hbgm

Hierarchical Bond Graph Modelling of Biochemical Networks

The bond graph approach to modelling biochemical networks is extended to allow hierarchical construction of complex models from simpler components. This is made possible by representing the simpler components as thermodynamically open systems exchanging mass and energy via ports. A key feature of this approach is that the resultant models are robustly thermodynamically compliant: the thermodynamic compliance is not dependent on precise numerical values of parameters. Moreover, the models are reusable due to the well-defined interface provided by the energy ports.

To extract bond graph model parameters from parameters found in the literature, general and compact formulae are developed to relate free-energy constants and equilibrium constants. The existence and uniqueness of solutions is considered in terms of fundamental properties of stoichiometric matrices. The approach is illustrated by building a hierarchical bond graph model of glycogenolysis in skeletal muscle.

Where is the publication?

Here is the arXiv link

How do I see the results and work with the code?

We suggest you use the Virtual Reference Environment for the project (what is this?), built using Vagrant. To do this, first install Vagrant and VirtualBox, then do:

$ git clone https://github.com/uomsystemsbiology/hbgm_vagrant.git
$ cd hbgm_vagrant
$ vagrant up

This will get the code for this project and build a virtual environment with scripts you can run to reproduce the computations and figures in the publication.