# MUFINS
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.