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, A. Funahashi, J. C. Doyle, H. Kitano

研究成果: Review article

156 引用 (Scopus)

抜粋

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.

元の言語English
ページ(範囲)41-53
ページ数13
ジャーナルSystems biology
1
発行部数1
DOI
出版物ステータスPublished - 2004 6

ASJC Scopus subject areas

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

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    Hucka, M., Finney, A., Bornstein, B. J., Keating, S. M., Shapiro, B. E., Matthews, J., Kovitz, B. L., Schilstra, M. J., Funahashi, A., Doyle, J. C., & Kitano, H. (2004). Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Systems biology, 1(1), 41-53. https://doi.org/10.1049/sb:20045008