Open Door Workshop, Cambridge, United Kingdom (1st - 3rd July 2013)

Working with the Human Genome Sequence

Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Ref: ODW-Hinxton

Course Summary

The Open Door Workshop provides an introduction to bioinformatics tools freely available on the internet, focussing primarily on the Human Genome data. The workshops provide hands-on training in the use of public databases and web-based sequence analysis tools, and are taught by experienced instructors.

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. The workshops run over three days and are without exception residential on the Wellcome Trust Genome Campus.

The Open Door Workshops were conceived jointly by The Wellcome Trust Sanger Institute and the Cold Spring Harbor Laboratories, and are being developed further by staff at these centres with assistance from staff at the European Bioinformatics Institute and the University of Cambridge.

The workshop is split into modules, each of which gives an overview of a given topic followed by a worked example and participant tasks.

The course is subsidised by the Wellcome Trust for scientists based in academic institutions anywhere in the world.

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 - The courses run at Hinxton are subsidised by the Wellcome Trust and for scientists based in academic institutions there is a charge towards board and lodging costs of £345. For applicants from industry, there is a charge of £1250 for tuition fees and board and lodging.
  • Applications - Application forms for this course can now be completed online. To apply, please go to the application portal. If you have any problems with the online application process, please email us.
    Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your supervisor or head of department. A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline.

Queries

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

Deadlines

  • Closing date for application is 12 April 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.

Topics

Sequence Formats and Retrieval:

  • DNA databases: Embl, Genbank, DDBJT
  • Protein databases: UniprotT
  • Entrez - seach sequence information, including RefseqT
  • 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
  • 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

Module material

To come.

Module presentations

To come.

Provisional timetable

Day one

Conference Centre Reception

  • 09.00 - 10.00: Registration

IT room, Conference Centre

  • 10.00 - 11.30 Introduction and Informal Participant talks
  • 11.30 - 12.30 Sanger Tour
  • 12.30 - 13.30 LUNCH
  • 13.30 - 15:30 Module 1: Sequence Formats and Retrieval
  • 15.30 - 16.00 COFFEE
  • 16.00 - 18.00 Module 2: Manual Annotation and de novo analysis of sequence

Hinxton Hall

  • 18:00 - 19:00 Welcome Drinks
  • 19.00 - DINNER and COFFEE

Day two

IT room, Conference Centre

  • 09.00 - 11.00 Module 3: Genome Browsing
  • 11.00 - 11.30 COFFEE
  • 11.30 - 13.00 Module 3: Genome Browsing (cont)
  • 13.00 - 14.00 LUNCH
  • 14.00 - 16.00 Module 4: Comparative Sequence Analysis
  • 16.00 - 16.30 TEA
  • 16.30 - 18.00 Own research/ask the instructors

Hinxton Hall

  • 19.00 - DINNER and COFFEE

Day three

IT room, Conference Centre

  • 09.00 - 10.45 Module 5: Exploring Function and Disease
  • 10.45 - 11.00 COFFEE
  • 11:00 - 13.00 Module 6: Sequence Variation
  • 13.00 - 14.00 LUNCH
  • 14.00 - 16.00 Own research/ask the instructors
  • 16.00 - 16.30 TEA
  • 16.30 - End of workshop
* quick link - http://q.sanger.ac.uk/rivlambm