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Bioinformatics Advance Access originally published online on August 24, 2009
Bioinformatics 2009 25(22):3012-3019; doi:10.1093/bioinformatics/btp495
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A method for visualizing CellML models

S. M. Wimalaratne 1,*, M. D. B. Halstead 1, C. M. Lloyd 1, M. T. Cooling 1, E. J. Crampin 1,2 and P. F. Nielsen 1,2

1Auckland Bioengineering Institute and 2Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand

*To whom correspondence should be addressed.


  Abstract

Motivation: The Physiome Project was established in 1997 to develop tools to facilitate international collaboration in the physiological sciences and the sharing of biological models and experimental data. The CellML language was developed to represent and exchange mathematical models of biological processes. CellML models can be very complicated, making it difficult to interpret the underlying physical and biological concepts and relationships captured/described in the mathematical model.

Results: To address this issue a set of ontologies was developed to explicitly annotate the biophysical concepts represented in the CellML models. This article presents a framework that combines a visual language, together with CellML ontologies, to support the visualization of the underlying physical and biological concepts described by the mathematical model and also their relationships with the CellML model. Automated CellML model visualization assists in the interpretation of model concepts and facilitates model communication and exchange between different communities.

Contact: sarala.dissanayake{at}auckland.ac.nz

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on May 23, 2009; revised on August 12, 2009; accepted on August 13, 2009

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