Metadata-Version: 1.1
Name: sbml_vis
Version: 0.1.2
Summary: SBML zoomable visualization utilities.
Home-page: https://github.com/annazhukova/mimoza
Author: Anna Zhukova
Author-email: zhutchok@gmail.com
License: UNKNOWN
Download-URL: https://github.com/annazhukova/mimoza/archive/0.1.2.zip
Description: # Mimoza
        
        *Mimoza* is a a Python library for metabolic model visualization and navigation that allows you
        to 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 metabolites
        and 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 model
          and their layout;
        * [SBGN](http://www.sbgn.org) representation of your model.
        
        
        ## Article
        
        Zhukova, 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:
        
        ```bash
        sudo pip3 install python-libsbml-experimental
        ```
        
        *Mimoza* uses [Model Generalization](https://github.com/annazhukova/mod_gen) library for python 
        to produce generalized views of the model and [Mod_SBML](https://github.com/annazhukova/mod_sbml) library.
        To install them
        
        ```bash
        sudo pip3 install mod_sbml
        sudo 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:
        
        ```bash
        sudo 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):
        
        ```bash
        sudo pip3 install sympy
        sudo pip3 install geojson
        sudo 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):
          
        ```bash
        sudo 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 Mimoza
        
        From the directory where you have extracted this archive, execute:
        
        ```bash
        python3 setup.py
        ```
        
        Do not forget to install the dependencies (see above).
        
        
        ## Running Mimoza
        
        Execute:
          
        ```bash
        python3 ./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 model
          and their layout;
        * SBGN representation of your model (if the SBGN bindings are installed, see Dependencies).
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Software Development :: Libraries :: Python Modules
