Shahidi Niloofar, Pan Michael, Tran Kenneth, Crampin Edmund J, Nickerson David P
Auckland Bioengineering Institute, University of Auckland, Auckland, 1010, New Zealand.
Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Melbourne, 3010, Victoria, Australia; School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, 3010, Victoria, Australia.
Math Biosci. 2022 Oct;352:108901. doi: 10.1016/j.mbs.2022.108901. Epub 2022 Sep 9.
The Systems Biology Markup Language (SBML) is a popular software-independent XML-based format for describing models of biological phenomena. The BioModels Database is the largest online repository of SBML models. Several tools and platforms are available to support the reuse and composition of SBML models. However, these tools do not explicitly assess whether models are physically plausible or thermodynamically consistent. This often leads to ill-posed models that are physically impossible, impeding the development of realistic complex models in biology. Here, we present a framework that can automatically convert SBML models into bond graphs, which imposes energy conservation laws on these models. The new bond graph models are easily mergeable, resulting in physically plausible coupled models. We illustrate this by automatically converting and coupling a model of pyruvate distribution to a model of the pentose phosphate pathway.
系统生物学标记语言（SBML）是一种流行的、独立于软件的基于XML的格式，用于描述生物现象模型。生物模型数据库是最大的SBML模型在线存储库。有几种工具和平台可用于支持SBML模型的重用和组合。然而，这些工具并未明确评估模型在物理上是否合理或在热力学上是否一致。这常常导致出现物理上不可能的不适定模型，阻碍了生物学中现实复杂模型的发展。在此，我们提出一个框架，该框架可以自动将SBML模型转换为键合图，从而将能量守恒定律应用于这些模型。新的键合图模型易于合并，从而产生物理上合理的耦合模型。我们通过将丙酮酸分布模型自动转换并耦合到磷酸戊糖途径模型来说明这一点。
