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| EPSRC Reference: |
GR/R67743/01 |
| Title: |
MYGRID: Directly Supporting the E-Scientist |
| Principal Investigator: |
Professor C Goble |
| Other Investigators: |
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| Researcher Co-investigator: |
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| Project Partner: |
| AstraZeneca |
Epistemics |
Geneticxchange, Inc |
| GlaxoSmithKline |
I B M United Kingdom Ltd |
Merck Ltd |
| Network Inference Ltd |
SUN Microsystems Ltd |
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| Department: |
Computer Science |
| Organisation: |
The University of Manchester |
| Scheme: |
Standard Research |
| Starts: |
01 October 2001 |
Ends: |
30 June 2005 |
Value (£): |
3,483,004
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| EPSRC Research Topic Classifications: |
| Artificial Intelligence Technologies |
Bioinformatics |
| Biological and Medicinal Chemistry |
Information and Knowledge Management |
| User Interface Technologies |
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| EPSRC Industrial Sector Classifications: |
| Creative Industries |
Pharmaceuticals and Biotechnology |
| Information Technologies |
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| Related Grants: |
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| Panel History: |
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Summary |
To date, Grid development has focused on the basic issues of storage, computation and resource management needed to make a global scientific community's information and tools accessible in a high performance environment. However, from an e-Science viewpoint, the purpose of the Grid is to deliver a collaborative and supportive environment that allows geographically distributed scientists to achieve research goals more effectively. MyGrid will design, develop and demonstrate higher level functionalities over an existing Grid infrastructure that support scientists in making use of complex distributed resources. The project will develop an e-Scientist's workbench that supports: (I) the scientific process of experimental investigation, evidence accumulation and result assimilation; (ii) the scientist's use of the community's information; and (iii) scientific collaboration, allowing dynamic groupings to tackle emergent research problems. The workbench will support individual scientists by providing personalisation facilities relating to resource selection, data management and process enactment. The design and development activity will be informed by and evaluated using problems in bioinformatics, which is characterised by a highly distributed community, with many shared tools resources. MyGrid will develop two application environments, one that supports individual scientists in the analysis of functional genomic data, and another that supports the annotation of a pattern database. Both of these tasks require explicit representation and enactment of scientific processes, and have challenging performance requirements.
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| Final Report Summary |
myGrid has developed open source high-level service-based middleware to support the construction, management and sharing of data-intensive in silico experiments in biology.
myGrid offers toolkit of components content and services that (a) enable scientific users and specialist middleware developers to interact and interoperate with applications and toolkits, and (b) actively support the scientific method. We mainly consider in silico experiments to be workflows. Our flagship application using these components is the Taverna e-Scientists workflow workbench, which has been designed with and for bioinformaticians, and has been widely adopted by Life Scientists in the UK, USA and throughout Europe many of whom who are independent external users. Taverna has been downloaded over 9000 times; it is a one click install application that is a gateway to over 1000 publicly available data sets and applications, and takes one hour for a bioinformatician to master.
Using our components middleware developers elsewhere can incorporate workflows, manage services and organise metadata. Using our Taverna e-Scientist's workbench, bioinformaticians can help one another to effectively take advantage of a communities resources and know-how, even when these were not originally designed to be shared. This allows the scientists to get on with the science.
Taverna has been used to build and run workflows to: identify a mutation associated with the autoimmune disorder Graves' Disease in the I kappa B-epsilon gene; identify and classify proteins secreted by the anthrax bacterium; produce the first complete and accurate map of the region of chromosome 7 involved in Williams-Beuren Syndrome; automatically identify targets for protein structure and function studies; assist in the automatic reconstruction of genome-scale yeast metabolic pathways from distributed data sets and to study the metagenomics of freshwater microorganisms.
Our research work on the use of semantic technologies for e-Science has made us acknowledged leaders in the Semantic Grid and the practical application of the Semantic Web. We have pioneered the use of knowledge technologies for representing experimental provenance, and the intelligent sharing and assembling of workflows. We currently have over 99 refereed publications including 15 journal articles.
During our work we have established and maintained international strategic alliances with service providers, middleware developers, bioinformaticians and tool builders. myGrid is now a key component of a range of follow-on Life Science and Health care application projects, middleware research projects and international platforms such as EGEE and OMII. We have attracted funds to sustain myGrids research and development, and the support of its user base.
Thus we have achieved our proposed objectives, successfully juggling the tensions between basic research, advanced development, ongoing user support and collaborations with national and international projects, and making a significant impact on our user and middleware communities
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| Further Information: |
http://www.mygrid.org.uk |
| Organisation Website: |
http://www.man.ac.uk |
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