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SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML).

Rodriguez N, Donizelli M, Le Novère N.

BMC Bioinformatics. 2007 Mar 6;8:79.PMID: 17341299 [PubMed - indexed for MEDLINE]Related articlesFree article

LibSBML: an API library for SBML.

Bornstein BJ, Keating SM, Jouraku A, Hucka M.

Bioinformatics. 2008 Mar 15;24(6):880-1. Epub 2008 Feb 5.PMID: 18252737 [PubMed - indexed for MEDLINE]Related articlesFree article

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

Zi Z, Zheng Y, Rundell AE, Klipp E.

BMC Bioinformatics. 2008 Aug 15;9:342.PMID: 18706080 [PubMed - indexed for MEDLINE]Related articlesFree article

SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

Zi Z, Klipp E.

Bioinformatics. 2006 Nov 1;22(21):2704-5. Epub 2006 Aug 22.PMID: 16926221 [PubMed - indexed for MEDLINE]Related articlesFree article

SBMLToolbox: an SBML toolbox for MATLAB users.

Keating SM, Bornstein BJ, Finney A, Hucka M.

Bioinformatics. 2006 May 15;22(10):1275-7. Epub 2006 Mar 30.PMID: 16574696 [PubMed - indexed for MEDLINE]Related articlesFree article

SBML export interface for the systems biology toolbox for MATLAB.

Schmidt H, Drews G, Vera J, Wolkenhauer O.

Bioinformatics. 2007 May 15;23(10):1297-8. Epub 2007 Mar 23.PMID: 17384017 [PubMed - indexed for MEDLINE]Related articlesFree article

A two-way interface between limited Systems Biology Markup Language and R.

Radivoyevitch T.

BMC Bioinformatics. 2004 Dec 7;5:190.PMID: 15585059 [PubMed - indexed for MEDLINE]Related articlesFree article

libAnnotationSBML: a library for exploiting SBML annotations.

Swainston N, Mendes P.

Bioinformatics. 2009 Sep 1;25(17):2292-3. Epub 2009 Jun 26.PMID: 19561017 [PubMed - indexed for MEDLINE]Related articlesFree article

An editor for pathway drawing and data visualization in the Biopathways Workbench.

Byrnes RW, Cotter D, Maer A, Li J, Nadeau D, Subramaniam S.

BMC Syst Biol. 2009 Oct 2;3:99.PMID: 19799790 [PubMed - indexed for MEDLINE]Related articlesFree article

Computer support for physiological cell modelling using an ontology on cell physiology.

Takao S, Kazuhiro K, Akira A, Takeshi I, Masanori K, Tetsuya M.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:4171-4.PMID: 17946607 [PubMed - indexed for MEDLINE]Related articles

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.

Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C.

Bioinformatics. 2006 Jun 1;22(11):1406-7. Epub 2006 Mar 9.PMID: 16527832 [PubMed - indexed for MEDLINE]Related articlesFree article

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum.

Bioinformatics. 2003 Mar 1;19(4):524-31.PMID: 12611808 [PubMed - indexed for MEDLINE]Related articlesFree article

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A.

Bioinformatics. 2009 Jun 1;25(11):1455-6. Epub 2009 Mar 23.PMID: 19307240 [PubMed - indexed for MEDLINE]Related articlesFree article

MathSBML: a package for manipulating SBML-based biological models.

Shapiro BE, Hucka M, Finney A, Doyle J.

Bioinformatics. 2004 Nov 1;20(16):2829-31. Epub 2004 Apr 15.PMID: 15087311 [PubMed - indexed for MEDLINE]Related articlesFree article

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

Schmidt H, Jirstrand M.

Bioinformatics. 2006 Feb 15;22(4):514-5. Epub 2005 Nov 29.PMID: 16317076 [PubMed - indexed for MEDLINE]Related articlesFree article

An automatic translation of SBML into Beta-binders.

Ciocchetta F, Priami C, Quaglia P.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):80-90.PMID: 18245877 [PubMed - indexed for MEDLINE]Related articles

A model diagram layout extension for SBML.

Gauges R, Rost U, Sahle S, Wegner K.

Bioinformatics. 2006 Aug 1;22(15):1879-85. Epub 2006 May 18.PMID: 16709586 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H.

Syst Biol (Stevenage). 2004 Jun;1(1):41-53. Review.PMID: 17052114 [PubMed - indexed for MEDLINE]Related articles

Automated manipulation of systems biology models using libSBML within Taverna workflows.

Li P, Oinn T, Soiland S, Kell DB.

Bioinformatics. 2008 Jan 15;24(2):287-9. Epub 2007 Dec 1.PMID: 18056069 [PubMed - indexed for MEDLINE]Related articlesFree article

The markup is the model: reasoning about systems biology models in the Semantic Web era.

Kell DB, Mendes P.

J Theor Biol. 2008 Jun 7;252(3):538-43. Epub 2007 Dec 3. Review.PMID: 18054049 [PubMed - indexed for MEDLINE]Related articles