ArticlePLoS computational biology2021
Modular assembly of dynamic models in systems biology.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- The Human Cardiac "Age-OME": Age-Specific Changes in Myocardial Molecular Expression.Aging cell · 2025Article
- 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
- Energy-based bond graph models of glucose transport with SLC transporters.Biophysical journal · 2025Article
- Energy-based modelling of single actin filament polymerization using bond graphs.Journal of the Royal Society, Interface · 2025Article
- A Prototype Software Framework for Transferable Computational Health Economic Models and Its Early Application in Youth Mental Health.PharmacoEconomics · 2024Article
- Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets.International journal of molecular sciences · 2023Review
- Sensitivity analysis of biochemical systems using bond graphs.Journal of the Royal Society, Interface · 2023Article
- Modelling speciation: Problems and implications.In silico biology · 2023Article
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- Physiologically Based Pharmacokinetic Modeling of Nanoparticle Biodistribution: A Review of Existing Models, Simulation Software, and Data Analysis Tools.International journal of molecular sciences · 2022Review
- Strategies and foundations for scientific discovery in longitudinal studies of bipolar disorder.Bipolar disorders · 2022Review
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the development of software tools to enhance model reusability, there has been a relative lack of consideration for how underlying biophysical principles can be applied to this space. Bond graphs combine the aspects of both modularity and physics-based modelling. In this paper, we argue that bond graphs are compatible with recent developments in modularity and abstraction in systems biology, and are thus a desirable framework for constructing large-scale models. We use two examples to illustrate the utility of bond graphs in this context: a model of a mitogen-activated protein kinase (MAPK) cascade to illustrate the reusability of modules and a model of glycolysis to illustrate the ability to modify the model granularity.
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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.