CellML2SBML: conversion of CellML into SBML

M. Schilstra; L. Li; J. Matthews; A. Finney; M. Hucka; N. Le Novere

doi:10.1093/bioinformatics/btl047

CellML2SBML: conversion of CellML into SBML

M. Schilstra, L. Li, J. Matthews, A. Finney, M. Hucka, N. Le Novere

Research output: Contribution to journal › Article › peer-review

25 Citations (Scopus)

77 Downloads (Pure)

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%

Original language	English
Pages (from-to)	1018-1020
Journal	Bioinformatics
Volume	22
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btl047
Publication status	Published - 2006

Access to Document

10.1093/bioinformatics/btl047

102145.pdf
“This is a pre-copy-editing, author produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version Schilstra, M. , Li, L. , Matthews, J. , Finney, A. and Hucka, M. (2006) 'CellML2SBML: conversion of CellML into SBML'. Bioinformatics 22 pp.1018-1020 is available online at: http://bioinformatics.oxfordjournals.org/archive/index.dtl" Copyright Oxford University Press DOI: 10.1093/bioinformatics/btl047

Cite this

@article{4160875c228b4bcba32e996f94141bd6,

title = "CellML2SBML: conversion of CellML into SBML",

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%",

author = "M. Schilstra and L. Li and J. Matthews and A. Finney and M. Hucka and {Le Novere}, N.",

note = "“This is a pre-copy-editing, author produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version Schilstra, M. , Li, L. , Matthews, J. , Finney, A. and Hucka, M. (2006) 'CellML2SBML: conversion of CellML into SBML'. Bioinformatics 22 pp.1018-1020 is available online at: http://bioinformatics.oxfordjournals.org/archive/index.dtl{"} Copyright Oxford University Press DOI: 10.1093/bioinformatics/btl047",

year = "2006",

doi = "10.1093/bioinformatics/btl047",

language = "English",

volume = "22",

pages = "1018--1020",

journal = "Bioinformatics",

publisher = "Oxford University Press (OUP)",

number = "8",

}

TY - JOUR

T1 - CellML2SBML

T2 - conversion of CellML into SBML

AU - Schilstra, M.

AU - Li, L.

AU - Matthews, J.

AU - Finney, A.

AU - Hucka, M.

AU - Le Novere, N.

N1 - “This is a pre-copy-editing, author produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version Schilstra, M. , Li, L. , Matthews, J. , Finney, A. and Hucka, M. (2006) 'CellML2SBML: conversion of CellML into SBML'. Bioinformatics 22 pp.1018-1020 is available online at: http://bioinformatics.oxfordjournals.org/archive/index.dtl" Copyright Oxford University Press DOI: 10.1093/bioinformatics/btl047

PY - 2006

Y1 - 2006

N2 - 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%

AB - 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%

U2 - 10.1093/bioinformatics/btl047

DO - 10.1093/bioinformatics/btl047

M3 - Article

VL - 22

SP - 1018

EP - 1020

JO - Bioinformatics

JF - Bioinformatics

IS - 8

ER -

CellML2SBML: conversion of CellML into SBML

Abstract

Access to Document

Fingerprint

Cite this