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Layering Toolbox

TPP, Moritz Lang & Antonis Papachristodoulou, PLoS Computational Biology, 2015

This work describes how to systematically decompose an SBML-encoded model of a biomolecular reaction network into functionalities, and investigate the behaviour of each functionality in the context of all combinations of the others. We have implemented this method in MATLAB through a toolbox, found here. Please check the documentation for licensing, requirements, and installation/usage instructions.

Model Reduction

TPP & Antonis Papachristodoulou, Journal of Theoretical Biology, 2012

This paper described how to implement a dissipativity analysis to estimate the model order reduction error. The attached MATLAB code is that referred to in the paper, used to estimate the error incurred by the reduction of the benchmark Michaelis-Menten enzyme kinetics. It has been developed for use with SOSTOOLS v2, which has recently been superseded by SOSTOOLS v3.