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Bioinformatics Advance Access originally published online on October 17, 2006
Bioinformatics 2006 22(24):3075-3081; doi:10.1093/bioinformatics/btl516
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Design and implementation of a tool for translating SBML into the biochemical stochastic {pi}-calculus

Claudio Eccher 1,2,* and Corrado Priami 1,3

1 DIT—University of Trento Trento, Italy
2 ITC-irst, Centre for Scientific and Technological Research Trento, Italy
3 The Microsoft Research—University of Trento Centre for Computational and Systems Biology Trento, Italy

*To whom correspondence should be addressed.

Motivation: SBML is becoming a standard ‘de-facto’ to represent and store biological models. Although SBML is very useful in defining ways of exchanging and storing biological information, it is not formal enough to allow direct translation into non ambiguous formal representation languages to perform analysis and simulation of models. We here suggest to map SBML models into process calculi representations.

Results: We implemented and validated a tool that translates SBML descriptions into stochastic {pi}-calculus specifications.

Availability: Source code is freely available for academic use by contacting the authors.

Contact: cleccher{at}itc.it

Received on June 14, 2006; revised on September 8, 2006; accepted on October 5, 2006

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