Ensembl API Workshop

Workshop Description

The Ensembl project (http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences.

This 1/2-day workshop is aimed at researchers and developers interested in exploring Ensembl beyond the browser.

Ensembl uses MySQL relational databases to store its information. A comprehensive set of Application Programming Interfaces (APIs) serve as a middle-layer between underlying database schemes and more specific application programmes. The APIs aim to encapsulate the database layout by providing efficient high-level access to data tables and isolate applications from data layout changes.

The workshop covers the Ensembl Core database and API. The database schema and the API design as well as its most important objects and their methods will be presented. Short presentations will be interspersed by hands-on exercises to put the learned into practice.

Ensembl Core databases and API

The set of species-specific Ensembl Core databases stores genome sequences and most of the annotation information. This includes the gene, transcript and protein models as annotated by the Ensembl automated genome analysis and annotation pipeline as well as assembly information, cDNA and protein alignments, external references and e.g. markers and repeat regions. The Core API also forms the basis for the Variation, Compara and Regulation APIs, that can be used retrieve variation, comparative genomics and regulation data from Ensembl, respectively.

Prerequisites

1. To attend this workshop participants should have a working knowledge of Perl and molecular biology / genetics. Participants without Ensembl knowledge are encouraged to also attend the Browser workshop.

2. Please test your iPlant credentials to ensure you have access. You can log-in from user.iplantcollaborative.org, click the button "iPlant Login"

• Once authenticated, click the "My Services" link
• Under "My Services" please ensure you have access to: Atmosphere, Discovery Environment, iPlant Data Store. You can also request access to other services here
• If you have account problems, please email support@iplantcollaborative.org

3. Please check your email and this wiki prior to the workshop, as this is the way we will communicate any important changes.

4. Please check this software requirement list and install the necessary software: Software Requirements

• Please contact your system administrator if you do not have permission to install software on your computer.

Workshop Agenda (Tentative)

Attendee List (20 max)