Open Door Workshop, Ho Chi Minh City, Vietnam (3rd-6th December 2012)

Working with the Human Genome Sequence

Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
Ref: ODW-Vietnam

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 NOTE: This workshop is aimed at regional researchers in Asia and Australasia. Scientists from outside these regions should apply to the workshops held regularly in Kenya/Malawi, Uruguay, and the UK as appropriate. Please contact us for further details or guidance.

There is no course fee and bursaries are available to assist with travel and accommodation costs. Please visit Bursaries for Wellcome Trust Advanced Courses and refer to the section 'Overseas courses (held outside the UK)' for more information and to download the overseas bursary application form. Please also see the course Terms and Conditions.

Course instructors

  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Simon Gregory (Duke University)
  • 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 are now closed

Queries

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

Deadlines

  • Closing date for applications is 7 September. 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

  • 10:00 - 10:30 Registration and coffee
  • 10:30 - 12:00 Introduction/participant talks
  • 12:00 - 13:00 Lunch
  • 13:00 - 15:00 Module 1 (sequence formats and retrieval)
  • 15:00 - 15:30 Tea
  • 15:30 - 17:30 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 - 14:00 Lunch
  • 14:00 - 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 - 14:00 Lunch
  • 14:00 - 16:00 Module 5 (Protein and Disease)
  • 16:00 - 16:30 Tea
  • 16:30 - 17:00 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 - 14:00 Lunch
  • 14:00 - 15:00 Mop-up session/End of workshop
* quick link - http://q.sanger.ac.uk/5fmjaswq