Mimoza: web-based semantic zooming and navigation in metabolic networks

Anna Zhukova (1, 2) , David James Sherman (2, 1)

1 PLEIADE - from patterns to models in computational biodiversity and biotechnology
2 LaBRI - Laboratoire Bordelais de Recherche en Informatique

Background: The complexity of genome-scale metabolic models makes them quite difficult for human users to read, since they contain thousands of reactions that must be included for accurate computer simulation. Interestingly, hidden similarities between groups of reactions can be discovered, and generalized to reveal higher-level patterns. Results: The web-based navigation system Mimoza allows a human expert to explore metabolic network models in a semantically zoomable manner: The most general view represents the compartments of the model; the next view shows the generalized versions of reactions and metabolites in each compartment; and the most detailed view represents the initial network with the generalization-based layout (where similar metabolites and reactions are placed next to each other). It allows a human expert to grasp the general structure of the network and analyze it in a top-down manner. Conclusions: Mimoza can be installed standalone, or used on-line at http://mimoza.bordeaux.inria.fr/, or installed in a Galaxy server for use in workflows. Mimoza views can be embedded in web pages, or downloaded as COMBINE archives.

Mots clés: Visualization; Metabolic modeling; Model generalization

Domaines: Bio-informatique [q-bio.QM]

Anna Zhukova, David James Sherman. Mimoza: web-based semantic zooming and navigation in metabolic networks. BMC Systems Biology, 2015, 9, pp.10. ⟨10.1186/s12918-015-0151-5⟩. ⟨hal-01123715⟩