Compartor

Compartor generates moment equations from user-defined interaction rules to represent stochastic dynamics of compartmentalized biochemical systems as a finite set of ordinary differential equations.

Key Features:

• Automatic Moment Equation Generation: Automatically derives moment equations from user-defined interaction rules for compartmentalized systems.
• Moment-to-ODE Conversion: Summarizes the time evolution of compartment populations using a finite set of ordinary differential equations (ODEs).
• Exportable Equations: Exports the generated ODEs as code in Python or Julia.
• Compartment Interaction Modeling: Handles compartments that interact and remodel over time to support stochastic population models.

Scientific Applications:

• Stochastic population analysis: Analyze stochastic population models via moment equations and ODE representations.
• Systems biology: Study dynamics of interacting compartments to elucidate cellular functions and mechanisms.
• Compartmentalized biochemical modeling: Model biochemical systems with compartments that interact and remodel over time.

Methodology:

Automatic derivation of moment equations from user-defined interaction rules, formulation of those moments as a finite set of ordinary differential equations, and export of the resulting ODEs as Python or Julia code.