Package: sbml_vis
# Mimoza*Mimoza* is a a Python library for metabolic model visualization and navigation that allows youto explore your metabolic models in a semantically zoomable manner.*Mimoza* combines the [model generalization method](http://metamogen.gforge.inria.fr)with the zooming user interface ([ZUI](http://en.wikipedia.org/wiki/Zooming_user_interface))paradigm and allows a human expert to explore metabolic network models in a semantically zoomable manner.*Mimoza* takes a metabolic model in [SBML](http://sbml.org) format, generalizes it to detect similar metabolitesand similar reactions, and automatically creates a 3-level zoomable map:1. the most detailed view represents the initial network with the generalization-based layout(similar metabolites and reactions are placed next to each other).2. the intermediate view shows the generalized versions of reactions and metabolites in each compartment;3. the general view represents the compartments and the transport reactions between them.*Mimoza* highlights the general model structure and the divergences from it, such as alternative paths or missing reactions,and allows a user to analyse it in a top-down manner.The network map can be browsed online or downloaded as a [COMBINE archive](http://co.mbine.org/documents/archive>), containing:* all the files needed for offline browsing;* SBML files with the groups and layout extensions, representing the initial and generalized versions of your modeland their layout;* [SBGN](http://www.sbgn.org) representation of your model.## ArticleZhukova, A., Sherman, D. J. (2015) **Mimoza: Web-Based Semantic Zooming and Navigation in Metabolic Networks** *BMC Systems Biology*, **9:**10[doi:10.1186/s12918-015-0151-5](http://identifiers.org/doi/10.1186/s12918-015-0151-5)## Dependencies*Mimoza* uses [libSBML](http://sbml.org/Software/libSBML) library for python with the groups and layout extensions.To install it:```bashsudo pip3 install python-libsbml-experimental```*Mimoza* uses [Model Generalization](https://github.com/annazhukova/mod_gen) library for pythonto produce generalized views of the model and [Mod_SBML](https://github.com/annazhukova/mod_sbml) library.To install them```bashsudo pip3 install mod_sbmlsudo pip3 install sbml_generalization```*Mimoza* uses [Tulip 4.4](http://tulip.labri.fr/Documentation/current/tulip-python/html/index.html) library for python to layout metabolic networks.To install it:```bashsudo pip3 install tulip-python```*Mimoza* uses [SymPy](http://www.sympy.org), Python bindings for [geojson](https://pypi.python.org/pypi/geojson),and [Jinja2] (http://jinja.pocoo.org):```bashsudo pip3 install sympysudo pip3 install geojsonsudo pip3 install Jinja2```If you want to have export of your maps in [SBGN PD](http://www.sbgn.org),install [libSBGN bindings for Python](https://github.com/matthiaskoenig/libsbgn-python):```bashsudo pip3 install libsbgnpy```*Mimoza* also uses [Leaflet](http://leafletjs.com/), [the ChEBI Ontology](http://www.ebi.ac.uk/chebi/),and [the Gene Ontology](http://geneontology.org), but you do not need to install them.*Mimoza* was developed using [PyCharm](http://www.jetbrains.com/pycharm).## Installing MimozaFrom the directory where you have extracted this archive, execute:```bashpython3 setup.py```Do not forget to install the dependencies (see above).## Running MimozaExecute:```bashpython3 ./main.py --model path_to_your_model.xml --verbose```This will produce a [COMBINE archive](http://co.mbine.org/documents/archive), containing:* the visualized model (You can see the result in your browser (index.html file inside the COMBINE archive));* SBML files with the groups and layout extensions, representing the initial and generalized versions of your modeland their layout;* SBGN representation of your model (if the SBGN bindings are installed, see Dependencies).