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CellML2SBML: conversion of CellML into SBML

Schilstra, Maria J. and Li, Lu and Matthews, Joanne and Finney, Andrew and Hucka, Michael and Le Novère, Nicolas (2006) CellML2SBML: conversion of CellML into SBML. Bioinformatics, 22 (8). pp. 1018-1020. ISSN 1367-4803. https://resolver.caltech.edu/CaltechAUTHORS:20110727-113447666

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Abstract

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%.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1093/bioinformatics/btl047DOIArticle
http://bioinformatics.oxfordjournals.org/content/22/8/1018PublisherArticle
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Le Novère, Nicolas0000-0002-6309-7327
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.
Issue or Number:8
Record Number:CaltechAUTHORS:20110727-113447666
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20110727-113447666
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:24569
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:27 Jul 2011 22:37
Last Modified:09 Mar 2020 13:18

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