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This article is part of the supplement: BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology

Open Access Poster presentation

SHARKview: a tool for the visualization of systems biology data

John W Pinney*, John M Starkovich, Peter Li and David L Robertson

Author Affiliations

University of Manchester, Manchester, UK

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BMC Systems Biology 2007, 1(Suppl 1):P33  doi:10.1186/1752-0509-1-S1-P33

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1752-0509/1/S1/P33


Published:8 May 2007

© 2007 Pinney et al; licensee BioMed Central Ltd.

Background

SHARKview is a freely available program to enable the interactive exploration of biological models encoded in the BioPAX or SBML exchange formats. This includes the ability to browse a model by pathway, physical entity, or interaction as well as the ability to overlay quantitative data such as gene expression levels onto the components of a model.

Results

Using Saccharomyces cerevisiae models obtained from online resources in conjunction with expression data from several different studies, we show how SHARKview can be used to visualise mRNA expression level changes for the proteins composing a pathway. Pathways analysed include both metabolic and genetic regulatory pathways.

Conclusion

Beyond simply displaying the model structure, the facility to incorporate and visualise transcriptomic, proteomic or metabolomic data in the context of a number of different cellular pathways will make SHARKview a very useful tool for systems biologists.

thumbnailFigure 1. Interface of the SHARKview