MUFINS: Multi-Formalism Interaction Network Simulator

We present MUFINS software, implementing a unique set of approaches for multi-formalism simulation of molecular interaction networks in the living cell. We extend the constraint-based modelling (CBM) framework by incorporation of linear inhibition constraints, enabling for the first time linear modelling of networks simultaneously describing gene regulation, signalling and whole-cell metabolism at steady state. We include an example where a logical hypergraph model of a regulatory network is expressed by linear constraints and integrated with a Genome Scale Metabolic Network (GSMN) of mouse macrophage. MUFINS incorporates an extended version of our Quasi Steady State Petri Net approach to integrate dynamic models with CBM, which we demonstrate through a dynamic model of cortisol signalling integrated with the human Recon 2 GSMN and a model of nutrient dynamics in physiological compartments. Finally, we implement a number of methods for deriving metabolic states from ~omics data, including our new variant of the iMAT congruency approach. The software provides graphics user interface with network visualisation, which facilitates use by researchers who are not experienced in coding and mathematical modelling environments.

MUFINS is available under GNU GPL license.