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MASSpy is a package for kinetic modeling and simulation of biological networks

Project description

MASSpy - Mass Action Stoichiometric Simulation in Python

PyPI

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 or github page.

Cite

A manuscript is in preparation for publication and will be the proper reference for citing the MASSpy in the future.

Installation

The recommended method is to install MASSpy is to use pip to install masspy from PyPI. It is recommended to do this inside a virtual environment):

pip install masspy

You can install all packages, including optional dependencies, directly by:

pip install masspy[all]

If you downloaded the source code, run:

pip install -e .

in the masspy source directory. For additional information, please refer to the the detailed installation instructions.

Contributing

Contributions are always welcome! Please read the contributions guideline to get started.

License

The MASSpy source is released under both the GPL and LGPL licenses. You may choose which license you choose to use the software under. However, please note that binary packages which include GLPK (such as the binary wheels distributed at https://pypi.python.org/pypi/cobra) and libRoadRunner will be bound by their licenses as well.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the Lesser GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Installation of MASSpy

All releases require Python 3.6+ to be installed before proceeding. Users without python can download and install python from the python website. Please note that though Anaconda and other python distributions may work with MASSpy, they are not explicitly supported.

Stable version installation

MASSpy can be installed with any recent installation of pip.

You can install all packages, including optional dependencies, directly by:

pip install masspy[all]

Instructions for several operating systems are below:

Mac OS X or Linux

  1. install pip.
  2. In a terminal, run sudo pip install masspy

We highly recommend updating pip beforehand (pip install pip --upgrade).

Microsoft Windows

The preferred installation method on Windows is also to use pip. The latest Windows installers for Python 3.4 and up include pip, so if you use those you will already have pip.

1. In a terminal, run C:\Python36\Scripts\pip.exe install masspy (you may need to adjust the path accordingly).

To install without pip, you will need to download and use the appropriate installer for your version of python from the python package index.

Installation for development

Get the detailed contribution instructions for contributing to MASSpy.

Testing your installation

Currently MASSpy is still under development and testing. We apologize for the inconvenience and provide further details on this page in a future update.

For now, if you have any questions or concerns, please email zhaiman@eng.ucsd.edu with “masspy concerns” in the subject line and we will get back to you as soon as we can.

Project details


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