Graduate School of Life Sciences Training

Bioinformatics: Ensembl API Workshop prerequisites 

Provided by: GSLS

Wed 4 Dec - Fri 6 Dec 2013  –  Department of Genetics, Room G12


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The following alternative date is available:
    Tue 2 Dec 2014
Register your interest - if you cannot make any of the currently scheduled dates and would be interested in additional dates being scheduled.

Description: This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers the core, compara, variation and functional genomics (regulation) databases and APIs. Each database schema and API design will be presented in association with practical sessions in which the participants will write their own Perl scripts. Further information concerning course content is available. A course timetable is also available here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience:

Duration: 3

Sessions:

Number of sessions: 3

Date Time Venue Trainer
Wed 4 Dec 09:30 - 17:00 Department of Genetics, Room G12 Magali Ruffier ,  Giulietta Spudich ,  Bert Overduin ,  Sarah Hunt ,  Alessandro Vullo
Thu 5 Dec 09:30 - 17:00 Department of Genetics, Room G12 Giulietta Spudich ,  Sarah Hunt ,  Bert Overduin ,  Thomas Juettemann
Fri 6 Dec 09:30 - 17:00 Department of Genetics, Room G12 Matthieu Muffato ,  Giulietta Spudich ,  Bert Overduin ,  Stephen Fitzgerald

Format: Presentations and practicals

Frequency: A number of times per year

Prerequisites:

  • A good grasp of programming concepts
  • Experience in coding in PERL
  • Familiarity with basic Molecular Biology and Genetics
  • Familiarity with the Ensembl would be advantageous

Aims:

  • To enable those with some experience in both Molecular Biology and Programming to use the Ensembl APIs competently

Topics covered (session 1):

  • a.m.: Core Database & API - Magali Ruffier, Alessandro Vullo
  • p.m.: Core Database & API - Magali Ruffier, Alessandro Vullo
  • p.m.: Variation Database & API - Sarah Hunt

Topics covered (session 2):

  • a.m.: Variation Database & API - Sarah Hunt
  • a.m.: Functional Genomics (Regulation) Database & API- Thomas Juettemann
  • p.m.: Functional Genomics (Regulation) Database & API- Thomas Juettemann

Topics covered (session 3):

  • a.m.: Compara Database & API - Gene Trees - Matthieu Muffato
  • p.m.: Compara Database & API - Alignments - Stephen Fitzgerald

Theme: SBS Practical Bioinformatics Training: Specialized Topics