Section: New Software and Platforms

Mimoza

Keywords: Systems Biology - Bioinformatics - Biotechnology

Functional Description: Mimoza uses metabolic model generalization and cartographic paradigms to allow human experts to explore a metabolic model in a hierarchical manner. Mimoza generalizes genome-scale metabolic models, by factoring equivalent reactions and metabolites while preserving reaction consistency. The software creates an zoomable representation of a model submitted by the user in SBML 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 , 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 resulting map can be explored on-line, or downloaded in a COMBINE archive. The zoomable representation is implemented using the Leaflet JavaScript library for mobile-friendly interactive maps. Users can click on reactions and compounds to see the information about their annotations.

News Of The Year: Mimoza is now available as a Docker image, and can be integrated with other containerized services using Pleiade's Alcyone system.

• Participants: Anna Zhukova and David James Sherman

• Contact: David James Sherman

• Publications: Knowledge-based generalization of metabolic models - Knowledge-based zooming for metabolic models - Knowledge-based generalization of metabolic networks: a practical study

• URL: http://mimoza.bordeaux.inria.fr/