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SBML zoomable visualization utilities.

Project 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](
with the zooming user interface ([ZUI](
paradigm and allows a human expert to explore metabolic network models in a semantically zoomable manner.

*Mimoza* takes a metabolic model in [SBML]( 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](>), 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]( 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

## Dependencies

*Mimoza* uses [libSBML]( library for python with the groups and layout extensions.
To install it:

sudo pip3 install python-libsbml-experimental

*Mimoza* uses [Model Generalization]( library for python
to produce generalized views of the model and [Mod_SBML]( library.
To install them

sudo pip3 install mod_sbml
sudo pip3 install sbml_generalization

*Mimoza* uses [Tulip 4.4]( library for python to layout metabolic networks.
To install it:

sudo pip3 install tulip-python

*Mimoza* uses [SymPy](, Python bindings for [geojson](,
and [Jinja2] (

sudo pip3 install sympy
sudo pip3 install geojson
sudo pip3 install Jinja2

If you want to have export of your maps in [SBGN PD](,
install [libSBGN bindings for Python](

sudo pip3 install libsbgnpy

*Mimoza* also uses [Leaflet](, [the ChEBI Ontology](,
and [the Gene Ontology](, but you do not need to install them.

*Mimoza* was developed using [PyCharm](

## Installing Mimoza

From the directory where you have extracted this archive, execute:


Do not forget to install the dependencies (see above).

## Running Mimoza


python3 ./ --model path_to_your_model.xml --verbose

This will produce a [COMBINE 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).

Project details

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