Compartor: a toolbox for the automatic generation of moment equations for dynamic compartment populations

Abstract

Abstract Summary Many biochemical processes in living organisms take place inside compartments that can interact with each other and remodel over time. In a recent work, we have shown how the stochastic dynamics of a compartmentalized biochemical system can be effectively studied using moment equations. With this technique, the time evolution of a compartment population is summarized using a finite number of ordinary differential equations, which can be analyzed very efficiently. However, the derivation of moment equations by hand can become time-consuming for systems comprising multiple reactants and interactions. Here we present Compartor, a toolbox that automatically generates the moment equations associated with a user-defined compartmentalized system. Through the moment equation method, Compartor renders the analysis of stochastic population models accessible to a broader scientific community. Availability and implementation Compartor is provided as a Python package and is available at https://pypi.org/project/compartor/. Source code and usage tutorials for Compartor are available at https://github.com/zechnerlab/Compartor.