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Short Description
Mimoza is a metabolic model visualization and navigation system
Full 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
doi:10.1186/s12918-015-0151-5

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] (http://jinja.pocoo.org):

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:

python3 setup.py

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

Running Mimoza

Execute:

python3 ./main.py --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).
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