Genome-scale Metabolic Modeling Tools



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CoReCo

CoReCo (Comparative ReConstruction) is useful for modeling metabolisms of multiple related species.

Year published: 2014

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FAME

FAME (The Flux Analysis and Modeling Environment) allows streamlined analysis of a newly built metabolic model using various simulation methods.

Year published: 2012

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GEMSiRV

GEMSiRV (GEnome-scale Metabolic models Simulation, Reconstruction and Visualization) allows metabolic model reconstruction, simulation and visualization.

Year published: 2012

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MEMOSys

MEMOSys (MEtabolic MOdel research and development System) allows management, storage, and development of metabolic models.

Year published: 2011

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Reference: * Pabinger, S., et al., 2011, BMC Syst. Biol. 5:20


merlin

merlin (Metabolic Models Reconstruction Using Genome-Scale Information) is the most recently released metabolic modeling program with comprehensive genome annotation functionalities necessary for model generation.

Year published: 2015

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MetaFlux in Pathway Tools

MetaFlux in Pathway Tools provides strong supports for predicting, modeling, curating and visualizing metabolic pathways in connection with various functionalities of Pathway Tools.

Year published: 2012

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Reference: Latendresse, M., et al., 2012, Bioinformatics 28:388-96


MicrobesFlux

MicrobesFlux (a semi-automatic, web-based platform) allows both flux balance analysis (FBA) and dynamic FBA of a newly generated metabolic model.

Year published: 2012

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Model SEED

Model SEED is the first online high-throughput metabolic modeling tool.

Year published: 2010

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Mueller et al.

A high-throughput metabolic modeling framework was developed and used to reconstruct metabolic models of Cyanobacteria species. The framework is not available online.

Year published: 2013

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RAVEN Toolbox

RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox allows metabolic model reconstruction, simulation and visualization in MATLAB environment.

Year published: 2013

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SuBliMinaL Toolbox

SuBliMinaL Toolbox has strengths in managing chemical information for metabolites in a metabolic model.

Year published: 2011

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