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.
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.
Denise Carvalho-Silva, EMBL-EBI
Audience and Prerequisites
- 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.
- Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
Syllabus, Tools and Resources
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.
- Regulation (day 3): 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.
- Compara (day 4): Access gene trees and homologues. Access multiple and pairwise genomic alignments.
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