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        "author": "Shuzhao Li, Andrei Todor",
        "author_email": "shuzhao.li@gmail.com",
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            "Development Status :: 4 - Beta",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Chemistry",
            "Topic :: Software Development :: Libraries :: Python Modules"
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        "description": "Mummichog\n=========\n\nMummichog is a Python program for analyzing data from high throughput, untargeted metabolomics. It leverages the organization of metabolic networks to predict functional activity directly from feature tables, bypassing metabolite identification. The features include\n\n* computing significantly enriched metabolic pathways\n* identifying significant modules in the metabolic network\n* visualization of top networks in web browser\n* visualization that also plugs into Cytoscape\n* tentative annotations\n* metabolic models for different species through plugins\n\nVersion 2 adds retention time for grouping ions, and improves adduct calculation and data tracking. The overall design has changed considerably to make the software more modular, easier to integrate into web services.\nThere is a separate version 1 package on PyPi as 'mummichog1'.\nThis package is provided for the convenience of developers and users, while the development of mummichog is swtiching more to web-based services.\n\n\nInstallation\n------------\nMummichog can be installed using pip (pip Installs Packages), the Python package manager:\n\n::\n\n    pip install mummichog\n\nThis is OS independent. To read more on pip `here <https://pip.pypa.io/en/stable/installing/#installing-with-get-pip-py>`.\n\nOne can also run mummichog without installing it. Direct python call on a downloaded copy will work.\nNote: a common error may come up in earlier versions as\n\n::\n\n    AttributeError: 'NoveView' object has no attribute 'sort'\n\nThis is caused by an incompatible update in networkx-2.0 library. It can be fixed by specifying\n\n::\n\n    sudo pip install networkx==1.10\n\nUsage\n-----\nInput data are a tab-delimited file with the first 4 columns in this order:\n\n::\n\n\tmz      rtime   p-value t-score\n\t186.0185697     463     0.000149751400132       3.82\n\t279.1773473     90      0.000399613326314       3.56\n\t344.1330624     124     0.000998323061251       -3.31\n\t215.9641894     132     0.00105418285794        -3.29\n\t177.0323244     77     0.00121065359218        3.25\n\nThe command line to run mummichog is like this:\n\n::\n\n\tmummichog -f testdata0710.txt -o myoutput\n\n\nThe initial paper on mummichog is described in Li et al. Predicting Network Activity from High Throughput Metabolomics. PLoS Computational Biology (2013); doi:10.1371/journal.pcbi.1003123.. More on `project website <http://mummichog.org>`.\n\n\n",
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        "license": "MIT",
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        "name": "mummichog",
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