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/.
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/.
Authors: Colin S Gillespie; Darren J Wilkinson; Carole J Proctor; Daryl P Shanley; Richard J Boys; Thomas B L Kirkwood Journal: Bioinformatics Date: 2006-01-12 Impact factor: 6.937
Authors: Nicolas Le Novère; Benjamin Bornstein; Alexander Broicher; Mélanie Courtot; Marco Donizelli; Harish Dharuri; Lu Li; Herbert Sauro; Maria Schilstra; Bruce Shapiro; Jacky L Snoep; Michael Hucka Journal: Nucleic Acids Res Date: 2006-01-01 Impact factor: 16.971
Authors: Endre T Somogyi; Jean-Marie Bouteiller; James A Glazier; Matthias König; J Kyle Medley; Maciej H Swat; Herbert M Sauro Journal: Bioinformatics Date: 2015-06-17 Impact factor: 6.937
Authors: T J Sego; Josua O Aponte-Serrano; Juliano Ferrari Gianlupi; Samuel R Heaps; Kira Breithaupt; Lutz Brusch; Jessica Crawshaw; James M Osborne; Ellen M Quardokus; Richard K Plemper; James A Glazier Journal: PLoS Comput Biol Date: 2020-12-21 Impact factor: 4.475
Authors: Christopher Schölzel; Valeria Blesius; Gernot Ernst; Alexander Goesmann; Andreas Dominik Journal: PLoS One Date: 2021-07-19 Impact factor: 3.240