Dubai, United Arab Emirates (Saturday 19th - Monday 21st March 2011)

The Wellcome Trust Sanger Institute Workshop

The American University in Dubai, United Arab Emirates
Ref: ODW-Dubai

APPLICATIONS NOW CLOSED

Course Summary

The workshop is being held at The American University in Dubai, as a post-meeting event to the HGM2011 conference, Dubai. This three-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 needs to bring their own laptop computer to use for the duration of the course.

This course is limited to 30 participants and will be held in English.

Please visit the application page for further details and on-line registration or expression of interest in future workshops. Applicants from industry should click here for further information. Successful applicants will be notified as soon as possible.

Course instructors

  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Pablo Rabinowicz (Institute for Genome Sciences, University of Maryland School of Medicine)
  • Robert Finn (Janelia Farm Research Campus)
  • Simon Gregory (Duke University)
  • Charles Steward (Welcome Trust Sanger Institute)
  • Xose Fernandez (European Bioinformatics 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. 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@sanger.ac.uk.

Deadlines

  • Closing date for application is Friday 21 January 2011. Applications will not be accepted after this date.
  • Notification of places will be as soon as possible 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

  • 09:00 - 09:30 Registration and coffee
  • 09:30 - 10:30 Introduction/participant talks
  • 10:30 - 11:00 Coffee
  • 11:00 - 13:00 Module 1 (sequence formats and retrieval)
  • 13:00 - 14:00 Lunch
  • 14:00 - 16:00 Module 2 (de novo analysis of sequence)
  • 16:00 - 16:30 Tea
  • 16:30 - 17:30 Own research

Day two

  • 09:00 - 11:00 Module 3 (Ensembl)
  • 11:00 - 11:30 Coffee
  • 11:30 - 12:30 Module 3 continued
  • 12:30 - 13:30 Lunch
  • 13:30 - 14:30 Own research
  • 14:30 - 16:30 Module 4 (Comparative)
  • 16:30 - 17:00 Coffee
  • 17:00 - 18:00 Tasks and own research

Day three

  • 09:00 - 11:00 Module 5 (Protein and expression)
  • 11:00 - 11:30 Coffee
  • 11:30 - 13:30 Module 6 (Variation)
  • 13:30 - 14:30 Lunch
  • 14:30 - 15:30 Own research
  • 15:30 - 16:00 Coffee
  • 16:00 - 17:00 mop-up session/end of workshop
* quick link - http://q.sanger.ac.uk/k1xe4ug4