{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T08:00:48Z","timestamp":1775808048477,"version":"3.50.1"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,8,10]],"date-time":"2010-08-10T00:00:00Z","timestamp":1281398400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1752-0509-4-109","type":"journal-article","created":{"date-parts":[[2010,8,10]],"date-time":"2010-08-10T18:15:23Z","timestamp":1281464123000},"source":"Crossref","is-referenced-by-count":47,"title":["DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results"],"prefix":"10.1186","volume":"4","author":[{"given":"Nail M","family":"Gizzatkulov","sequence":"first","affiliation":[]},{"given":"Igor I","family":"Goryanin","sequence":"additional","affiliation":[]},{"given":"Eugeny A","family":"Metelkin","sequence":"additional","affiliation":[]},{"given":"Ekaterina A","family":"Mogilevskaya","sequence":"additional","affiliation":[]},{"given":"Kirill V","family":"Peskov","sequence":"additional","affiliation":[]},{"given":"Oleg V","family":"Demin","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,8,10]]},"reference":[{"key":"498_CR1","volume-title":"Taylor & Francis (United States)","author":"O Demin","year":"2008","unstructured":"Demin O, Goryanin I: Kinetic Modelling in Systems Biology. Taylor & Francis (United States). 2008"},{"key":"498_CR2","unstructured":"Teranode design suite., http:\/\/www.gerbsmanpartners.com\/email120.html"},{"key":"498_CR3","unstructured":"COPASI - software for simulation and modeling of biochemical networks., http:\/\/www.copasi.org"},{"key":"498_CR4","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1049\/sb:20045018","volume":"1","author":"U Rost","year":"2004","unstructured":"Rost U, Kummer U: Visualisation of biochemical network simulations with SimWiz. Systems Biology, IEE Proceedings. 2004, 1: 184-189. 10.1049\/sb:20045018.","journal-title":"Systems Biology, IEE Proceedings"},{"key":"498_CR5","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1093\/bioinformatics\/15.9.749","volume":"15","author":"I Goryanin","year":"1999","unstructured":"Goryanin I, Hodgman C, Selkov E: Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics. 1999, 15: 749-758. 10.1093\/bioinformatics\/15.9.749","journal-title":"Bioinformatics"},{"key":"498_CR6","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"19","author":"M Hucka","year":"2003","unstructured":"Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 19: 524-31. 10.1093\/bioinformatics\/btg015","journal-title":"Bioinformatics"},{"key":"498_CR7","unstructured":"GNU parser generator., http:\/\/www.gnu.org\/software\/bison\/"},{"key":"498_CR8","unstructured":"A fast lexical analyzer generator., http:\/\/flex.sourceforge.net\/"},{"key":"498_CR9","first-page":"55","volume":"1","author":"AC Hindmarsh","year":"1983","unstructured":"Hindmarsh AC: A systematized collection of ODE solvers. Scientific Computing. North Holland. 1983, 1: 55-64.","journal-title":"North Holland"},{"key":"498_CR10","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1016\/0167-2789(93)90294-B","volume":"62","author":"A Khibnik","year":"1993","unstructured":"Khibnik A, Kuznetsov Y, Levitin V, Nikolaev E: Continuation techniques and interactive software for bifurcation analysis of ODEs and iterated maps. Physica D. 1993, 62: 360-370. 10.1016\/0167-2789(93)90294-B.","journal-title":"Physica D"},{"key":"498_CR11","volume-title":"Springer-Verlag","author":"J Guckenheimer","year":"1983","unstructured":"Guckenheimer J, Holmes P: Nonlinear Oscillations, Dynamical Systems, Bifurcations of Vector Fields. Springer-Verlag. 1983"},{"key":"498_CR12","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1145\/321062.321069","volume":"8","author":"R Hooke","year":"1944","unstructured":"Hooke R, Jeeves TA: Direct search solution of numerical and statistical problems. J Ass Comput Mach. 8: 212-229.","journal-title":"J Ass Comput Mach"},{"key":"498_CR13","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1090\/qam\/10666","volume":"2","author":"K Levenberg","year":"1944","unstructured":"Levenberg K: A method of solution of certain nonlinear problems in least squares. Q Appl Math. 1944, 2: 164-168.","journal-title":"Q Appl Math"},{"key":"498_CR14","first-page":"431","volume":"11","author":"DW Marquardt","year":"1963","unstructured":"Marquardt DW: An algorithm for least square estimation of non-linear parameters. SIAM J. 1963, 11: 431-441.","journal-title":"SIAM J"},{"key":"498_CR15","unstructured":"Chart component for Borland Builder., http:\/\/www.steema.com"},{"key":"498_CR16","unstructured":"2D and 3D Graphics library., http:\/\/www.opengl.org"},{"key":"498_CR17","unstructured":"XML schema of the DBSolve Optimum static map xml file., http:\/\/biokinetics.ru\/images\/dbsolve\/glShema.xsd"},{"key":"498_CR18","first-page":"441","volume":"9","author":"HM Sauro","year":"1993","unstructured":"Sauro HM: SCAMP: a generalpurpose simulator and metabolic control analysis program. Comp Appl Biosci. 