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    "info": {
        "author": "Anna Zhukova",
        "author_email": "zhutchok@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Visualization",
            "Topic :: Software Development :: Libraries :: Python Modules"
        ],
        "description": "# Mimoza\n\n*Mimoza* is a a Python library for metabolic model visualization and navigation that allows you\nto explore your metabolic models in a semantically zoomable manner.\n\n*Mimoza* combines the [model generalization method](http://metamogen.gforge.inria.fr)\nwith the zooming user interface ([ZUI](http://en.wikipedia.org/wiki/Zooming_user_interface))\nparadigm and allows a human expert to explore metabolic network models in a semantically zoomable manner.\n\n*Mimoza* takes a metabolic model in [SBML](http://sbml.org) format, generalizes it to detect similar metabolites\nand similar reactions, and automatically creates a 3-level zoomable map:\n\n1. the most detailed view represents the initial network with the generalization-based layout\n  (similar metabolites and reactions are placed next to each other).\n2. the intermediate view shows the generalized versions of reactions and metabolites in each compartment;\n3. the general view represents the compartments and the transport reactions between them.\n\n*Mimoza* highlights the general model structure and the divergences from it, such as alternative paths or missing reactions,\nand allows a user to analyse it in a top-down manner.\n\nThe network map can be browsed online or downloaded as a [COMBINE archive](http://co.mbine.org/documents/archive>), containing:\n\n* all the files needed for offline browsing;\n* SBML files with the groups and layout extensions, representing the initial and generalized versions of your model\n  and their layout;\n* [SBGN](http://www.sbgn.org) representation of your model.\n\n\n## Article\n\nZhukova, A., Sherman, D. J. (2015) **Mimoza: Web-Based Semantic Zooming and Navigation in Metabolic Networks** *BMC Systems Biology*, **9:**10\n[doi:10.1186/s12918-015-0151-5](http://identifiers.org/doi/10.1186/s12918-015-0151-5)\n\n\n## Dependencies\n\n*Mimoza* uses [libSBML](http://sbml.org/Software/libSBML) library for python with the groups and layout extensions.\nTo install it:\n\n```bash\nsudo pip3 install python-libsbml-experimental\n```\n\n*Mimoza* uses [Model Generalization](https://github.com/annazhukova/mod_gen) library for python \nto produce generalized views of the model and [Mod_SBML](https://github.com/annazhukova/mod_sbml) library.\nTo install them\n\n```bash\nsudo pip3 install mod_sbml\nsudo pip3 install sbml_generalization\n```\n\n*Mimoza* uses [Tulip 4.4](http://tulip.labri.fr/Documentation/current/tulip-python/html/index.html) library for python to layout metabolic networks.\nTo install it:\n\n```bash\nsudo pip3 install tulip-python\n```\n\n*Mimoza* uses [SymPy](http://www.sympy.org), Python bindings for [geojson](https://pypi.python.org/pypi/geojson),\nand [Jinja2] (http://jinja.pocoo.org):\n\n```bash\nsudo pip3 install sympy\nsudo pip3 install geojson\nsudo pip3 install Jinja2\n```\n\nIf you want to have export of your maps in [SBGN PD](http://www.sbgn.org), \ninstall [libSBGN bindings for Python](https://github.com/matthiaskoenig/libsbgn-python):\n  \n```bash\nsudo pip3 install libsbgnpy\n```\n\n*Mimoza* also uses [Leaflet](http://leafletjs.com/), [the ChEBI Ontology](http://www.ebi.ac.uk/chebi/),\nand [the Gene Ontology](http://geneontology.org), but you do not need to install them.\n\n*Mimoza* was developed using [PyCharm](http://www.jetbrains.com/pycharm).\n\n\n## Installing Mimoza\n\nFrom the directory where you have extracted this archive, execute:\n\n```bash\npython3 setup.py\n```\n\nDo not forget to install the dependencies (see above).\n\n\n## Running Mimoza\n\nExecute:\n  \n```bash\npython3 ./main.py --model path_to_your_model.xml --verbose\n```\n\nThis will produce a [COMBINE archive](http://co.mbine.org/documents/archive), containing:\n\n* the visualized model (You can see the result in your browser (index.html file inside the COMBINE archive));\n* SBML files with the groups and layout extensions, representing the initial and generalized versions of your model\n  and their layout;\n* SBGN representation of your model (if the SBGN bindings are installed, see Dependencies).",
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