User:Jarle Pahr/Metabolic modelling: Difference between revisions
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=Software= | |||
RAVEN | ==COBRA Toolbox== | ||
==CobraPy== | |||
See [[User:Jarle Pahr/CobraPy|CobraPy]] | |||
==RAVEN== | |||
http://129.16.106.142/tools.php?c=raven | |||
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002980 | http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002980 | ||
BioMet Toolbox | ==BioMet Toolbox== | ||
http://www.sysbio.se/BioMet/ / http://129.16.106.142/ | |||
iMAT | BioMet Toolbox: genome-wide analysis of metabolism: http://www.ncbi.nlm.nih.gov/pubmed/20483918 | ||
==ScrumPy== | |||
See [[User:Jarle Pahr/ScrumPy|ScrumPy]] | |||
==Integrative Metabolic Analysis Tool (iMAT)== | |||
imat.cs.tau.ac.il | |||
http://csbl.bitbucket.org/tiger/doc/tiger/tie/imat.html | 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. | 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 | 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 | ||
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Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism: http://www.sciencedirect.com/science/article/pii/S0014579311004765 | 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= | =Bibliography= | ||
Latest revision as of 08:48, 18 August 2013
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