1993, 9: 441-450.","journal-title":"Comp Appl Biosci"},{"key":"498_CR19","unstructured":"The Institute for Systems Biology SPb., http:\/\/www.insysbio.ru"},{"key":"498_CR20","first-page":"332","volume-title":"Proceedings of the IMACS Symposium on Mathematical Modelling: 1994; Austria","author":"I Goryanin","year":"1994","unstructured":"Goryanin I, Serdyuk K: Automation of Modelling of Multienzyme Systems Using Databanks on Enzyme and Metabolic pathways (EMP). Proceedings of the IMACS Symposium on Mathematical Modelling: 1994; Austria. 1994, 332-336."},{"key":"498_CR21","first-page":"252","volume-title":"Biothermokinetics of the Living Cell: 1996; Amsterdam","author":"I Goryanin","year":"1996","unstructured":"Goryanin I: NetSolve: integrated development environment software for metabolic and enzymatic systems modeling. Biothermokinetics of the Living Cell: 1996; Amsterdam. Edited by: Westerhoff HV, Snoep JL, Sluse FE, Wijker JE, Holodenko BN. 1996, 252-254."},{"key":"498_CR22","volume-title":"ISMB\/ECCB Conference: 31 July-5 August 2004; Glasgow","author":"N Gizzatkulov","year":"2004","unstructured":"Gizzatkulov N, Klimov A, Lebedeva G, Demin O: DBSolve7: new update version to develop and analyze models of complex biological systems. ISMB\/ECCB Conference: 31 July-5 August 2004; Glasgow. 2004"},{"key":"498_CR23","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1007\/978-1-4020-9394-4_10","volume-title":"Systems Biology and Biotechnology of Esherichia coli","author":"E Mogilevskaya","year":"2009","unstructured":"Mogilevskaya E, Peskov K, Metelkin E, Plyusnina T, Lebedeva G, Goryanin I, Demin O: Kinetic modeling of E. coli enzymes: integration of in vitro data. Systems Biology and Biotechnology of Esherichia coli. Edited by: Sang Yup Lee. 2009, 177-207. full_text. Netherlands: Springer"},{"key":"498_CR24","doi-asserted-by":"publisher","first-page":"6942","DOI":"10.1111\/j.1742-4658.2009.07394.x","volume":"276","author":"E Metelkin","year":"2009","unstructured":"Metelkin E, Demin O, Kovecs Z, Christos C: Modeling of ATP-ADP steady-state exchange rate mediated by the adenine nucleotide translocase in isolated mitochondria. FEBS J. 2009, 276: 6942-6955. 10.1111\/j.1742-4658.2009.07394.x","journal-title":"FEBS J"},{"key":"498_CR25","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1021\/bi011506c","volume":"41","author":"G Moehren","year":"2002","unstructured":"Moehren G, Markevic N, Demin OV, Kiyatkin A, Goryain I, Kholodenko BN: Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model. Biochemistry. 2002, 41: 306-320. 10.1021\/bi011506c","journal-title":"Biochemistry"},{"key":"498_CR26","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1049\/sb:20045003","volume":"1","author":"NI Markevich","year":"2004","unstructured":"Markevich NI, Moehren G, Demin OV, Kiyatkin A, Hoek JB, Kholodenko BN: Signal processing at the ras circuit: what shapes ras activation patterns?. Systems Biology. 2004, 1: 104-113. 10.1049\/sb:20045003","journal-title":"Systems Biology"},{"key":"498_CR27","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.ejps.2008.10.015","volume":"36","author":"A Goltsov","year":"2009","unstructured":"Goltsov A, Maryashkin A, Swat M, Kosinsky Y, Humphery-Smith I, Goryanin I, Lebedeva G: Kinetic modelling of NSAID action on COX-1: focus on in vitro\/in vivo aspects and drug combinations. Europ J Pharmac Sciences. 2009, 36: 122-136. 10.1016\/j.ejps.2008.10.015.","journal-title":"Europ J Pharmac Sciences"},{"key":"498_CR28","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1002\/0471973165.ch23","volume":"49","author":"II Goryanin","year":"2006","unstructured":"Goryanin II, Lebedeva GV, Mogilevskaya EA, Metelkin EA, Demin OV: Cellular kinetic modeling of the microbial metabolism. Methods Biochem Anal. 2006, 49: 437-488.","journal-title":"Methods Biochem Anal"},{"key":"498_CR29","first-page":"452","volume":"45","author":"GY Riznichenko","year":"2000","unstructured":"Riznichenko GY, Lebedeva GV, Demin OV, Rubin AB: Regulatory levels of photosynthetic processes. Biophysics. 2000, 45: 452-460.","journal-title":"Biophysics"},{"key":"498_CR30","first-page":"1897","volume":"74","author":"GV Lebedeva","year":"2000","unstructured":"Lebedeva GV, Belyaeva NE, Riznichenko GY, Rubin AB, Demin OV: Kinetic model of photosystem II of high plants. J Physical Chemistry. 