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

被引：1959
|
作者：
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
机构：
[1] CALTECH, Pasadena, CA 91125 USA
[2] ERATO, Kitano Symbiot Syst Project, Tokyo, Japan
[3] Univ Hertfordshire, Hatfield AL10 9AB, Herts, England
[4] Syst Biol Inst, Tokyo, Japan
[5] Univ Calif Berkeley, Berkeley, CA 94720 USA
[6] NASA, JPL, Pasadena, CA USA
[7] Univ Cambridge, Cambridge, England
[8] CNRS, BIP, Marseille, France
[9] Univ Auckland, Auckland 1, New Zealand
[10] GlaxoSmithKline, Stevenage, Herts, England
[11] Max Planck Inst Complex Tech Syst, Magdeburg, Germany
[12] Univ Stellenbosch, ZA-7600 Stellenbosch, South Africa
[13] EML, Heidelberg, Germany
[14] Univ Connecticut, Ctr Hlth, Farmington, CT USA
[15] Virginia Bioinformat Inst, Blacksburg, VA USA
[16] Keio Univ, Tokyo, Japan
[17] Physiome Sci Inc, Princeton, NJ USA
[18] Sony Comp Sci Labs Inc, Tokyo, Japan
[19] LION Biosci AG, Heidelberg, Germany
[20] Univ Calif Irvine, Sch Informat & Comp Sci, Irvine, CA USA
来源：
BIOINFORMATICS | 2003年 / 19卷 / 04期
关键词：
D O I：
10.1093/bioinformatics/btg015
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. Results: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.
引用
收藏
页码：524 / 531
页数：8
相关论文
共 50 条
  • [1] SBMLeditor:: effective creation of models in the Systems Biology Markup Language (SBML)
    Rodriguez, Nicolas
    Donizelli, Marco
    Le Novere, Nicolas
    BMC BIOINFORMATICS, 2007, 8 (1)
  • [2] SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)
    Nicolas Rodriguez
    Marco Donizelli
    Nicolas Le Novère
    BMC Bioinformatics, 8
  • [3] Integrating Systems Biology Markup Language(SBML) with NEURON
    Anna S Bulanova
    Robert A McDougal
    Samuel A Neymotin
    Victor K Mutai
    William W Lytton
    Michael L Hines
    BMC Neuroscience, 15 (Suppl 1)
  • [4] SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool
    Zhike Zi
    Yanan Zheng
    Ann E Rundell
    Edda Klipp
    BMC Bioinformatics, 9
  • [5] SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool
    Zi, Zhike
    Zheng, Yanan
    Rundell, Ann E.
    Klipp, Edda
    BMC BIOINFORMATICS, 2008, 9 (1)
  • [6] The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
    Hucka, Michael
    Bergmann, Frank T.
    Hoops, Stefan
    Keating, Sarah M.
    Sahle, Sven
    Schaff, James C.
    Smith, Lucian P.
    Wilkinson, Darren J.
    JOURNAL OF INTEGRATIVE BIOINFORMATICS, 2015, 12 (02) : 266
  • [7] The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core
    Hucka, Michael
    Bergmann, Frank T.
    Draeger, Andreas
    Hoops, Stefan
    Keating, Sarah M.
    Le Novere, Nicolas
    Myers, Chris J.
    Olivier, Brett G.
    Sahle, Sven
    Schaff, James C.
    Smith, Lucian P.
    Waltemath, Dagmar
    Wilkinson, Darren J.
    JOURNAL OF INTEGRATIVE BIOINFORMATICS, 2018, 15 (01)
  • [8] SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models
    Zi, Zhike
    BIOINFORMATICS, 2011, 27 (07) : 1028 - 1029
  • [9] The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints
    Olivier, Brett G.
    Bergmann, Frank T.
    JOURNAL OF INTEGRATIVE BIOINFORMATICS, 2015, 12 (02): : 269
  • [10] The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core
    Gauges, Ralph
    Rost, Ursula
    Sahle, Sven
    Wengler, Katja
    Bergmann, Frank T.
    JOURNAL OF INTEGRATIVE BIOINFORMATICS, 2015, 12 (02): : 267
12345