MASSpy: Modeling Dynamic Biological Processes in Python

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Welcome to MASSpy’s Documentation!

The Mass Action Stoichiometric Simulation python (MASSpy) package contains modules for the construction, simulation, and analysis of kinetic models of biochemical reaction systems.

MASSpy is built to integrate seamlessly with COBRApy [ELPH13], a widely used modeling software package for constraint-based reconstruction and analysis of biochemical reaction systems. MASSpy can be used separately from or in conjunction with COBRApy, providing a vast assortment of modeling techniques and tools that enable different workflows. Additional information about COBRApy can be found in its documentation or GitHub page.


A manuscript is in preparation for publication and will be the proper reference for citing the MASSpy software package in the future. In the meantime, feel free to cite the preprint [HZK+20], which can be found at bioRxiv.

The code and instsructions to reproduce the results presented in the publication is located in the MASSpy-publication GitHub Repository.

Installation and Setup

There are various ways to get started with the MASSpy package. The guides below provide instructions on how to set up a MASSpy environment best suited to your needs.

Quick Start Guide:

Ready to dive into MASSpy right away? Check out the Quick Start Guide.

Optimization Solvers:

In order to utilize certain MASSpy features, additional optimization capabilities (e.g., quadratic programming) are necessary. Read more at Optimization Solvers.

Docker Containers:

Need a standardized, ready-to-deploy container for your project? Learn how to set up Using MASSpy with Docker for MASSpy.

Once MASSpy is installed, check out the step-by-step tutorials below to learn how to use MASSpy!

Educational Resources

Need to review the basic principles of dynamic simulation and analysis? Educational resources utilizing MASSpy are outlined below and available for academic purposes.


Not sure how to use a specific method or function? Try searching the API Reference!

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