ENSEMBL Developers Workshop: CORE and COMPARA

   Deadline for applications: March 16th 2009
   Notification of acceptance dates:
        EARLY: March 6th 2009
        NORMAL: March 17th 2009
   Course date: April 2nd - April 3rd 2009


Bert Overduin is a member of the PANDA Coordination and Outreach team at the European Bioinformatics Institute in Hinxton, United Kingdom. He has a background in plant molecular biology and genetics and has worked both in science and IT consultancy. Currently he spends most of his time answering questions from Ensembl users or travelling around the world to give Ensembl workshops.

Javier Herrero is the coordinator of the Ensembl Compara team, the Ensembl sub-group focused on comparative genomics. He has a master degree in Chemistry (Universidad Complutense de Madrid) and a PhD in Molecular Biology (Universidad Autonoma de Madrid). Before joining the EBI, he was working at the CNIO where he developed the first versions of GEPAS, a web tool for the analysis of expression array data. He has combined his work in the team with teaching in many Ensembl API workshops in several locations around the world.

Affiliation: European Bioinformatics Institute, Hinxton, UK

Course description:

Ensembl (http://www.ensembl.org) uses MySQL relational databases to store its information. A comprehensive set of Application Programme 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. This 2-day workshop is aimed at developers interested in exploring Ensembl beyond the website. The workshop covers various Ensembl databases and APIs. For each of them the database schema and the API design as well as its most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put the learned into practice by writing their own Perl scripts. 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 annotated by the Ensembl automated genome analysis and annotation pipeline. Ensembl Core databases also store assembly information, cDNA and protein alignments, external references, markers and repeat regions data sets. Ensembl Compara database and API The Ensembl Compara multi-species database stores the results of genome-wide species comparisons re-calculated for each release. The comparative genomics set includes pairwise whole genome alignments and synteny regions. The comparative proteomics data set contains orthologue predictions and protein family clusters.

Course Pre-requisites:

The only prerequisite for this workshop is a basic knowledge of UNIX and Perl.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated:  March 2nd 2009