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The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.
If you are using RAVEN in any scientific work, please cite: R. Agren, et. al, “The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum,” PLoS Comput. Biol., vol. 9, no. 3, p. e1002980, Mar. 2013..
A manuscript describing RAVEN Toolbox 2 is currently being prepared. Citation details will therefore be updated in the near future.
Please report any technical issues and bugs here. For other issues, please contact Eduard Kerkhoven.
For more systems biology related software and recently published genome-scale models from the Systems and Synthetic Biology group at Chalmers University of Technology, please visit the Github page. For more information and publications by the Systems and Synthetic Biology please visit SysBio.