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Bioinformatics. 2014 Apr 1;30(7):903-7. doi: 10.1093/bioinformatics/btt641. Epub 2013 Nov 8.

SBML and CellML translation in antimony and JSim.

Author information

  • 1Department of Bioengineering, University of Washington, Seattle, WA, USA.

Abstract

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.

PMID:
24215024
[PubMed - indexed for MEDLINE]
PMCID:
PMC3967103
[Available on 2015-04-01]
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