2000, 74: 1897-1906.","journal-title":"J Physical Chemistry"},{"key":"498_CR31","first-page":"103","volume-title":"Metabolic Engineering in the Post Genomic Era: 2003; UK","author":"II Goryanin","year":"2003","unstructured":"Goryanin II, Demin OV, Tobin F: Applications of Whole Cell and Large Pathway Mathematical Models in the Pharmaceutical Industry. Metabolic Engineering in the Post Genomic Era: 2003; UK. Edited by: Kholodenko B, Westerhoff H. 2003, 103-129. Horison Bioscience"},{"key":"498_CR32","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1002\/bit.20772","volume":"95","author":"M Noble","year":"2006","unstructured":"Noble M, Sinha Y, Kolupaev A, Demin O, Earnshaw D, Tobin F, West J, Martin JD, Qiu C, Liu WS, DeWolf JWE, Tew D, Goryanin II: The kinetic model of the shikimate pathway as a tool to optimize enzyme assays for high-throughput screening. Biotechnology and Bioengineering. 2006, 95: 560-571. 10.1002\/bit.20772","journal-title":"Biotechnology and Bioengineering"},{"key":"498_CR33","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1142\/S0219720008003771","volume":"65","author":"K Peskov","year":"2008","unstructured":"Peskov K, Goryanin I, Prank K, Tobin F, Demin O: Kinetic Modeling of ace operon genetic regulation in Escherichia coli. J Bioinform Comput Biol. 2008, 65: 933-959. 10.1142\/S0219720008003771.","journal-title":"J Bioinform Comput Biol"},{"key":"498_CR34","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.ejps.2008.10.017","volume":"36","author":"S Smirnov","year":"2009","unstructured":"Smirnov S, Belashov A, Demin O: Optimization of antimicrobial drug gramicidin S dosing regime using biosimulations. Europ J Pharmac Sciences. 2009, 36: 105-109. 10.1016\/j.ejps.2008.10.017.","journal-title":"Europ J Pharmac Sciences"},{"key":"498_CR35","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/s10867-006-9015-y","volume":"32","author":"E Mogilevskaya","year":"2006","unstructured":"Mogilevskaya E, Demin O, Goryanin I: Kinetic Model of Mitochondrial Krebs Cycle: Unraveling the Mechanism of Salicylate Hepatotoxic Effects. Journal of Biological Physics. 2006, 32: 245-271. 10.1007\/s10867-006-9015-y","journal-title":"Journal of Biological Physics"},{"key":"498_CR36","unstructured":"The systems biology markup language site., http:\/\/www.sbml.org"},{"key":"498_CR37","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1529\/biophysj.105.061986","volume":"90","author":"E Metelkin","year":"2006","unstructured":"Metelkin E, Goryanin I, Demin O: Mathematical modeling of mitochondrial adenine nucleotide translocase. Biophys J. 2006, 90: 423-432. 10.1529\/biophysj.105.061986","journal-title":"Biophys J"},{"key":"498_CR38","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1142\/S0219720008003643","volume":"6","author":"K Peskov","year":"2008","unstructured":"Peskov K, Goryanin I, Demin O: Kinetic Model of Phosphofructokinase-1 from Escherichia coli. J Bioinform Comput Biol. 2008, 6: 843-67. 10.1142\/S0219720008003643","journal-title":"J Bioinform Comput Biol"},{"key":"498_CR39","doi-asserted-by":"publisher","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","volume":"22","author":"S Hoops","year":"2006","unstructured":"Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U: COPASI a COmplex PAthway Simulator. Bioinformatics. 2006, 22: 3067-3074. 10.1093\/bioinformatics\/btl485","journal-title":"Bioinformatics"},{"key":"498_CR40","unstructured":"Example of (XML and PLT) visualization files can be found in DBSolve Optimum distribution using followng path from root of installation folder \"Institute for Systems Biology Spb\\DBSolve\\Player\\Examples\\\"., http:\/\/biokinetics.ru\/images\/dbsolve\/DBSolveOptimum.zip"},{"key":"498_CR41","unstructured":"Free software application allow to run Windows applications on Unix-like computers., http:\/\/www.winehq.org\/"},{"key":"498_CR42","unstructured":"DBSolve Optimum installation package incudes DBSolve Optimum, user manual, examples of knetic models and aimation of simulation results. This installation package can be dowloaded at., http:\/\/biokinetics.ru\/images\/dbsolve\/DBSolveOptimum.zip"},{"key":"498_CR43","unstructured":"DBSolve Optimum license., http:\/\/biokinetics.ru\/images\/dbsolve\/license\/license"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-109.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-4-109\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-109.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,29]],"date-time":"2024-03-29T08:40:27Z","timestamp":1711701627000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-4-109"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,10]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["498"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-4-109","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,8,10]]},"article-number":"109"}}