Ensembl API workshop, Cambridge, June 2016
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Date:
Monday 27 - Thursday 30 June 2016Venue:
University of Cambridge - Downing Site, Cambridge, CB2 3AR, United KingdomApplication opens:
Wednesday 27 January 2016Application deadline:
Friday 24 June 2016Participation:
First come, first servedContact:
Gabriella RusticiRegistration fee:
freeRegistration closed
Course Overview
The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. 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.
http://www.ensembl.org/info/docs/api/index.html
For each of these the database schema and the API design as well as the most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put theoretical learning into practice by writing their own Perl scripts.
Note: Some basic obect-oriented Perl experience is a prerequisite for the course.
Beginner and regular users of the Ensembl API are welcome. Please make sure you sign up for Day 1 (Core) if you are unfamiliar with our APIs.
Quotes from participants: API workshops Dec, 2013
"I really enjoyed the course, and the ENSEMBL API will become a very relevant part of my toolset."
"Wish I'd taken the course years ago! Many tasks I have done in the past could have been completed in considerably less time had I taken this course."
If you think you'd like to host a similar course at your institute, you can find out more on the Ensembl workshops page.
Audience
Bioinformaticians and wet-lab biologists who can program in Perl.
Learning outcomes
- Understanding of the data types accessible through the Ensembl APIs
- Understanding of objects and methods in the Ensembl APIs
- Ability to navigate the Ensembl API documentation to find available methods
- Practice using the Ensembl APIs to access data
Programme
Day 1 – Core: Principles of the Ensembl Perl API, using the documentation, accessing genomic regions (slices), genes, transcripts, translations and repeats.
Day 2 – Variation: Accessing genomic variants, their alleles and allele frequencies, genotypes, phenotypes, linkage disequilibrium and genes they hit.
Day 3 – Compara: Access gene trees and homologues. Access multiple and pairwise genomic alignments.
Day 4 – Regulation: How we make regulatory features (eg promoters and enhancers) in the Ensembl regulatory build, accessing them and the evidence behind them through the Ensembl API.