Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

SBML to bond graphs: from conversion to composition

View ORCID ProfileNiloofar Shahidi, View ORCID ProfileMichael Pan, View ORCID ProfileKenneth Tran, Edmund J Crampin, View ORCID ProfileDavid P Nickerson
doi: https://doi.org/10.1101/2022.05.25.493355
Niloofar Shahidi
aAuckland Bioengineering Institute, University of Auckland,, Auckland, 1010, Auckland, New Zealand
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Niloofar Shahidi
  • For correspondence: nsha457@aucklanduni.ac.nz
Michael Pan
bSystems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne,, Melbourne, 3010, Victoria, Australia
cSchool of Mathematics and Statistics, Faculty of Science, University of Melbourne,, Melbourne, 3010, Victoria, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Michael Pan
Kenneth Tran
aAuckland Bioengineering Institute, University of Auckland,, Auckland, 1010, Auckland, New Zealand
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kenneth Tran
Edmund J Crampin
bSystems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne,, Melbourne, 3010, Victoria, Australia
cSchool of Mathematics and Statistics, Faculty of Science, University of Melbourne,, Melbourne, 3010, Victoria, Australia
dARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne,, Melbourne, 3010, Victoria, Australia
eSchool of Medicine, University of Melbourne,, Melbourne, 3010, Victoria, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David P Nickerson
aAuckland Bioengineering Institute, University of Auckland,, Auckland, 1010, Auckland, New Zealand
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for David P Nickerson
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

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.

Figure
  • Download figure
  • Open in new tab

Highlights

  • A 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 Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/Niloofar-Sh/SBMLtoBGs

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted May 29, 2022.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
SBML to bond graphs: from conversion to composition
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
SBML to bond graphs: from conversion to composition
Niloofar Shahidi, Michael Pan, Kenneth Tran, Edmund J Crampin, David P Nickerson
bioRxiv 2022.05.25.493355; doi: https://doi.org/10.1101/2022.05.25.493355
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
SBML to bond graphs: from conversion to composition
Niloofar Shahidi, Michael Pan, Kenneth Tran, Edmund J Crampin, David P Nickerson
bioRxiv 2022.05.25.493355; doi: https://doi.org/10.1101/2022.05.25.493355

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioengineering
Subject Areas
All Articles
  • Animal Behavior and Cognition (4230)
  • Biochemistry (9123)
  • Bioengineering (6766)
  • Bioinformatics (23968)
  • Biophysics (12109)
  • Cancer Biology (9509)
  • Cell Biology (13753)
  • Clinical Trials (138)
  • Developmental Biology (7622)
  • Ecology (11674)
  • Epidemiology (2066)
  • Evolutionary Biology (15490)
  • Genetics (10630)
  • Genomics (14310)
  • Immunology (9473)
  • Microbiology (22821)
  • Molecular Biology (9086)
  • Neuroscience (48914)
  • Paleontology (355)
  • Pathology (1480)
  • Pharmacology and Toxicology (2566)
  • Physiology (3839)
  • Plant Biology (8322)
  • Scientific Communication and Education (1468)
  • Synthetic Biology (2295)
  • Systems Biology (6180)
  • Zoology (1299)