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Wed 4 Dec - Fri 6 Dec 2013
09:30 - 17:00

Venue: Department of Genetics, Room G12

Provided by: Graduate School of Life Sciences


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Bioinformatics: Ensembl API Workshop
Prerequisites

Wed 4 Dec - Fri 6 Dec 2013

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
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
Sessions

Number of sessions: 3

# Date Time Venue Trainers
1 Wed 4 Dec 2013   09:30 - 17:00 09:30 - 17:00 Department of Genetics, Room G12 map Magali Ruffier,  Giulietta Spudich,  Bert Overduin,  Sarah Hunt,  Alessandro Vullo
2 Thu 5 Dec 2013   09:30 - 17:00 09:30 - 17:00 Department of Genetics, Room G12 map Sarah Hunt,  Giulietta Spudich,  Bert Overduin,  Thomas Juettemann
3 Fri 6 Dec 2013   09:30 - 17:00 09:30 - 17:00 Department of Genetics, Room G12 map Matthieu Muffato ,  Giulietta Spudich,  Bert Overduin,  Stephen Fitzgerald
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
Aims
  • To enable those with some experience in both Molecular Biology and Programming to use the Ensembl APIs competently
Format

Presentations and practicals

Duration

3

Frequency

A number of times per year

Theme
SBS Practical Bioinformatics Training: Specialized Topics

Booking / availability