Section: New Software and Platforms

Mimoza: Generalizing and Visualizing Metabolic Models

Participants : David James Sherman [correspondant] , Anna Zhukova.

Mimoza uses metabolic model generalization and cartographic paradigms to allow human experts to explore a metabolic model in a hierarchical manner. The software creates an zoomable representation of a model submitted by the user in SBML (http://sbml.org ) format. The most general view represents the compartments of the model; the next view shows the visualization of generalized versions of reactions and metabolites in each compartment (see section 6.3); and the most detailed view visualizes the initial model with the generalization-based layout (where similar metabolites and reactions are placed next to each other). The zoomable representation is implemented using the Leaflet (http://leafletjs.com ) JavaScript library for mobile-friendly interactive maps. Users can click on reactions and compounds to see the information about their annotations. The resulting map can be explored on-line, or downloaded in a COMBINE archive. The software and examples are available at http://mimoza.bordeaux.inria.fr .