20 de abril de 2011

curso APIs de Ensembl

en línea con la anterior entrada del blog os paso este anuncio de Miguel Pérez-Enciso (miguel.perez@uab.es ) :

Del 4 al 6 de octubre organizo el siguiente curso en el CRAG, más detalles + adelante. Lo darán dos personas del EBI. Se requiere conocimientos sólidos de perl. Máximo 20 personas.

"Ensembl 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. Participants will be expected to have experience in writing Perl programs. A background in object oriented programming techniques and familiarity with databases (MySQL) would be an advantage.

The workshop covers the following four 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 bypractical 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 Variation databases and API

The large amount of genetic variation information is organised in a set of species-specific Ensembl Variation databases. This includes basic variation information (alleles, flanking sequences, genotypes), the functional consequence of a variation and more complex data such as LD values from genotype data and tagged SNPs in a population.

**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. "

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