Ensembl API workshop

Prerequisites

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. The Ensembl Perl API Documentation can be found here.

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.

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

• Bioinformaticians and wet-lab biologists who can program in Perl.
• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Further details regarding eligibility criteria are available here
• Further details regarding the charging policy are available here

• Some basic object-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.

Number of sessions: 4

Bioinformatics, Data retrieval, Database search

After this course you should be able to:

• Understand the data types accessible through the Ensembl APIs
• Understand objects and methods in the Ensembl APIs
• Navigate the Ensembl API documentation to find available methods
• Practice using the Ensembl APIs to access data

During this course you will learn about:

• Core (day 1): Principles of the Ensembl Perl API, using the documentation, accessing genomic regions (slices), genes, transcripts, translations and repeats.
• Variation (day 2): Accessing genomic variants, their alleles and allele frequencies, genotypes, phenotypes, linkage disequilibrium and genes they hit.
• Compara (day 3): Access gene trees and homologues. Access multiple and pairwise genomic alignments.
• Regulation (day 4): 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.

• Presentations and practicals
• One mandatory one day session plus three optional one day sessions

4 days

A number of times per year

• An Introduction to Solving Biological Problems with PERL
• Software Carpentry: Instructor training