MOTIVATION: The creation and exchange of biologically relevant models is of great interest to many researchers. When multiple standards are in use, models are more readily used and re-used if there exist robust translators between the various accepted formats. SUMMARY: Antimony 2.4 and JSim 2.10 provide translation capabilities from their own formats to SBML and CellML. All provided unique challenges, stemming from differences in each format's inherent design, in addition to differences in functionality. AVAILABILITY AND IMPLEMENTATION: Both programs are available under BSD licenses; Antimony from http://antimony.sourceforge.net/and JSim from http://physiome.org/jsim/. CONTACT: lpsmith@u.washington.edu.
MOTIVATION: The creation and exchange of biologically relevant models is of great interest to many researchers. When multiple standards are in use, models are more readily used and re-used if there exist robust translators between the various accepted formats. SUMMARY: Antimony 2.4 and JSim 2.10 provide translation capabilities from their own formats to SBML and CellML. All provided unique challenges, stemming from differences in each format's inherent design, in addition to differences in functionality. AVAILABILITY AND IMPLEMENTATION: Both programs are available under BSD licenses; Antimony from http://antimony.sourceforge.net/and JSim from http://physiome.org/jsim/. CONTACT: lpsmith@u.washington.edu.
Authors: M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang Journal: Bioinformatics Date: 2003-03-01 Impact factor: 6.937
Authors: Maria J Schilstra; Lu Li; Joanne Matthews; Andrew Finney; Michael Hucka; Nicolas Le Novère Journal: Bioinformatics Date: 2006-02-10 Impact factor: 6.937
Authors: Andrew K Miller; Justin Marsh; Adam Reeve; Alan Garny; Randall Britten; Matt Halstead; Jonathan Cooper; David P Nickerson; Poul F Nielsen Journal: BMC Bioinformatics Date: 2010-04-08 Impact factor: 3.169
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