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Bioinformatics Advance Access published online on February 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl047
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 3, 2006
Revised February 6, 2006
Accepted February 6, 2006

Applications note

CellML2SBML: conversion of CellML into SBML

Maria J. Schilstra 1 *, Lu Li 2, Joanne Matthews 1, Andrew Finney 3, Michael Hucka 4, and Nicolas Le Novère 2

1 Biological and Neural Computation Group, STRI, University of Hertfordshire, Hatfield, AL10 9AB, UK
2 Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
3 Physiomics PLC, Magdalen Centre, Oxford Science Park, Oxford, OX4 4GA, UK
4 Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA

* To whom correspondence should be addressed.
Maria J. Schilstra, E-mail: m.j.1.schilstra{at}herts.ac.uk


  Abstract

Summary: CellML and SBML are XML-based languages for storage and exchange of molecular biological and physiological reaction models. They use very similar subsets of MathML to specify the mathematical aspects of the models. CellML2SBML is implemented as a suite of XSLT stylesheets that, when applied consecutively, convert models expressed in CellML into SBML without significant loss of information. The converter is based on the most recent stable versions of the languages (CellML version 1.1; SBML Level 2 Version 1), and the XSLT used in the stylesheets adheres to the XSLT version 1.0 specification. Of all 306 models in the CellML repository in April 2005, CellML2SBML converted 91% automatically into SBML. Minor manual changes to the unit definitions in the originals raised the percentage of successful conversions to 96%.

Availability: http://sbml.org/software/cellml2sbml/.

Supplementary information: Instructions for use and further documentation available on http://sbml.org/software/cellml2sbml/.

Associate Editor: Thomas Lengauer
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