Genome-scale Metabolic Modeling Tools¶

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antiSMASH¶

please see antiSMASH page.

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BiGMeC¶

BiGMeC (Biosynthetic Gene cluster Metabolic pathway Construction) is a pipeline that leverages antiSMASH results to create the metabolic pathway corresponding to a PKS or NRPS biosynthetic gene cluster.

Year published: 2021

Link:

• https://github.com/AlmaasLab/BiGMeC

Reference:

• Sulheim, S., Fossheim, F.A., Wentzel, A. et al., 2021, BMC Bioinform, 22:81

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CoReCo¶

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

Year published: 2014

Link:

• https://github.com/esaskar/CoReCo

Reference:

• Pitkanen, E., et al., 2014, PLoS Comput. Biol. 10:e1003465

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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

Link:

• http://f-a-m-e.fame-vu.vm.surfsara.nl/ajax/page1.php

Reference:

• Boele, J., et al., 2012, BMC Syst. Biol. 6:8

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GEMSiRV¶

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

Year published: 2012

Link:

• http://sb.nhri.org.tw/GEMSiRV/en/GEMSiRV

Reference:

• Liao, Y. C., et al., 2012, Bioinformatics 28:1752-8

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MEMOSys¶

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

Year published: 2011

Link:

• https://memosys.i-med.ac.at/MEMOSys/home.seam

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

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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

Link:

• http://www.merlin-sysbio.org/

Reference:

• Dias, O., et al., 2015, Nucleic Acids Res. 43:3899-910

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

Link:

• http://bioinformatics.ai.sri.com/ptools/

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

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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

Link:

• http://www.microbesflux.org/

Reference:

• Feng, X., et al., 2012, BMC Syst. Biol. 6:94

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Model SEED¶

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

Year published: 2010

Reference:

• Henry, C. S., et al., 2010, Nat. Biotechnol. 28:977-82

Link:

• http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView

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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

Reference:

• Mueller, T. J., et al., 2013, BMC Syst. Biol. 7:142

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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

Link:

• http://biomet-toolbox.org/index.php?page=downtools-raven

Reference:

• Agren, R., et al., 2013, PLoS Comput. Biol. 9:e1002980

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SuBliMinaL Toolbox¶

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

Year published: 2011

Link:

• http://www.mcisb.org/resources/subliminal/

Reference:

• Swainston, N., et al., 2011, J Integr Bioinform 8:186

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