index.rst

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.

Citation

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 /references.rst and /additional/code_repositories.rst 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 /installation/quickstart.rst.

Optimization Solvers:

In order to utilize certain MASSpy features, additional optimization capabilities (e.g., quadratic programming) are necessary. Read more at /installation/solvers.rst.

Docker Containers:

Need a standardized, ready-to-deploy container for your project? Learn how to set up /installation/docker.rst for MASSpy.

installation/quickstart.rst installation/solvers.rst installation/docker.rst installation/docker_detailed.rst

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

tutorials/getting_started_with_masspy.ipynb tutorials/constructing_models.ipynb tutorials/reading_writing_models.ipynb tutorials/dynamic_simulation.ipynb tutorials/plot_visualization.ipynb tutorials/enzyme_modules.ipynb tutorials/thermo_concentrations.ipynb tutorials/ensemble_modeling.ipynb tutorials/network_visualization.ipynb tutorials/quality_assurance.ipynb tutorials/global_configuration.ipynb tutorials/cobra_to_mass.ipynb tutorials/compartments.ipynb tutorials/import_export_optimization.ipynb

Example Gallery

Interested in seeing more of MASSpy in action? Browse through the Gallery </gallery/index.rst>.

gallery/index.rst

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.

• /education/sb2/index.rst

education/sb2/index.rst

API

Not sure how to use a specific method or function? Try searching the /autoapi/index.rst!

autoapi/index.rst

Additional Resources

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

additional/faqs.ipynb additional/code_repositories.rst references.rst

Indices and tables

• genindex
• modindex
• search