Welcome

The aim of this BBSRC Bioinformatics and E-Science funded project is to create an informatics platform for proteomics using Grid-based technologies, and to use this to address specific biological problems. To this end we have constructed an In Silico Proteome Integrated Data Environment Resource (ISPIDER).

We refer to proteomics in the most general sense, considering data from gel/mass spectrometry based proteomics through protein-protein interaction data, to structure-based proteome informatics and sequence-based proteome/genome annotation. We are developing tools, standards and infrastructure that will integrate these data types to enable novel queries and analyses to be performed.

3 major centres of bioinformatics innovation in the UK are involved Manchester University , UCL / Birkbeck and the EBI

Main Objectives:

1. 1. To develop an integrated platform of proteomic data resources enabled as Grid and Web services for the storage, dissemination and management of proteomic data, using existing standards from proteomics, bioinformatics and e-Science.
2. 2. To produce appropriate middleware technologies to bring existing proteome-related databases into the integrated proteome platform, enabling them as Grid and/or Web services.
3. 3. To develop novel, proteome-specific databases to form part of 1. above, delivered as Grid and/or Web services, as well as browser-based user interfaces.
4. 4. To develop middleware and support to enable distributed querying, workflows and other integrated data analysis tasks across this range of novel and existing proteome databases
5. 5. To demonstrate the effectiveness of the resulting infrastructure through a series of systematic studies in proteomics, including clients for the visualisation of proteomic data, analyses for fungal species of industrial interest, and protein structural/functional trends in experimental proteomics