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MASSpy is a package for dynamic modeling of biological processes.

Project description

MASSpy - Mass Action Stoichiometric Simulation in Python

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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 seemlessly with COBRApy, a widely used modeling software package for constraint-based reconstruction and analysis of biochemical reaction systems. Therefore MASSpy can be used seperately from or in conjuction with COBRApy, thereby providing a wide range of modeling workflows and techniques. Additional information about COBRApy can be found in its documentation.

Installation

Check out the following information from the Quick Start guide to get started using MASSpy!

With Python 3.7+

The recommended method is to install MASSpy is to use pip to install the software from the Python Package Index It is recommended to do this inside a virtual environment::

pip install "masspy"

To install MASSpy with visualization dependencies:

pip install "masspy[visualization]"

To install MASSpy with all optional dependencies:

pip install "masspy[all]"

With Docker

To quickly get started with the latest version of MASSpy using Docker, run the following commands in a shell:

docker pull sbrg/masspy
docker run --rm \
    --mount type=volume,src=licenses,dst=/home/masspy_user/opt/licenses \
    --mount type=volume,src=mass_project,dst=/home/masspy_user/mass_project \
    --publish 8888:8888 \
    -it sbrg/masspy

From within the container, either run python or jupyter notebook --ip=0.0.0.0 --port=8888 depending on the desired Python workspace. Don't forget to change the port number if it is already being used!

Additional installation details

For additional details about how to set up an environment for MASSpy, including how to set up commercial optimizers and optional dependencies, check out the detailed Installation guide in the documentation!

Documentation

The documentation for MASSpy is found at https://masspy.rtfd.io with installation instructions and several tutorials for getting started. All documentation is generated using Sphinx and hosted by ReadTheDocs.

Cite

To cite the MASSpy software publication:

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.

Support

Not sure how to file an issue, want to contribute to MASSpy, or just looking for some general guidance? Check out the Support page!

License

The MASSpy source is released under the MIT license. However, please note that binary packages (e.g., GLPK, CPLEX, etc.) and other dependencies (e.g. openCOBRA packages, libRoadRunner, etc.) will be bound by their respective license agreements as well.

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