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Bioinformatics Advance Access originally published online on July 3, 2009
Bioinformatics 2009 25(18):2452-2454; doi:10.1093/bioinformatics/btp401
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Antimony: a modular model definition language

Lucian P. Smith *, Frank T. Bergmann , Deepak Chandran and Herbert M. Sauro

Department of Bioengineering, University of Washington, Seattle, WA, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Model exchange in systems and synthetic biology has been standardized for computers with the Systems Biology Markup Language (SBML) and CellML, but specialized software is needed for the generation of models in these formats. Text-based model definition languages allow researchers to create models simply, and then export them to a common exchange format. Modular languages allow researchers to create and combine complex models more easily. We saw a use for a modular text-based language, together with a translation library to allow other programs to read the models as well.

Summary: The Antimony language provides a way for a researcher to use simple text statements to create, import, and combine biological models, allowing complex models to be built from simpler models, and provides a special syntax for the creation of modular genetic networks. The libAntimony library allows other software packages to import these models and convert them either to SBML or their own internal format.

Availability: The Antimony language specification and the libAntimony library are available under a BSD license from http://antimony.sourceforge.net/

Contact: lpsmith{at}u.washington.edu

Associate Editor: Limsoon Wong

Received on March 23, 2009; revised on May 27, 2009; accepted on June 26, 2009

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