Michael Pan

Energy-based advection modelling using bond graphs

Peter J Gawthrop, Michael Pan

Journal article  |  2022  |  JOURNAL OF THE ROYAL SOCIETY INTERFACE

Advection, the transport of a substance by the flow of a fluid, is a key process in biological systems. The energy-based bond grap..

Network thermodynamics of biological systems: A bond graph approach

Peter J Gawthrop, Michael Pan

Journal article  |  2022  |  MATHEMATICAL BIOSCIENCES

Edmund Crampin (1973-2021) was at the forefront of Systems Biology research and his work will influence the field for years to com..

SBML to bond graphs: From conversion to composition

Niloofar Shahidi, Michael Pan, Kenneth Tran, Edmund J Crampin, David P Nickerson

Journal article  |  2022  |  MATHEMATICAL BIOSCIENCES

The Systems Biology Markup Language (SBML) is a popular software-independent XML-based format for describing models of biological ..

The Cell Physiome: What Do We Need in a Computational Physiology Framework for Predicting Single-Cell Biology?

Vijay Rajagopal, Senthil Arumugam, Peter J Hunter, Afshin Khadangi, Joshua Chung, Michael Pan

Journal article  |  2022  |  ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE

Modern biology and biomedicine are undergoing a big data explosion, needing advanced computational algorithms to extract mechanist..

A semantics, energy-based approach to automate biomodel composition

Niloofar Shahidi, Michael Pan, Kenneth Tran, Edmund J Crampin, David P Nickerson

Journal article  |  2022  |  PLOS ONE

Hierarchical modelling is essential to achieving complex, large-scale models. However, not all modelling schemes support hierarchi..

Analysing and simulating energy-based models in biology using BondGraphTools

Peter Cudmore, Michael Pan, Peter J Gawthrop, Edmund J Crampin

Journal article  |  2021  |  EUROPEAN PHYSICAL JOURNAL E

Like all physical systems, biological systems are constrained by the laws of physics. However, mathematical models of biochemistry..

Modular assembly of dynamic models in systems biology

Michael Pan, Peter J Gawthrop, Joseph Cursons, Edmund J Crampin

Journal article  |  2021  |  PLOS COMPUTATIONAL BIOLOGY

It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling proble..

Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data

Peter J Gawthrop, Michael Pan, Edmund J Crampin

Journal article  |  2021  |  JOURNAL OF THE ROYAL SOCIETY INTERFACE

Renewed interest in dynamic simulation models of biomolecular systems has arisen from advances in genome-wide measurement and appl..

Hierarchical semantic composition of biosimulation models using bond graphs

Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran, Edmund J Crampin, David P Nickerson

Journal article  |  2021  |  PLOS COMPUTATIONAL BIOLOGY

Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challen..

Analysing and simulating energy-based models in biology using BondGraphTools

Peter Cudmore, Michael Pan, Peter Gawthrop, Edmund Crampin

Journal article  |  2021

Like all physical systems, biological systems are constrained by the laws of physics. However, mathematical models of biochemistry..