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

M. Hucka, A. Finney, B. J. Bornstein, S. M. Keating, B. E. Shapiro, J. Matthews, B. L. Kovitz, M. J. Schilstra, Akira Funahashi, J. C. Doyle, H. Kitano

Research output: Contribution to journalArticle

154 Citations (Scopus)

Abstract

Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

Original languageEnglish
Pages (from-to)41-53
Number of pages13
JournalSystems biology
Volume1
Issue number1
DOIs
Publication statusPublished - 2004 Jun
Externally publishedYes

Fingerprint

Markup languages
Systems Biology
Computational Biology
Language
Software
Infrastructure
Biochemical Networks
Reaction Network
Regulatory Networks
Computational Modeling
Software Tools
Experimental Data
Model

ASJC Scopus subject areas

  • Modelling and Simulation
  • Biotechnology
  • Cell Biology
  • Molecular Biology
  • Molecular Medicine
  • Genetics

Cite this

Evolving a lingua franca and associated software infrastructure for computational systems biology : the Systems Biology Markup Language (SBML) project. / Hucka, M.; Finney, A.; Bornstein, B. J.; Keating, S. M.; Shapiro, B. E.; Matthews, J.; Kovitz, B. L.; Schilstra, M. J.; Funahashi, Akira; Doyle, J. C.; Kitano, H.

In: Systems biology, Vol. 1, No. 1, 06.2004, p. 41-53.

Research output: Contribution to journalArticle

Hucka, M, Finney, A, Bornstein, BJ, Keating, SM, Shapiro, BE, Matthews, J, Kovitz, BL, Schilstra, MJ, Funahashi, A, Doyle, JC & Kitano, H 2004, 'Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.', Systems biology, vol. 1, no. 1, pp. 41-53. https://doi.org/10.1049/sb:20045008
Hucka, M. ; Finney, A. ; Bornstein, B. J. ; Keating, S. M. ; Shapiro, B. E. ; Matthews, J. ; Kovitz, B. L. ; Schilstra, M. J. ; Funahashi, Akira ; Doyle, J. C. ; Kitano, H. / Evolving a lingua franca and associated software infrastructure for computational systems biology : the Systems Biology Markup Language (SBML) project. In: Systems biology. 2004 ; Vol. 1, No. 1. pp. 41-53.
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