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xBASE: A Bioinformatics Resource for the AgriFood Bacteriology Community

Institutions
University of Birmingham
Start date
2007
End date
2012
Objective
Bacteria play important roles at every stage in the human food chain, from improving the productivity of the soil to infecting the human consumer. The era of genomics and systems biology brings the promise of unparalleled progress in the study of bacteria of agricultural importance. However, if the average bacteriologist is unable to exploit the new flood of new sequence and interaction data, the whole genomics enterprise risks becoming expensive molecular stamp-collecting exercise. In recent years, we have met this challenge by providing bacteriologists with user-friendly tools for visualising, analysing and exploiting genome sequence data from bacteria that affect the human food chain. Our most recent effort is coliBASE, a web site and database dedicated to the comparative genomics of E. coli and related bacteria of relevance in the AgriFood context . As evidence of its success, this site is receiving greater than 1000 visitors a month.

In this proposal, we aim to sustain these facilities into the second decade of the twenty-first century by the development of xBASE, a series of taxon-specific databases, in which we add breadth (by covering a wider range of organisms) and add depth (by adding additional analytical and visualization tools, including new tools to cope with data from bacterial Systems Biology and meta-genomics projects) to our current repertoire. xBASE will be implemented through the use of a MySQL database running on a Linux cluster, augmented with visualization, graphing and other software.

Funding Source
Biotechnology and Biological Sciences Research Council
Project source
View this project
Project number
BBE0111791
Categories
Bacterial Pathogens
Escherichia coli
Natural Toxins