ArticleThe European physical journal. E, Soft matter2021
Analysing and simulating energy-based models in biology using BondGraphTools.
Article in The European physical journal. E, Soft matter, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- A thermodynamically consistent approach to modeling epithelial solute and water transport in the proximal convoluted tubule.Journal of biological physics · 2026Article
- Thermodynamically consistent, reduced models of gene regulatory networks.Royal Society open science · 2025Article
- Energy-based analysis of biochemical oscillators using bond graphs and linear control theory.Royal Society open science · 2025Article
- Sensitivity analysis of biochemical systems using bond graphs.Journal of the Royal Society, Interface · 2023Article
- The transition between acute and chronic infections in light of energy control: a mathematical model of energy flow in response to infection.Journal of the Royal Society, Interface · 2022Article
- Article
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
- Hierarchical semantic composition of biosimulation models using bond graphs.PLoS computational biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Like all physical systems, biological systems are constrained by the laws of physics. However, mathematical models of biochemistry frequently neglect the conservation of energy, leading to unrealistic behaviour. Energy-based models that are consistent with conservation of mass, charge and energy have the potential to aid the understanding of complex interactions between biological components, and are becoming easier to develop with recent advances in experimental measurements and databases. In this paper, we motivate the use of bond graphs (a modelling tool from engineering) for energy-based modelling and introduce, BondGraphTools, a Python library for constructing and analysing bond graph models. We use examples from biochemistry to illustrate how BondGraphTools can be used to automate model construction in systems biology while maintaining consistency with the laws of physics.
Indexed as
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.