{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:19:19Z","timestamp":1764688759349},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Studying biological systems, not just at an individual component level but at a system-wide level, gives us great potential to understand fundamental functions and essential biological properties. Despite considerable advances in the topological analysis of metabolic networks, inadequate knowledge of the enzyme kinetic rate laws and their associated parameter values still hampers large-scale kinetic modelling. Furthermore, the integration of gene expression and protein levels into kinetic models is not straightforward.<\/jats:p>\n               <jats:p>Results: The focus of our research is on streamlining the construction of large-scale kinetic models. A novel software tool was developed, which enables the generation of generic rate equations for all reactions in a model. It encompasses an algorithm for estimating the concentration of proteins for a reaction to reach a particular steady state when kinetic parameters are unknown, and two robust methods for parameter estimation. It also allows for the seamless integration of gene expression or protein levels into a reaction and can generate equations for both transcription and translation. We applied this methodology to model the yeast glycolysis pathway; our results show that the behaviour of the system can be accurately described using generic kinetic equations.<\/jats:p>\n               <jats:p>Availability and implementation: The software tool, together with its source code in Java, is available from our project web site at http:\/\/www.bioinf.manchester.ac.uk\/schwartz\/grape<\/jats:p>\n               <jats:p>Contact: \u00a0jean-marc.schwartz@manchester.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq136","type":"journal-article","created":{"date-parts":[[2010,4,1]],"date-time":"2010-04-01T00:17:47Z","timestamp":1270081067000},"page":"1324-1331","source":"Crossref","is-referenced-by-count":16,"title":["Streamlining the construction of large-scale dynamic models using generic kinetic equations"],"prefix":"10.1093","volume":"26","author":[{"given":"Delali A.","family":"Adiamah","sequence":"first","affiliation":[{"name":"Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK"}]},{"given":"Julia","family":"Handl","sequence":"additional","affiliation":[{"name":"Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK"}]},{"given":"Jean-Marc","family":"Schwartz","sequence":"additional","affiliation":[{"name":"Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK"}]}],"member":"286","published-online":{"date-parts":[[2010,3,30]]},"reference":[{"key":"2023012507503784600_B1","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1016\/S1872-2075(08)60046-1","article-title":"Towards kinetic modeling of global metabolic networks: Methylobacterium extorquens AM1 growth as validation","volume":"24","author":"Ao","year":"2008","journal-title":"Chin. J. Biotechnol."},{"key":"2023012507503784600_B2","doi-asserted-by":"crossref","first-page":"W466","DOI":"10.1093\/nar\/gkl308","article-title":"BiologicalNetworks: visualization and analysis tool for systems biology","volume":"34","author":"Baitaluk","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012507503784600_B3","doi-asserted-by":"crossref","first-page":"3207","DOI":"10.1074\/jbc.272.6.3207","article-title":"Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes","volume":"272","author":"Bakker","year":"1997","journal-title":"J. Biol. Chem."},{"key":"2023012507503784600_B4","first-page":"29","article-title":"Modeling gene expression with differential equations","volume":"4","author":"Chen","year":"1999","journal-title":"Pac. Symp. Biocomput."},{"key":"2023012507503784600_B5","first-page":"30","volume-title":"Fundamentals of Enzyme Kinetics.","author":"Cornish-Bowden","year":"2004","edition":"3rd"},{"key":"2023012507503784600_B6","first-page":"41","article-title":"Linear modeling of mRNA expression levels during CNS development and injury","volume":"4","author":"D'haeseleer","year":"1999","journal-title":"Pac. Symp. Biocomput."},{"key":"2023012507503784600_B7","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1093\/bioinformatics\/bth067","article-title":"Grid Cellware: The first Grid-enabled tool for modeling and simulating cellular processes","volume":"20","author":"Dhar","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012507503784600_B8","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1752-0509-2-39","article-title":"SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks","volume":"2","author":"Dr\u00e4ger","year":"2008","journal-title":"BMC Syst. Biol."},{"key":"2023012507503784600_B9","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1101\/gr.234503","article-title":"Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network","volume":"13","author":"F\u00f6rster","year":"2003","journal-title":"Genome Res."},{"key":"2023012507503784600_B10","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S1478-5382(03)02370-9","article-title":"CellDesigner: a process diagram editor for gene-regulatory and biochemical networks","volume":"1","author":"Funahashi","year":"2003","journal-title":"BIOSILICO"},{"key":"2023012507503784600_B11","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/1471-2105-5-175","article-title":"Computation of elementary modes: a unifying framework and the new binary approach","volume":"5","author":"Gagneur","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012507503784600_B12","doi-asserted-by":"crossref","first-page":"R222","DOI":"10.1186\/gb-2007-8-10-r222","article-title":"Common gene expression strategies revealed by genome-wide analysis in yeast","volume":"8","author":"Garcia-Martinez","year":"2007","journal-title":"Genome Biol."},{"key":"2023012507503784600_B13","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1371\/journal.pcbi.0030189","article-title":"Universally sloppy parameter sensitivities in systems biology models","volume":"3","author":"Gutenkunst","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2023012507503784600_B14","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/S0301-4622(01)00229-0","article-title":"Full scale model of glycolysis in Saccharomyces cerevisiae","volume":"94","author":"Hynne","year":"2001","journal-title":"Biophys. Chem."