BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=curation_notes.txthttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=BIOMD0000000473.pdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=BIOMD0000000473-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=BIOMD0000000473-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=manifest.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=BIOMD0000000473_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=BIOMD0000000473-matlab.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=metadata.rdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=BIOMD0000000473_url.sedmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=BIOMD0000000473.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=BIOMD0000000473.odehttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000473?filename=curation_image.pngprimary200OKKieran SmallboneManually curatedordinary differential equation modelL2V4https://www.ebi.ac.uk/biomodels/BIOMD0000000473falseBioModelsBIOMD0000000172 biomodels.dbModelsSBMLSmallbone2013 Yeast metabolic model with modular rate law, merged with Pritchard 20022013MODEL1302140005Messiha HLMessiha HL, Kent E, Malys N, Carroll KM, Mendes P, Smallbone K.10.1089/ind.2013.0003, Genome-scale kinetic models of metabolism are important for rational design of the metabolic engineering required for industrial biotechnology applications. They allow one to predict the alterations needed to optimize the flux or yield of the compounds of interest, while keeping the other functions of the host organism to a minimal, but essential, level. We define a pipeline for the generation of genome-scale kinetic models from reconstruction data. To build such a model, inputs of all concentrations, fluxes, rate laws, and kinetic parameters are required. However, we propose typical estimates for these numbers when experimental data are not available. While little data are required to produce the model, the pipeline ensures consistency with any known flux or concentration data, or any kinetic constants. We apply the method to create genome-scale models of Escherichia coli and Saccharomyces cerevisiae. We go on to show how these may be used to expand a detailed model of yeast glycolysis to the genome level.. null, null. Manchester Centre for Integrative Systems Biology and School of Computer Science, University of Manchester, Manchester Institute of Biotechnology, Manchester, UKkieran.smallbone@ncl.ac.uk10.1089/ind.2013.0003Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK.BIOMD0000000473biochemical pathways, host organism, scale tissue, Obligation, Ghrfr, Metabolic Process, Jurisprudence, Metabolic Concepts, Mbp1, bacterium E3, Embden-Meyerhof, sci, Embden Meyerhof Parnas Pathway, Status, Techniques, judicial aspects, Method, Constitutional Law, Concepts, HOW, How, Embden-Meyerhof Pathway, Enterococcus coli, Metabolism Concept, myd, Phenomenon, l(3)j5D5, 24B, Escherichia/Shigella coli, Genomes, catabolism, plant peltate hair, medicolegal aspects, stru, Mbp-1, E coli, Saccharomyes cerevisiae, Pathways, metabolic process resulting in cell growth, Baker, l(3)S053606, Court Decision, Saccharomyces uvarum var. melibiosus, CG10293, E. coli, Eschericia coli, Enteroaggregative Escherichia coli, l(3)j5B5, Legal Obligation, Methodological Studies, Saccharomyces capensis, Decision, Baker's, biotransformation, Legal Aspect, Mycoderma cerevisiae, juridical aspects, brewer's yeast, Catabolism, 0904/17, Pathway, Process, gyltl1b-b, metabolism resulting in cell growth, Court, Interest, anaerobic glycolysis, lit, Procedure, Embden-Meyerhof-Parnas, Enteroaggregative E. coli, Baker's Yeasts, Embden-Meyerhof-Parnas Pathway, Diffusely Adherent E. coli, Saccharomyces diastaticus, SZ1, MDDGA6, mKIAA0609, secretion, State, KIAA0609, little, fg, Yeast, Diffusely Adherent Escherichia coli, gyltl1b, Legal, Enteroinvasive E. coli, jurisprudence, mdc1d, expanded, whole genome, Methodological, Methodological Study, Embden-Meyerhof pathway, Biotechnologies, MDC1D, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, glycolysis, enr, enlarged, State Interests, Constitutional, anon-EST:Liang-2.39, litigation, Brewer's Yeast, Embden-Meyerhof Pathways, big, Procedures, ordinances, Processes, Aspect, P62, Interests, peltate hair, Legal Status, Brewer's, baker's yeast, Laws, Medical Jurisprudence, Metabolic Processes, Saccharomyces italicus, froggy, Gyltl1a, legislation and jurisprudence, laws, large, method, civil suits, Metabolism, Litigations, method used in an experiment, Escherchia coli, yeast, modified Embden-Meyerhof pathway, Studies, Obligations, Enteroinvasive Escherichia coli, Metabolism Phenomena, Medical, Technique, lager beer yeast, Genomes., Decisions, l(3)s2612, MDDGB6, Metabolic Concept, LARGE, S. cerevisiae, Study, BPFD#36, S cerevisiae, Constitutional Laws, Candida robusta, great, DmelCG10293, lawsuits, 1883, regulations, statutes, State Interest, Alkalescens-Dispar Group, Law, Bacterium coli, Embden Meyerhof Pathway, degradation, Saccharomyces cerevisiae 'var. diastaticus', clone 2.39, Legal Aspects, EAggEC, qkr, l(3)S090417, Saccaromyces cerevisiae, Concept, Metabolic Phenomena, Court Decisions, Sccharomyces cerevisiae, Metabolism Concepts, government regulations, Bacillus coli, KH93F, Phenomena, scales, legal aspects, metabolism, Metabolic Phenomenon, who, Saccharomyces oviformis, multicellular organism metabolic process, scale, biodegradation, Metabolic, Engineering, Who/How, Embden-Meyerhof-Parnas pathway, court decisions, plan specification, Legal Obligations, Litigation, Bacterium coli commune, concentration, qkr[93F], Aspects, Baker's Yeast, Baker Yeast, AnabolismSaccharomyces oviformis, Sccharomyces cerevisiae, Yeast, Candida robusta, Saccharomyces capensis, yeast, joined with., fused to, Saccharomyes cerevisiae, baker's yeast, brewer's yeast, fused, Saccharomyces uvarum var. melibiosus, merged with, coalesced, Saccharomyces italicus, Saccaromyces cerevisiae, lager beer yeastfalseSmallbone2013 - Yeast metabolic model with modular rate law, merged with Pritchard 2002Kieran Smallbone & Pedro Mendes. Large-Scale Metabolic Models: From Reconstruction to Differential Equations. Industrial Biotechnology 9, 4 (2013). Genome-scale kinetic models of metabolism are important for rational design of the metabolic engineering required for industrial biotechnology applications. They allow one to predict the alterations needed to optimize the flux or yield of the compounds of interest, while keeping the other functions of the host organism to a minimal, but essential, level. We define a pipeline for the generation of genome-scale kinetic models from reconstruction data. To build such a model, inputs of all concentrations, fluxes, rate laws, and kinetic parameters are required. However, we propose typical estimates for these numbers when experimental data are not available. While little data are required to produce the model, the pipeline ensures consistency with any known flux or concentration data, or any kinetic constants. We apply the method to create genome-scale models of Escherichia coli and Saccharomyces cerevisiae. We go on to show how these may be used to expand a detailed model of yeast glycolysis to the genome 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