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e-science tools for the genomic scale characterisation of bacterial secreted proteins

Lookup NU author(s): Tracy Craddock, Dr Phillip Lord, Professor Colin Harwood, Professor Anil Wipat

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Abstract

Within bioinformatics, a considerable amount of time is spent dealing with three problems; heterogeneity, distribution and autonomy - concerns that are mirrored in this study and which eScience technologies should help to address. We describe the design and architecture of a system which makes predictions about the secreted proteins of bacteria, describing both the strengths and some weaknesses of current e-Science technology. The focus of this study was on the development and application of e-Science workflows and a service oriented approach to the genomic scale detection and characterisation of secreted proteins from Bacillus species. Members of the genus Bacillus show a diverse range of properties, from the non-pathogenic B. subtilis to the causative agent of anthrax, B. anthracis. Protein predictions were automatically integrated into a custom relational database with an associated Web portal to facilitate expert curation, results browsing and querying. We describe the use of workflow technology to arrange secreted proteins into families and the subsequent study of the relationships between and within these families. The design of the workflows, the architecture and the reasoning behind our approach are discussed.


Publication metadata

Author(s): Craddock T, Lord P, Harwood C, Wipat A

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: Proceedings of the UK e-Science All Hands Meeting 2006

Year of Conference: 2006

Pages: 788-795

Publisher: National e-Science Centre

URL: http://www.allhands.org.uk/2006/proceedings/proceedings/proceedings.pdf

Library holdings: Search Newcastle University Library for this item

ISBN: 0955398800


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