KEMRI/Wellcome Trust Programme, Kilifi, Kenya (31st Oct-2nd Nov 2011)

Working with the Human Genome Sequence

KEMRI/Wellcome Trust Programme, Kilifi, Kenya
Ref: ODW-Kenya

APPLICATIONS NOW CLOSED

Course Summary

This 3-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 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. Please also read the workshop terms and conditions.

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.

Course instructors

  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Matthew Clark (The Genome Analysis Centre)
  • Bert Overduin (The 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 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 22 July 2011. 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 - Splign, Est2genome, SIM4
  • Multiple Sequence Alignment - MUSCLE, CLUSTALW
  • Alignment viewing and Editing- Jalview, GeneDoc

Exploring Function and Disease:

  • Understanding Protein Function - from domains to structure (covering Pfam, InterPro, PDB)
  • 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
  • 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, ECR browserVISTA

Day One

  • 09:00 - 10:00 Registration and coffee
  • 10:00 - 11:30 Welcome, Introduction and participant talks
  • 11:30 - 12:30 Tour of Facility
  • 12:30 - 13:30 LUNCH
  • 13:30 - 15:00 Module 1: Sequence formats and retrieval
  • 15:00 - 15:20 break
  • 15:20 - 17:00 Module 2: Manual genome annotation and de novo sequence analysis

Day Two

  • 09:00 - 10:45 Module 3: Ensembl genome browser
  • 10:45 - 11:00 break
  • 11:00 - 12:30 Module 3: Ensembl genome browser (cont.)
  • 12:30 - 13:30 LUNCH
  • 13:30 - 15:30 Module 4: Comparative sequence analysis
  • 15:30 - 16:00 break
  • 15:30 - 17:00 Own research/ask the instructors
  • 19:00 - Beach barbeque

Day Three

  • 09:00 - 10:45 Module 5: Exploring Protein Function and Disease
  • 10:45 - 11:00 break
  • 11:00 - 12:30 Module 6: Sequence Variation
  • 12:30 - 13:30 LUNCH
  • 13:30 - 15:00 Own research/ask the instructors
  • 15:00 - Close of workshop
* quick link - http://q.sanger.ac.uk/pc756bqg