Skip Navigation


Bioinformatics Advance Access originally published online on February 10, 2006
Bioinformatics 2006 22(8):1018-1020; doi:10.1093/bioinformatics/btl047
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
22/8/1018    most recent
btl047v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (7)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Schilstra, M. J.
Right arrow Articles by Le Novère, N.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schilstra, M. J.
Right arrow Articles by Le Novère, N.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CellML2SBML: conversion of CellML into SBML

Maria J. Schilstra 1,*, Lu Li 2, Joanne Matthews 3, Andrew Finney 4, Michael Hucka 5 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 Biological and Neural Computation Group, STRI, University of Hertfordshire Hatfield AL10 9AB, UK
4 Physiomics PLC, Magdalen Centre Oxford Science Park, Oxford OX4 4GA, UK
5 Control and Dynamical Systems, California Institute of Technology Pasadena, CA 91125, USA

*To whom correspondence should be addressed.

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/

Contact: m.j.1.schilstra{at}herts.ac.uk

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

Received on January 3, 2006; revised on February 6, 2006; accepted on February 6, 2006

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J R Soc InterfaceHome page
L. Endler, N. Rodriguez, N. Juty, V. Chelliah, C. Laibe, C. Li, and N. Le Novere
Designing and encoding models for synthetic biology
J R Soc Interface, August 6, 2009; 6(Suppl_4): S405 - S417.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
E. Antezana, M. Kuiper, and V. Mironov
Biological knowledge management: the emerging role of the Semantic Web technologies
Brief Bioinform, July 1, 2009; 10(4): 392 - 407.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc AHome page
D. P. Nickerson and M. L. Buist
A physiome standards-based model publication paradigm
Phil Trans R Soc A, May 28, 2009; 367(1895): 1823 - 1844.
[Abstract] [Full Text] [PDF]

Home page
 J. Exp. Biol.Home page
N. P. Smith, E. J. Crampin, S. A. Niederer, J. B. Bassingthwaighte, and D. A. Beard
Computational biology of cardiac myocytes: proposed standards for the physiome
J. Exp. Biol., May 1, 2007; 210(9): 1576 - 1583.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
L. Stromback, V. Jakoniene, H. Tan, and P. Lambrix
Representing, storing and accessing molecular interaction data: a review of models and tools
Brief Bioinform, December 1, 2006; 7(4): 331 - 338.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
A. Ng, B. Bursteinas, Q. Gao, E. Mollison, and M. Zvelebil
Resources for integrative systems biology: from data through databases to networks and dynamic system models
Brief Bioinform, December 1, 2006; 7(4): 318 - 330.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.