Home Page:	http://www.e-protein.org/
Date Submitted:	2007-01-18 15:34:02.0
Last Updated:	2007-01-18 15:34:56.0
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Keywords:	proteomes;pipeline

Project Summary

To provide a fully automated distributed pipeline for large-scale structural and functional annotation of all major proteomes via the use of cutting edge computer GRID technologies.

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Project Description

Software used:

GridSAM : Provides the web service job execution interface to run the simulations.

Taverna : Workflow environment of myGrid.

Description

e-Protein is a BBSRC/DTI Grid pilot project entitled "A Distributed Pipeline for Structure-based Proteome Annotation using Grid Technology". The project involves seven groups at three locations -- Imperial College London (Profs Sternberg & Darlington), University College London (UCL) (Prof. Jones, Prof. Orengo and Dr Sorensen) and the European Bioinformatics Institute (EBI) (Prof. Thornton and Dr Birney).

The aim of e-Protein is to provide a structure-based annotation of all proteins in major sequenced genomes, linking computational and database resources at the three sites by Grid technology to achieve this goal.

The major results of the project to date are:

• The development and analysis of databases of proteome annotation at Imperial (3D-Genomics) and UCL (GTD and Gene3D).
• The development of databases providing functional annotation of all proteins in Uniprot KnowledgeBase using structural information (EBI).
• Adaptation of the Distributed Annotation System for use with protein annotations.
• Provision of a web-based portal combining protein annotations from all project sites.
• The development and demonstration of the JYDE software (UCL) for inter-site distributed computing, focusing on applications to proteome annotation.
• The application of JYDE to annotate 32,000 unique protein sequences in the human genome within one day, using 500 computer processors at UCL and Imperial.
• The development of the ICENI protocol (Imperial) to capture the workflow of proteome annotation pipelines and split the work between multiple Grid resources, providing the capability of true resource brokering.

Organisation Details

Investigator(s):	Professor Michael Sternberg (ICL), Professor David Jones (UCL), Professor Janet Thornton (EBI)
Organisation:	Imperial College London, University College London, European Bioinformatics Institute
Address:
Contact Email Address:	s.ali@imperial.ac.uk
Administrators:	s.ali@imperial.ac.uk

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