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Published April 15, 2006 | Published
Journal Article Open

CellML2SBML: conversion of CellML into SBML


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%.

Additional Information

© 2006 The Author. Published by Oxford University Press. Received on January 3, 2006; revised and accepted on February 6, 2006. Advance Access publication February 10, 2006. The authors would like to thank Poul Nielsen and Autumn Cuellar of the CellML team, and the SBML Forum, for fruitful discussions. Associate Editor: Thomas Lengauer.

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