User:Jarle Pahr/Metabolic modelling

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Contents

Software

COBRA Toolbox

CobraPy

See CobraPy

RAVEN

http://129.16.106.142/tools.php?c=raven

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002980

BioMet Toolbox

http://www.sysbio.se/BioMet/ / http://129.16.106.142/

BioMet Toolbox: genome-wide analysis of metabolism: http://www.ncbi.nlm.nih.gov/pubmed/20483918

ScrumPy

See ScrumPy

Integrative Metabolic Analysis Tool (iMAT)

imat.cs.tau.ac.il

http://csbl.bitbucket.org/tiger/doc/tiger/tie/imat.html

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. http://www.ncbi.nlm.nih.gov/pubmed?cmd=Retrieve&list_uids=23870272


Human metabolic modelling

http://genomebiology.com/2004/6/1/r2

Medical metabolic modelling

http://www.cs.tau.ac.il/~ruppin/ccr_review.pdf


Comparative metabolic modelling

MultiMetEval:


Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism: http://www.sciencedirect.com/science/article/pii/S0014579311004765


Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001116

Network reconstruction

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003126

MEMOSys: http://www.biomedcentral.com/1752-0509/5/20


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

Bibliography

iMAT: an integrative metabolic analysis tool: http://bioinformatics.oxfordjournals.org/content/26/24/3140.long

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0045635


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. http://www.nature.com/ncomms/journal/v3/n7/full/ncomms1928.html

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. : http://www.nature.com/msb/journal/v9/n1/full/msb201318.html

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