},{"key":"2023012507503784600_B15","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507503784600_B16","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/msb.2008.8","article-title":"Formulating genome-scale kinetic models in the post-genome era","volume":"4","author":"Jamshidi","year":"2008","journal-title":"Mol. Syst. Biol."},{"key":"2023012507503784600_B17","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1093\/bib\/4.3.228","article-title":"Inferring gene networks from time series microarray data using dynamic Bayesian networks","volume":"4","author":"Kim","year":"2003","journal-title":"Brief. Bioinform."},{"key":"2023012507503784600_B18","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/1471-2105-8-37","article-title":"Boolean networks using the chi-square test for inferring large-scale gene regulatory networks","volume":"8","author":"Kim","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012507503784600_B19","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1021\/j150544a010","article-title":"A schematic method of deriving the rate laws for enzyme-catalyzed reactions","volume":"60","author":"King","year":"1956","journal-title":"J. Phys. Chem."},{"key":"2023012507503784600_B20","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1126\/science.1069492","article-title":"Systems biology: a brief overview","volume":"295","author":"Kitano","year":"2002","journal-title":"Science"},{"key":"2023012507503784600_B21","doi-asserted-by":"crossref","first-page":"4071","DOI":"10.1093\/nar\/gkg461","article-title":"CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle","volume":"31","author":"Kurata","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012507503784600_B22","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1114\/1.1492813","article-title":"A computational model for glycogenolysis in skeletal muscle","volume":"30","author":"Lambeth","year":"2002","journal-title":"Ann. Biomed. Eng."},{"issue":"Suppl. 7","key":"2023012507503784600_B23","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1186\/1471-2105-8-S7-S13","article-title":"Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks","volume":"8","author":"Li","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012507503784600_B24","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"COPASI: a COmplex PAthway SImulator","volume":"22","author":"Mendes","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012507503784600_B25","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1007\/b98874","volume-title":"Numerical Optimization.","author":"Nocedal","year":"1999"},{"key":"2023012507503784600_B26","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1093\/bioinformatics\/bth200","article-title":"Web-based kinetic modelling using JWS Online","volume":"20","author":"Olivier","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012507503784600_B27","doi-asserted-by":"crossref","first-page":"3894","DOI":"10.1046\/j.1432-1033.2002.03055.x","article-title":"Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis","volume":"269","author":"Pritchard","year":"2002","journal-title":"Eur. J. Biochem."},{"key":"2023012507503784600_B28","first-page":"S37","article-title":"Storing and annotating of kinetic data","volume":"7","author":"Rojas","year":"2007","journal-title":"In Silico Biol."},{"key":"2023012507503784600_B29","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/S0968-0004(01)02027-8","article-title":"BRENDA: a resource for enzyme data and metabolic information","volume":"27","author":"Schomburg","year":"2002","journal-title":"Trends Biochem. Sci."},{"key":"2023012507503784600_B30","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1186\/1471-2105-7-186","article-title":"Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis","volume":"7","author":"Schwartz","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012507503784600_B31","doi-asserted-by":"crossref","first-page":"5576","DOI":"10.1111\/j.1742-4658.2007.06076.x","article-title":"Something from nothing: bridging the gap between constraint-based and kinetic modelling","volume":"274","author":"Smallbone","year":"2007","journal-title":"FEBS J."},{"key":"2023012507503784600_B32","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/S0896-6273(00)81194-0","article-title":"Mathematical modeling of gene networks","volume":"26","author":"Smolen","year":"2003","journal-title":"Neuron"},{"key":"2023012507503784600_B33","doi-asserted-by":"crossref","first-page":"11868","DOI":"10.1073\/pnas.0600013103","article-title":"Structural kinetic modelling of metabolic networks","volume":"103","author":"Steuer","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507503784600_B34","doi-asserted-by":"crossref","first-page":"5313","DOI":"10.1046\/j.1432-1327.2000.01527.x","article-title":"Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry","volume":"267","author":"Teusink","year":"2000","journal-title":"Eur. J. Biochem."},{"key":"2023012507503784600_B35","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1093\/bioinformatics\/15.1.72","article-title":"E-CELL: software environment for whole cell simulation","volume":"15","author":"Tomita","year":"1999","journal-title":"Bioinformatics"},{"key":"2023012507503784600_B36","doi-asserted-by":"crossref","first-page":"3680","DOI":"10.1093\/bioinformatics\/bth422","article-title":"The JigCell model builder and run manager","volume":"18","author":"Vass","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012507503784600_B37","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/bth428","article-title":"GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data","volume":"20","author":"Wu","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012507503784600_B38","doi-asserted-by":"crossref","first-page":"2704","DOI":"10.1093\/bioinformatics\/btl443","article-title":"SBML-PET: a Systems Biology Markup Language-based parameter estimation tool","volume":"22","author":"Zi","year":"2006","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/10\/1324\/48850957\/bioinformatics_26_10_1324.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/10\/1324\/48850957\/bioinformatics_26_10_1324.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:51:08Z","timestamp":1674633068000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/10\/1324\/193431"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,3,30]]},"references-count":38,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2010,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq136","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,5,15]]},"published":{"date-parts":[[2010,3,30]]}}}