Open Door Workshop, Montevideo, Uruguay (24th - 27th March 2014)

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.

Please visit the application page for on-line registration. There is no course fee for applicants from non-commercial institutes. A number of bursaries are available for each overseas course. These are awarded by the selection committee according to merit.

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.

Course instructors

  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Pablo Rabinowicz (Independent Consultant)
  • Simon Gregory (Duke University)
  • Emily Pritchard (The European Bioinformatics Institute)
  • Robert Finn (European Bioinformatics 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 is no course fee for applicants from non-commercial institutes. Bursaries are available for travel and accommodation, these are subject to a selection process and are awarded by merit. Applicants may apply for a bursary during the online application process.
  • Applications - APPLICATIONS NOW CLOSED

Queries

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

Deadlines

  • Closing date for application is 29th November 2013. 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

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
* quick link - http://q.sanger.ac.uk/v8etmbcp