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Abstract
BackgroundThe 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.ResultsThe 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 mannerConclusionsMimoza 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-015-0151-5) contains supplementary material, which is available to authorized users.
Highlights
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
Mimoza web server [71] lets one test visualization for smaller SBML models, with the possibility to download the result as a COMBINE archive [72], including the SBML file with groups and layout extensions, GeoJSON files with the coordinates of model elements, and the HTML, CSS and JavaScript files that are needed to view the visualization in a browser
Embedding After the visualization with Mimoza is done, we provide a link for embedding the view in another web page
Summary
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 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
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