Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
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DOI：
10.1049/sb:20045008
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发表时间：
2004-06-01
期刊：
影响因子：
--
通讯作者：
Kitano, H.
中科院分区：
文献类型：
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作者：
Hucka, M.;Finney, A.;Kitano, H.
生物学家越来越认识到，计算建模对于理解现在正在收集的大量复杂实验数据至关重要。如果要共享，评估和开发模型，则系统生物学领域需要商定的信息标准。在过去的四年中，我们的团队一直与国际建模者和软件开发人员合作开发系统生物学标记语言（SBML）。 SBML已成为事实上的标准格式，用于在生化反应和调节网络的水平上代表形式，定量和定性模型。在本文中，我们总结了SBML的当前和即将发布的版本，以及我们为开发用于支持和扩大其使用的软件基础架构的努力。我们还简要概述了当今可用的许多SBML兼容软件工具。
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.