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Tue 2 Dec - Fri 5 Dec 2014
09:30 - 17:00

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Graduate School of Life Sciences


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Bioinformatics: Ensembl API Workshops
Prerequisites

Tue 2 Dec - Fri 5 Dec 2014

Description
  • This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website.
  • The workshop covers the Core (Day 1), Variation (Day 2), Functional Genomics (Regulation) (Day3), and Compara (Day4) 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.
  • This course is comprised of 4 one day sessions.
  • The first Core API session (or equivalent experience) is a mandatory prerequisite to the other 3 sessions.
  • Please specify which of the optional sessions you wish to attend when booking. The default is "all three of them".
  • Participants are requested to give us a little information about their background & requirements by registering here.
  • The course fee, for those participants required to pay, will be £100 independent of the number of sessions attended.
  • The course timetable can be viewed 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
  • The Core API session is required to fully benefit from any of the other three sessions.
Sessions

Number of sessions: 4

# Date Time Venue Trainers
1 Tue 2 Dec 2014   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Alessandro Vullo
2 Wed 3 Dec 2014   09:30 - 17:00 * 09:30 - 17:00 * Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Anja Thormann
3 Thu 4 Dec 2014   09:30 - 17:00 * 09:30 - 17:00 * Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Thomas Juettemann
4 Fri 5 Dec 2014   09:30 - 17:00 * 09:30 - 17:00 * Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Matthieu Muffato ,  Stephen Fitzgerald
* Optional session.
Topics covered
  • Day 1: Core Database & API
  • Day 2: Variation Database & API
  • Day 3: Functional Genomics (Regulation) Database & API
  • Day 4: Compara Database & API - Gene Trees
  • Day 4: Compara Database & API - Alignments
Aims
  • To enable those with some experience in both Molecular Biology and Programming to use the Ensembl APIs competently
Format
  • Presentations and practicals
  • Four full day sessions in total
  • One mandatory one day session plus three optional one day sessions
Notes

A recent version of this course has been recorded and is available for viewing, in part or in its entirety, from here.

Duration

4

Frequency

A number of times per year

Related courses

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