User:Jarle Pahr/Metabolic modelling

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COBRA Toolbox


See CobraPy


BioMet Toolbox /

BioMet Toolbox: genome-wide analysis of metabolism:


See ScrumPy

Integrative Metabolic Analysis Tool (iMAT)

Thermodynamic approaches

Biophys J. 2013 Jul 16;105(2):512-22. doi: 10.1016/j.bpj.2013.06.011. Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.

Human metabolic modelling

Medical metabolic modelling

Comparative metabolic modelling


Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism:

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis:

Network reconstruction

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM:


Metabolic maintenance

Maurice Cheung et al, A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions. The Plant Journa


iMAT: an integrative metabolic analysis tool:

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

Lerman JA*, Hyduke DR*, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. 2012 In silico method for modelling metabolism and gene product expression at genome scale. Nature Communications 3:929.

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Molecular Systems Biology 9 Article number: 661 doi:10.1038/msb.2013.18 Published online: 30 April 2013. :