideo, Uruguay (16th-19th April 2012)

Working with the Human Genome Sequence

Instituto de Higiene, Montevideo, Uruguay
Ref: ODW-Uruguay

APPLICATIONS NOW CLOSED

Course Summary

This 4-day Workshop provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be available on the web, and students will have the opportunity to ask questions of the instructors as they apply what they have learned. Each student will have access to a desk-top PC for the duration of the course.

This course is limited to 20 participants and will be held in English.

A number of bursaries are available for each overseas course. These are awarded by the selection committee according to merit. There is no course fee. The bursary will cover travel, accommodation and sustenance. The maximum award for travel (in economy/second class) will be £750. Successful applicants will be notified as soon as possible.

Please visit Bursaries for Wellcome Trust Advanced Courses for more information. Please also see the course Terms and Conditions.

Information
Topics
Course manuals
Course urls
Timetable

Course instructors

Jane Loveland (Wellcome Trust Sanger Institute)
Pablo Rabinowicz (Institute for Genome Sciences, University of Maryland School of Medicine)
Simon Gregory (Duke University)
Giulietta Spudich (The European Bioinformatics Institute)
Robert Finn (Wellcome Trust Sanger Institute)
Charles Steward (Wellcome Trust Sanger Institute)

How to apply

Pre-requisites - The workshops are aimed at research scientists with a minimum of a degree in a biological discipline, including laboratory and clinical staff as well as specialists in related fields. Acceptance will be subject to selection process.
Cost - There will be no course fee for academics. Bursaries are available for travel and accommodation, these are subject to a selection process and are awarded by merit. You must state in the 'Summary' section below if you are applying for a bursary and also fill out a bursary application form that is available from the Bursaries for Wellcome Trust Advanced Courses section of the Wellcome Trust website. The bursary form must be signed by your scientific sponsor and sent to Wellcome Trust Advanced Courses by the application deadline. The course fee for commercial applicants is £1000.
Applications - Applicants will be required to complete an online application form together with a 250-word outline of the relevance of the course to their work. Please note that documentation supporting the application will be required from the applicant's Supervisor/Head of Department.

Queries

Any queries should be sent to opendoor@hinxton.wellcome.ac.uk.

Deadlines

Closing date for application is 20 January 2012. Applications will not be accepted after this date.
Notification of places will be as soon as possible ( TBA - but after the closing date ).
Full payment (if required) due on TBA.

Sequence Formats and Retrieval:

DNA databases: Embl, Genbank, DDBJT
Protein databases: Uniprot
Entrez - seach sequence information, including Refseq
BLAST

Genome Browsing:

Ensembl - full coverage including BioMart
VEGA
UCSC

De novo analysis of Sequence:

VEGA
DNA analysis - ORF finder
Alignment of splicing cDNA to genomic DNA - Spidey, Est2genome, SIM4
Multiple Sequence Alignment - CLUSTALW
Alignment viewing and Editing- Jalview, GeneDoc

Exploring Function and Disease:

Understanding Protein Function - from domains to structure (covering Pfam, InterPro, TreeFam CDD, CATH, SCOP, PDB, MSD)
Proteins as part of functional networks - iPfam, IntAct
Secondary Structure predictions
Disease databases COSMIC, OMIM, DECIPHER
Mapping disease associated SNPs to Proteins - Polyphen, SNPs 3D Rfam and microRNAs (miRBase)

Sequence Variation:

Ensembl SNP information, Geneview in dbSNP
Glovar, JSNP, HGVBase
Genotyping
Haplotypes and HapMap
Haploview

Comparative Sequence Analysis:

Homologous gene identification - Paralogues and Orthologues
Ensembl - orthologue prediction, MultiContigView
EntrezGene - BLink, Homologene
Comparative Genome Analysis - UCSC, Zpicture, VISTA

General Overview

Contents

Module material

Module presentations

Course URLs

Module 1

Module 2

Module 3

The VEGA Vertebrate Genome Annotation Database
Direct comparison between Ensembl and Vega annotation

InterPro Analyses included in InterPro that may be run separately.
- PROSITE
- PROSITE: Profiles
- Pfam
- PRINTS
- ProDom
- SMART
- TIGRFAMs
- UniProt
- PIR Superfamily
- Superfamily
- MSD
- CATH
- SCOP

Promoter Prediction Programs:

Module 4

Human

Trace Archives

At NCBI

Comparative Gene Analysis

Comparative Genome Analysis

Phylogeny

Module 5

Module 6

Day one

10:30 - 11:30 Registration and coffee
11:30 - 13:00 Introduction/participant talks
13:00 - 14:30 Lunch
14:30 - 16:30 Module 1 (sequence formats and retrieval)
16:30 - 17:00 Tea
17:00 - 18:00 Own research

Day two

09:00 - 11:00 Module 2 (Ensembl)
11:00 - 11:30 Coffee
11:30 - 13:00 Module 2 continued
13:00 - 14:30 Lunch
14:30 - 15:00 Own research
15:00 - 16:30 Module 3 (De novo analysis)
16:30 - 17:00 Coffee
17:00 - 18:00 Tasks and own research

Day three

09:00 - 11:00 Module 4 (Comparative)
11:00 - 11:30 Coffee
11:30 - 13:00 Tasks and own research
13:00 - 14:30 Lunch
14:30 - 16:30 Module 5 (Expression and disease)
16:30 - 17:00 Tea
17:00 - 18:00 Tasks and own research

Day four

09:00 - 11:00 Module 6 (SNPs)
11:00 - 11:30 Coffee
11:30 - 13:00 Tasks and own research
13:00 - 14:30 Lunch
14:30 - 15:30 Mop-up session
15:30 Coffee/End of workshop