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        "author": "Rob Edwards",
        "author_email": "raedwards@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: POSIX :: Linux",
            "Operating System :: Unix",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.0",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "PyFBA\n=====\n\nA python implementation of flux balance analysis to model microbial\nmetabolism\n\nAbout PyFBA\n-----------\n\nPyFBA is a Python flux-balance-analysis package that allows you to build\nmodels from genomes, gapfill models, and run flux-balance-analysis on\nthat model. The aim of PyFBA is to provide an extensible, python-based\nplatform for FBA work.\n\nPyFBA is being developed by Daniel Cuevas, Taylor O'Connell, and Rob\nEdwards in Rob's bioinformatics group at San Diego State University\ntogether with help from Janaka Edirisinghe, Chris Henry, Ross Overbeek\nand others at Argonne National Labs.\n\nInstalling PyFBA\n----------------\n\nTo use PyFBA you need Python 2.7 or greater, and you need to install the\nGNU GLPK and a Python wrapper for that program, pyGLPK available from\ngithub.\n\nWe also leverage the Model SEED GitHub repository with all the latest\nbiochemistry tables.\n\nOur installation page has detailed instructions on installing PyFBA and\ngetting everything running.\n\nGetting Started with PyFBA\n--------------------------\n\nOnce you have installed GLPK, PyGLPK, and PyFBA, you will most likely\nwant to build a model from a genome, gap fill that model, and test it\nfor growth on different media. We have detailed instructions that walk\nyou through the step-by-step procedures that you need to use to run flux\nbalance analysis on your own genome.\n\nCopyright and License\n\nPyFBA is copyright Daniel Cuevas, Taylor O'Connell, and Rob Edwards, and\nis released under the MIT license.\n\n\n\nVERSION 1.2\n\n\nCrucial edit to setup.py file\n\nAdding PyFBA.model package to list.\n\n\n\nVERSION 1.1\n\n\nUpdated all the code to work with Python 3.\n\nHowever, this breaks compatibility with Python 2 because of the \"errors\"\nkeyword in open.\n\nThe main changes include relative imports, a new class in the tests/\npackage to allow deep assertions,\nand using this type of construct with the open command to ignore unicode\nerrors in ModelSeed:\n\n    with open(ssfile, 'r', errors='replace') as sin:\n\nAdded function to obtain Model SEED complexes from a set of roles\n\n-   PyFBA/filters/roles_and_complexes.py\n\nAdded gap-fill step to add reactions based on existent EC numbers\n\n-   PyFBA/gapfill/ecnumbers.py\n\nOptimized and fixed bugs during gap-fill reaction minimization process\n\n-   PyFBA/gapfill/reaction_minimization.py\n\nNew Model class objects\n\nModel object contains functionality to make common processes easier to\nfacilitate.\n\n-   Generate model from RAST annotations\n-   Save model to hard disk location\n-   Load model from hard disk location\n-   Run FBA\n-   Run FBA and obtain flux values\n-   Run FBA and obtain flux values according to SEED subsystems\n-   Run gap-fill\n-   Remember which reactions were gap-filled reactions and which media\n\nNew iPython Notebooks\n\n-   Find a metabolite.ipynb\n-   PATRIC to FBA.ipynb\n-   Gap-fill_a_model.ipynb\n-   Saving_and_loading_a_model.ipynb\n\n\n\nVERSION 1.0\n\n\nAdded a CITATION.md\n\nPlease cite us if you use PyFBA\n\nAdded the iPython Notebook directory\n\nExample code showing:\n\nimporting an SBML file and running FBA\n\n-   iPythonNotebooks/Using_an_SBML_model.ipynb\n\nhow to build your model from functional roles and how to gap-fill that\nmodel on a media\n\n-   iPythonNotebook/From_functional_roles_to_gap-filling.ipynb\n\nAdded minimization by accuracy\n\nRemoved PyFBA/gapfill/minimize_additional_reactions.py and created\nreaction_minimization.py\n\nExample gap-fill pipeline\n\n-   example_code/gapfill_from_reactions_multiple_conditions.py\n\n\n\nVERSION 0.951\n\n\nRemoved the author tag\n\nIt is superflous, that is what versioning is for.\n\n\n\nVERSION 0.95\n\n\nSeveral changes to files:\n\nUpdated the subsystem functions and changed the name to a generic name. The date is handled by versioning!\n\n-   PyFBA/Biochemistry/SEED/Subsystems/SS_functions.txt\n-   PyFBA/Biochemistry/SEED/Subsystems/SS_functions_Oct_2015.txt\n\nChanging the version number\n\n-   PyFBA/INIT.py\n\nAdding reaction flux information that can be pulled after the sm has been solved\n\n-   PyFBA/fba/INIT.py\n-   PyFBA/fba/fluxes.py\n\nExternal reactions\n\nFixed an issue where we were over-incorporating reactions based on\nthings in the media\n\n-   PyFBA/fba/bounds.py\n-   PyFBA/parse/model_seed.py\n\nAdding verboseness\n\n-   PyFBA/fba/run_fba.py\n-   PyFBA/gapfill/roles.py\n-   PyFBA/parse/read_media.py\n\nReduced complexity\n\nWe only test the right half of the reactions if the left half do not\ngrow, and once we have <10 reactions\nto search through we just iterate and knock out each reaction\nsequentially. It is faster than the shuffle\napproach.\n\n-   PyFBA/gapfill/minimize_additional_reactions.py\n\nChanged the way we read roles\n\nSEED has a notion of multifunctional roles, and we added splitting those\nfunctions into roles\n\n-   PyFBA/gapfill/subsystem.py\n\nGap generation code\n\nTesting each of the individual reactions in a model\n\n-   PyFBA/gapgeneration/test_reactions.py\n-   example_code/test_individual_reactions.py\n\nShifted the order of gapfilling\n\nThis order makes more logical sense!\n\n-   example_code/gapfill_from_reactions.py\n\nUpdated the tests\n\nWith all these changes, the tests were not right\n\n-   PyFBA/tests/reaction_list.txt\n-   PyFBA/tests/test_fba.py\n-   PyFBA/tests/test_suggestions.py\n\n\n\nVERSION 0.9\n\n\nRefactored separating roles to functions. SEED has a concept of\nmultifunctional roles and this separates out our roles before we search\nfor them.\n\n\n\nVERSION 0.8\n\n\n\nVERSION 0.7\n\n\n\nVERSION 0.6\n\n\n-   Removed installation dependencies from setup.py because they break\n    installation! You need to install the dependencies manually\n-   Refactored the code to remove the os.environ dependencies\n\n\n\nVERSION 0.5\n\n\n-   Initial release\n\n",
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