SBML to bond graphs: from conversion to composition
SBML to bond graphs: from conversion to composition
Abstract 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 plausibile 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. Graphical Abstractbiorxiv;2022.05.25.493355v1/UFIG1F1ufig1 HighlightsA framework to convert suitable SBML models of biochemical networks into bond graphs is developed.The framework is applied here to two interconnecting models of metabolism pathways.We automatically integrate the generated bond graph modules.We qualitatively illustrate the functionality of the composed model.
Pan Michael、Shahidi Niloofar、Tran Kenneth、Crampin Edmund J、Nickerson David P
Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne||School of Mathematics and Statistics, Faculty of Science, University of MelbourneAuckland Bioengineering Institute, University of AucklandAuckland Bioengineering Institute, University of AucklandSystems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne||School of Mathematics and Statistics, Faculty of Science, University of Melbourne||ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne||School of Medicine, University of MelbourneAuckland Bioengineering Institute, University of Auckland
生物科学研究方法、生物科学研究技术生物化学生物物理学
SBMLBioModelsbond graphsautomatic conversionautomatic compositionglycolysispentose phosphate pathway
Pan Michael,Shahidi Niloofar,Tran Kenneth,Crampin Edmund J,Nickerson David P.SBML to bond graphs: from conversion to composition[EB/OL].(2025-03-28)[2025-06-06].https://www.biorxiv.org/content/10.1101/2022.05.25.493355.点此复制
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