{ "info": { "author": "Zachary B. Haiman", "author_email": "zhaiman@eng.ucsd.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)", "License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)", "Operating System :: OS Independent", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: Implementation :: CPython", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Build Tools" ], "description": "masspy - Mass Action Stoichiometric Simulation in Python\n========================================================\n\nWhat is masspy?\n~~~~~~~~~~~~~~~\nThe **M**\\ass **A**\\ction **S**\\toichiometric **S**\\imulation for **Py**\\thon\n(**masspy**) is a modeling software package for the construction and\nanalysis of kinetic models of biochemical reaction systems.\n\nOne of the main goals of masspy is to integrate seamlessly with **cobrapy**,\na widely used constraint-based reconstruction and analysis python package in\norder to provide a wide range of modeling techniques that can be utilized\nseperately or together. For further information about cobrapy, please visit\ntheir `github page `_.\n\nCite\n----\nA manuscript is in preparation for publication and will be the proper reference\nfor citing the masspy in the future.\n\nInstallation\n~~~~~~~~~~~~\n\nThe recommended method to install masspy is to use pip to `install masspy from\nPyPI `_ (we recommend doing this\ninside a `virtual environment\n`_)::\n\n\tpip install masspy\n\nIf you downloaded the source code, run::\n\n\tpip install -e .\n\nin the ``masspy`` directory. For additional information, please refer to the\nthe `detailed installation instructions `_.\n\nContributing\n~~~~~~~~~~~~\n\nContributions are always welcome! Please read the `contributions\nguideline <.github/CONTRIBUTING.rst>`_\nto get started.\n\nLicense\n-------\n\nThe masspy source is released under both the GPL and LGPL licenses. You\nmay choose which license you choose to use the software under.\n\nThis program is free software: you can redistribute it and/or modify it\nunder the terms of the GNU General Public License or the Lesser GNU\nGeneral Public License as published by the Free Software Foundation,\neither version 2 of the License, or (at your option) any later version.\n\nThis program is distributed in the hope that it will be useful, but\nWITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General\nPublic License for more details.\n\n\nInstallation of masspy\n=======================\n\nAll releases require Python 3.4+ to be installed before proceeding.\nMac OS X (10.7+) and Ubuntu ship with Python. Windows users without python can\ndownload and install python from the `python website\n`_.\nPlease note that though Anaconda and other python distributions may work\nwith masspy, they are not explicitly supported (yet!).\n\nStable version installation\n~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nmasspy can be installed with any recent installation of pip.\nInstructions for several operating systems are below:\n\nMac OS X or Linux\n-----------------\n\n1. `install pip `_.\n2. In a terminal, run ``sudo pip install mass``\n\nWe highly recommend updating ``pip`` beforehand\n(``pip install pip --upgrade``).\n\nMicrosoft Windows\n-----------------\n\nThe preferred installation method on Windows is also to use pip. The\nlatest Windows installers for Python 3.4 and up include pip, so if you\nuse those you will already have pip.\n\n1. In a terminal, run ``C:\\Python36\\Scripts\\pip.exe install masspy``\n(you may need to adjust the path accordingly).\n\nTo install without pip, you will need to download and use the\nappropriate installer for your version of python from the `python\npackage index `_.\n\nInstallation for development\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nGet the `detailed contribution instructions `_ for\ncontributing to masspy.\n\nInstallation of optional dependencies\n=====================================\n\nOptional dependencies\n~~~~~~~~~~~~~~~~~~~~~\n\nOn windows, these can downloaded from `this site\n`_. On Mac/Linux, they can be\ninstalled using pip, or from the OS package manager (e.g brew, apt, yum).\n\n1. `libsbml `_ >= 5.10 to read/write SBML level 2\n files\n\n - `Windows libsbml installer `_\n - Use ``sudo pip install python-libsbml`` on Mac/Linux\n\n2. `lxml `_ to speed up read/write of SBML level 3 files.\nYou can install all packages directly by::\n\n pip install \"masspy[all]\"\n\nTesting your installation\n=========================\n\nCurrently masspy is still under development and testing. We apologize\nfor the inconvenience and provide further details on this page in a\nfuture update.\n\nFor now, if you have any questions or concerns, please email\nzhaiman@eng.ucsd.edu with \"masspy concerns\" in the subject line and we will\nget back to you as soon as we can.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "https://pypi.python.org/pypi/masspy", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/SBRG/masspy", "keywords": "metabolism biology kinetic modeling simulation programmingcobra", "license": "LGPL/GPL v2+", "maintainer": "Zachary B. 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