Ensembl is an online database for the annotation, analysis and display of vertebrate species. Ensembl Genomes has expanded the taxonomic range of Ensembl to include non-vertebrate species. Projects cover a broad range of topics, from groups that are sequencing a genome and want to implement the Ensembl annotation pipeline, to people interested in developing new tools based on the Ensembl platform. Visitors may be based at the EBI or the Wellcome Trust Sanger Institute (co-developers of Ensembl and our neighbours on the Genome Campus). For more information, see the Ensembl Geek for a Week page.
ArrayExpress is a data resource developed and run by the Functional Genomics team. It is a database of functional genomics data, with the main emphasis on gene expression. We are developing and running tools for functional genomics data submission, management, annotation, access and analysis. We are interested in applications of ontologies to bioinformatics and biomedical data, including de novo ontology development, ontology manipulation tools, ontology-data mapping tools, and knowledge bases for gene expression and phenotype information.
The Proteomics Services Team offers Geek for a Week placements within two main areas:
1) Molecular interactions data management. The molecular interactions workgroup of HUPO’s (Human Proteome Organisation) Proteomics Standards Initiative (PSI-MI) develops community standards for the representation of molecular interaction data. The open source IntAct database provides a reference implementation of these standards and the supporting tools. A recent, highly dynamic project is PSICQUIC, the PSI Common Query Interface, a now widely implemented API for access to molecular interaction data.
We invite Geek for a Week projects either to become familiar with the available IntAct and PSI open source software, with the aim of local deployment, or advanced projects aimed at joint further development of a particular software tool.
2) Distributed Annotation System. The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. The idea behind this system is that such annotations should not be provided by a single centralised database, but should instead be spread over multiple sites. We are interested in tools, services as well as new ideas to facilitate data integration using the DAS protocol. We welcome developers to define and work on projects of mutual interest. For more information, see the UniProt Protein DAS Server page.
