MASSpy: Modeling Dynamic Biological Processes in Python
What is MASSpy?
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.
To cite the MASSpy software publication [HZK+21]:
Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT, Palsson BO (2021) MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. PLOS Computational Biology 17(1): e1008208. https://doi.org/10.1371/journal.pcbi.1008208
Additionally, please consider citing COBRApy, libRoadRunner, and other software dependencies of MASSpy! Citations and links to several dependencies as well as other useful literature sources are found in the Works Cited and Code Repositories sections of the documentation.
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!
- 1. Getting Started with MASSpy
- 2. Constructing Models
- 3. Reading and Writing Models
- 4. Dynamic Simulation of Models
- 5. Plotting and Visualization
- 6. Enzyme Modules
- 7. Thermodynamic Feasibility and Sampling of Metabolite Concentrations
- 8. Ensemble Modeling
- 9. Network Visualization
- 10. Checking Model Quality
- 11. Global Configuration
- 12. Using COBRApy with MASSpy
- 13. Modeling Volumes and Multiple Compartments
- 14. Import and Export of Optimization Problems
Interested in seeing more of MASSpy in action? Browse through the Gallery.
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!
The code and instsructions to reproduce the results presented in the publication is located in the MASSpy-publication GitHub Repository.