ISPIDER - A Pilot Grid for Integrative Proteomics

Project Aims

This is a BBSRC-funded project in collaboration with the University of Manchester, University College London and the European Bioinformatics Institute. Please see the main ISPIDER website for further details of the people who are working on this project, our ongoing research, software and publications. The aims of the project are as follows:

  • 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.
  • To produce appropriate middleware technologies to bring existing proteome-related databases into the integrated proteome platform, enabling them as Grid and/or Web services.
  • 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. These will be:
    • A repository for experimental proteome data
    • A proteome protein identification server and database
    • A phosphoproteome specific database
  • 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
  • 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

Project Outputs

  • Publications: a complete list of ISPIDER-related publications can be found on the publications page of the ISPIDER Central website
  • Services: a service deployed over the ISPIDER integrated resource can be accessed directly here, or through the services page of the ISPIDER Central website
  • Integrated resource: A performance evaluation of the ISPIDER integrated resource can be found in the Birkbeck technical report BBKCS-08-05. The zip file contains the following files, required to reproduce the experiments described in the report. Note that this does not include the data sources, since permission has to be granted on an individual basis from the data source providers.
    • automed_ispider_2008_07_16.jar: snapshot from the AutoMed CVS used to conduct the experiments
    • source.zip: source code used to wrap data sources, create the integrated schema, create the integrated resource and query it
    • gs.sql: SQL DDL file used to create the PostgreSQL database that is used to generate the integrated schema

 

BBSRC - the Biotechnology and Biological Sciences Research Council Birkbeck College European Bioinformatics Institute University College London University of Manchester