Anna Zhukova1, David J Sherman2. 1. Inria/Université Bordeaux/CNRS joint project-team MAGNOME, 351, cours de la Libération, Talence, F-33405, France. anna.zhukova@inria.fr. 2. Inria/Université Bordeaux/CNRS joint project-team MAGNOME, 351, cours de la Libération, Talence, F-33405, France. david.sherman@inria.fr.
Abstract
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.
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.
Authors: Ron Caspi; Tomer Altman; Kate Dreher; Carol A Fulcher; Pallavi Subhraveti; Ingrid M Keseler; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Lukas A Mueller; Quang Ong; Suzanne Paley; Anuradha Pujar; Alexander G Shearer; Michael Travers; Deepika Weerasinghe; Peifen Zhang; Peter D Karp Journal: Nucleic Acids Res Date: 2011-11-18 Impact factor: 16.971
Authors: Esa Pitkänen; Paula Jouhten; Jian Hou; Muhammad Fahad Syed; Peter Blomberg; Jana Kludas; Merja Oja; Liisa Holm; Merja Penttilä; Juho Rousu; Mikko Arvas Journal: PLoS Comput Biol Date: 2014-02-06 Impact factor: 4.475