Antimony: a modular model definition language.
BACKGROUND
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.


CONCLUSIONS
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.


BACKGROUND
The Antimony language specification and the libAntimony library are available under a BSD license from http://antimony.sourceforge.net/.
Smith
Lucian P
LP
Department of Bioengineering, University of Washington, Seattle, WA, USA. lpsmith@u.washington.edu
Bergmann
Frank T
FT
Chandran
Deepak
D
Sauro
Herbert M
HM
D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D012984:Software; D049490:Systems Biology