PT  - JOURNAL ARTICLE
AU  - Niloofar Shahidi
AU  - Michael Pan
AU  - Kenneth Tran
AU  - Edmund J Crampin
AU  - David P Nickerson
TI  - SBML to bond graphs: from conversion to composition
AID  - 10.1101/2022.05.25.493355
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.05.25.493355
4099  - http://biorxiv.org/content/early/2022/05/29/2022.05.25.493355.short
4100  - http://biorxiv.org/content/early/2022/05/29/2022.05.25.493355.full
AB  - 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.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.Competing Interest StatementThe authors have declared no competing interest.