Tobias Pietzsch1,2, Lorenzo Duso1,2, Christoph Zechner1,2,3. 1. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany. 2. Center for Systems Biology Dresden, Dresden, 01307, Germany. 3. Cluster of Excellence Physics of Life, TU Dresden, Dresden, 01062, Germany.
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 (Duso and Zechner, 2020), 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/. Usage tutorials for Compartor are provided as Jupyter notebooks at https://github.com/zechnerlab/Compartor.
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 (Duso and Zechner, 2020), 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/. Usage tutorials for Compartor are provided as Jupyter notebooks at https://github.com/zechnerlab/Compartor.