{ "info": { "author": "Huan Jin", "author_email": "hji236@g.uky.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7" ], "description": "moiety_modeling\n===============\n\n.. image:: https://img.shields.io/pypi/v/moiety_modeling.svg\n :target: https://pypi.org/project/moiety_modeling\n :alt: Current library version\n\n.. image:: https://img.shields.io/pypi/pyversions/moiety_modeling.svg\n :target: https://pypi.org/project/moiety_modeling\n :alt: Supported Python versions\n\n.. image:: https://api.travis-ci.org/MoseleyBioinformaticsLab/moiety_modeling.svg?branch=master\n :target: https://travis-ci.org/MoseleyBioinformaticsLab/moiety_modeling\n :alt: Travis CI status\n\n\n`moiety_modeling` package provides facilities for moiety model representation, model optimization and model selection.\n\n\nCitation\n~~~~~~~~\n\nPlease cite the GitHub repository until our manuscript is accepted for \npublication: https://github.com/MoseleyBioinformaticsLab/moiety_modeling.git\n\n\nInstallation\n~~~~~~~~~~~~\n\n'moiety_modeling' runs under Python 3.6+ and is available through python3-pip.\nInstall via pip or clone the git repo and install the following depencies and \nyou are ready to go!\n\n\nInstall on Linux\n~~~~~~~~~~~~~~~~\n\nPip installation\n----------------\n\n.. code:: bash\n\n python3 -m pip install moiety-modeling\n\nGitHub Package installation\n---------------------------\n\nMake sure you have git_ installed:\n\n.. code:: bash\n\n git clone https://github.com/MoseleyBioinformaticsLab/moiety_modeling.git\n\n\nDependencies\n------------\n\n'moiety_modeling' requires the following Python libraries:\n\n * docopt_ for creating the command-line interface.\n * jsonpickle_ for saving Python objects in a JSON serializable form and outputting to a file.\n * numpy_ and matplotlib_ for visualization of optimized results.\n * scipy_ for application of optimization methods.\n * SAGA-optimize_ for parameters optimization. \n\n\nQuickstart\n~~~~~~~~~~\n\nUsing moiety_modeling to optimize parameters of moiety model.\n\n.. code:: bash\n\n python3 -m moiety_modeling modeling --models= --datasets= --optimizations= --repetition=100 --split --multiprocess --energyFunction=logDifference\n\nUsing moiety_modeling to analyze optimized results and select the optimal model.\n\n.. code:: bash\n\n python3 -m moiety_modeling analyze optimizations --a \n python3 -m moiety_modeling analyze rank --rankCriteria=AICc\n\nUsing moiety_modeling to visualize the optimzed results.\n\n.. code:: bash \n\n python3 -m moiety_modeling plot moiety \n\n.. note:: Read the User Guide and the ``moiety_modeling`` Tutorial on ReadTheDocs_ to learn more and to see code examples on using the ``moiety_modeling`` as a library and as a command-line tool.\n\nLicense\n~~~~~~~\n\nMade available under the terms of The modified Clear BSD License. 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