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bioRxiv · 10.1101/2022.05.25.493355

SBML to bond graphs: from conversion to composition

Shahidi, N.·Pan, M.·Tran, K.·Crampin, E.·Nickerson, D. P.
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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 Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/493355v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@16f5998org.highwire.dtl.DTLVardef@1630beborg.highwire.dtl.DTLVardef@1a37309org.highwire.dtl.DTLVardef@1d582df_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA framework to convert suitable SBML models of biochemical networks into bond graphs is developed. C_LIO_LIThe framework is applied here to two interconnecting models of metabolism pathways. C_LIO_LIWe automatically integrate the generated bond graph modules. C_LIO_LIWe qualitatively illustrate the functionality of the composed model. C_LI

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Shahidi, N., Pan, M., Tran, K., Crampin, E., Nickerson, D. P.. 2022-05-29. SBML to bond graphs: from conversion to composition. https://doi.org/10.1101/2022.05.25.493355

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