Welcome to Mimoza, a metabolic model visualization and navigation system!

Try Mimoza now by submitting your model (in SBML format):

Select SBML file

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:

  • the most detailed view represents the initial network with the generalization-based layout (similar metabolites and reactions are placed next to each other).
  • the intermediate view shows the generalized versions of reactions and metabolites in each compartment;
  • the general view represents the compartments and the transport reactions between them.

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 the model and their layouts;
  • SBGN representation of the model.

To learn more about or to cite Mimoza, see:
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.

Mimoza is developed by the MAGNOME team at the Inria Bordeaux research center. For any questions and comments please contact zhutchok@gmail.com.

Mimoza.zip - download the Mimoza code. You can install it locally, or as a Galaxy tool (download the config file).

The README file inside the Mimoza.zip archive provides the installation and usage instructions.

This is a peroxisome of a yeast Y. lipolytica. Zoom in to see the details.

Or have a look at the visualizations of:

Mimoza is powered by Leaflet, Model generalization library, ChEBI, Tulip, GeoJSON, jQuery, Python, libSBML, Python API for libSBGN, Codrops, IcoMoon, and PyCharm.