Open Door Workshop, Cambridge, United Kingdom (11th - 13th May 2015)

Human and Vertebrate Genomics: Bioinformatics Tools and Resources.

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.

Course instructors

  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Matthew Clark (The Genome Analysis Centre)
  • Emily Perry (The European Bioinformatics Institute)
  • Rob Finn (The European Bioinformatics Institute)
  • Jen Harrow (Wellcome Trust Sanger Institute)
  • Bert Overduin (Edinburgh Genomics, The University of Edinburgh)

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 TBA. 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

Genome Browsing:

  • Ensembl
  • VEGA
  • UCSC

Comparative Sequence Analysis:

  • Homologous gene identification - Paralogues and Orthologues
  • Ensembl - orthologue prediction, MultiContigView
  • EntrezGene - BLink, Homologene
  • Comparative Genome Analysis - UCSC, ECR browser

Working with Encode Data:

  • Epigenetics
  • ENCODE project
  • ENCODE portal
  • Browsing ENCODE data with UCSC
  • Browsing ENCODE data with Ensembl
  • Ensembl Regulatory Build

Proteins, Complexes and Pathways:

  • UniProt
  • InterPro/Pfam protein
  • PDBe/PDBSum
  • IntAct
  • Reactome/Metacyc

ncRNA:

  • Rfam
  • MicroRNA/targets
  • lncRNA db and Vega
  • RNACentral

More Complex Genome Browsing:

  • Ensembl Biomart
  • UCSC Table Browser
  • Uploading your own data

Genomic Variation:

  • Ensembl SNP information, Geneview in dbSNP
  • Genotyping
  • Haplotypes and HapMap
  • Haploview

Variation, Function and Disease:

  • Polyphen, SIFT
  • Ensembl VEP
  • OMIM
  • COSMIC
  • DECIPHER
  • GEO
  • ONTOLOGIES

Module material

To come.

Module presentations

To come.

Timetable

Day 1:

  • 09:00 - 09:30 Registration
  • 09:30 - 10:30 Introductory talk
  • 10:30 - 11:30 Sanger Tour
  • 11:30 - 13:00 Module 1(Intro Ensembl)
  • 13:00 - 14:00 Lunch
  • 14:00 - 15:30 Module 2 (intro UCSC and other browsers)
  • 15:00 - 15:30 Coffee
  • 15:30 - 17:00 Module 3 (Comparative Genomics)

Day 2:

  • 09:00 - 10:30 Module 4 (Working with Encode data)
  • 10:30 - 11:00 Coffee
  • 11:00 - 12:30 Module 5 (More complex genome browsing)
  • 12:30 - 13:30 Lunch
  • 13:30 - 15:00 Module 6 (Genomic Variation)
  • 15:00 - 15:30 Coffee
  • 15:30 - 16:30 Talk (Next Gen Sequencing)

Day 3:

  • 09:00 - 10:30 Module 7 (Variation and Disease)
  • 10:30 - 11:00 Coffee
  • 11:00 - 12:30 Module 8 (Proteins, Complexes and Pathways)
  • 12:30 - 13:30 Lunch
  • 13:30 - 15:00 Module 9 (ncRNA)
  • 15:00 - 15:30 Coffee
  • 15:30 - 16:30 Talk (Metagenomics)
  • 16:30 - 17:00 Own research / ask the instructors
  • End of Workshop
* quick link - http://q.sanger.ac.uk/rivlambm