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Items: 1 to 20 of 459

1.

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.

2.

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
3.
4.

SBMLToolbox: an SBML toolbox for MATLAB users.

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

Bioinformatics. 2006 May 15;22(10):1275-7.

5.

A model diagram layout extension for SBML.

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

Bioinformatics. 2006 Aug 1;22(15):1879-85.

6.

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).

Yeh I, Karp PD, Noy NF, Altman RB.

Bioinformatics. 2003 Jan 22;19(2):241-8.

7.
8.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ.

J Integr Bioinform. 2015 Sep 4;12(2):266. doi: 10.2390/biecoll-jib-2015-266.

PMID:
26528564
9.

SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks.

Dräger A, Hassis N, Supper J, Schröder A, Zell A.

BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39.

10.

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

Zi Z, Klipp E.

Bioinformatics. 2006 Nov 1;22(21):2704-5.

11.

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

Li F, Li M, Xiao Z, Zhang P, Li J, Chen Z.

BMC Bioinformatics. 2006 Jan 11;7:13.

12.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2015 Sep 4;12(2):271. doi: 10.2390/biecoll-jib-2015-271.

PMID:
26528569
13.

An XML message broker framework for exchange and integration of microarray data.

Tjandra D, Wong S, Shen W, Pulliam B, Yu E, Esserman L.

Bioinformatics. 2003 Sep 22;19(14):1844-5.

14.

Supporting SBML as a model exchange format in software applications.

Keating SM, Le Novère N.

Methods Mol Biol. 2013;1021:201-25. doi: 10.1007/978-1-62703-450-0_11.

PMID:
23715987
15.

Systems biology markup language: Level 2 and beyond.

Finney A, Hucka M.

Biochem Soc Trans. 2003 Dec;31(Pt 6):1472-3.

PMID:
14641091
16.

The design of Jemboss: a graphical user interface to EMBOSS.

Carver T, Bleasby A.

Bioinformatics. 2003 Sep 22;19(14):1837-43.

17.

PIML: the Pathogen Information Markup Language.

He Y, Vines RR, Wattam AR, Abramochkin GV, Dickerman AW, Eckart JD, Sobral BW.

Bioinformatics. 2005 Jan 1;21(1):116-21.

18.

CellML2SBML: conversion of CellML into SBML.

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

Bioinformatics. 2006 Apr 15;22(8):1018-20.

19.

SBMLmerge, a system for combining biochemical network models.

Schulz M, Uhlendorf J, Klipp E, Liebermeister W.

Genome Inform. 2006;17(1):62-71. Review.

PMID:
17503356
20.

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.

Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C.

J Biomed Inform. 2004 Feb;37(1):43-53.

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