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Volumn 4, Issue , 2010, Pages

DBSolve Optimum: A software package for kinetic modeling which allows dynamic visualization of simulation results

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPUTER GRAPHICS; COMPUTER PROGRAM; KINETICS;

EID: 77955290623     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-109     Document Type: Article
Times cited : (39)

References (43)
  • 2
    • 77956172829 scopus 로고    scopus 로고
    • Teranode design suite
    • Teranode design suite. , http://www.gerbsmanpartners.com/email120.html
  • 3
    • 77956172709 scopus 로고    scopus 로고
    • COPASI - software for simulation and modeling of biochemical networks
    • COPASI - software for simulation and modeling of biochemical networks. , http://www.copasi.org
  • 4
    • 33746143171 scopus 로고    scopus 로고
    • Visualisation of biochemical network simulations with SimWiz
    • Rost U, Kummer U. Visualisation of biochemical network simulations with SimWiz. Systems Biology, IEE Proceedings 2004, 1:184-189.
    • (2004) Systems Biology, IEE Proceedings , vol.1 , pp. 184-189
    • Rost, U.1    Kummer, U.2
  • 5
    • 0032825010 scopus 로고    scopus 로고
    • Mathematical simulation and analysis of cellular metabolism and regulation
    • 10.1093/bioinformatics/15.9.749, 10498775
    • 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, 10498775.
    • (1999) Bioinformatics , vol.15 , pp. 749-758
    • Goryanin, I.1    Hodgman, C.2    Selkov, E.3
  • 6
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    • 10.1093/bioinformatics/btg015, 12611808
    • 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, 12611808.
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.C.5    Kitano, H.6
  • 7
    • 77956177833 scopus 로고    scopus 로고
    • GNU parser generator
    • GNU parser generator. , http://www.gnu.org/software/bison/
  • 8
    • 77956174250 scopus 로고    scopus 로고
    • A fast lexical analyzer generator
    • A fast lexical analyzer generator. , http://flex.sourceforge.net/
  • 9
    • 0001811061 scopus 로고
    • A systematized collection of ODE solvers. Scientific Computing
    • Hindmarsh AC. A systematized collection of ODE solvers. Scientific Computing. North Holland 1983, 1:55-64.
    • (1983) North Holland , vol.1 , pp. 55-64
    • Hindmarsh, A.C.1
  • 10
    • 4544313738 scopus 로고
    • Continuation techniques and interactive software for bifurcation analysis of ODEs and iterated maps
    • 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.
    • (1993) Physica D , vol.62 , pp. 360-370
    • Khibnik, A.1    Kuznetsov, Y.2    Levitin, V.3    Nikolaev, E.4
  • 11
    • 84944978720 scopus 로고
    • Nonlinear Oscillations, Dynamical Systems, Bifurcations of Vector Fields
    • Guckenheimer J, Holmes P. Nonlinear Oscillations, Dynamical Systems, Bifurcations of Vector Fields. Springer-Verlag 1983,
    • (1983) Springer-Verlag
    • Guckenheimer, J.1    Holmes, P.2
  • 12
    • 84938447945 scopus 로고    scopus 로고
    • Direct search solution of numerical and statistical problems
    • Hooke R, Jeeves TA. Direct search solution of numerical and statistical problems. J Ass Comput Mach 8:212-229.
    • J Ass Comput Mach , vol.8 , pp. 212-229
    • Hooke, R.1    Jeeves, T.A.2
  • 13
    • 0000873069 scopus 로고
    • A method of solution of certain nonlinear problems in least squares
    • Levenberg K. A method of solution of certain nonlinear problems in least squares. Q Appl Math 1944, 2:164-168.
    • (1944) Q Appl Math , vol.2 , pp. 164-168
    • Levenberg, K.1
  • 14
    • 0000169232 scopus 로고
    • An algorithm for least square estimation of non-linear parameters
    • Marquardt DW. An algorithm for least square estimation of non-linear parameters. SIAM J 1963, 11:431-441.
    • (1963) SIAM J , vol.11 , pp. 431-441
    • Marquardt, D.W.1
  • 15
    • 77956176433 scopus 로고    scopus 로고
    • Chart component for Borland Builder
    • Chart component for Borland Builder. , http://www.steema.com
  • 16
    • 77956174903 scopus 로고    scopus 로고
    • 2D and 3D Graphics library
    • 2D and 3D Graphics library. , http://www.opengl.org
  • 17
    • 77956178145 scopus 로고    scopus 로고
    • XML schema of the DBSolve Optimum static map xml file
    • XML schema of the DBSolve Optimum static map xml file. , http://biokinetics.ru/images/dbsolve/glShema.xsd
  • 18
    • 0027178664 scopus 로고
    • SCAMP: a generalpurpose simulator and metabolic control analysis program
    • Sauro HM. SCAMP: a generalpurpose simulator and metabolic control analysis program. Comp Appl Biosci 1993, 9:441-450.
    • (1993) Comp Appl Biosci , vol.9 , pp. 441-450
    • Sauro, H.M.1
  • 19
    • 84885687318 scopus 로고    scopus 로고
    • The Institute for Systems Biology SPb
    • The Institute for Systems Biology SPb. , http://www.insysbio.ru
  • 21
    • 77956178386 scopus 로고    scopus 로고
    • NetSolve: integrated development environment software for metabolic and enzymatic systems modeling
    • Westerhoff HV, Snoep JL, Sluse FE, Wijker JE, Holodenko BN
    • Goryanin I. NetSolve: integrated development environment software for metabolic and enzymatic systems modeling. Biothermokinetics of the Living Cell: 1996; Amsterdam 1996, 252-254. Westerhoff HV, Snoep JL, Sluse FE, Wijker JE, Holodenko BN.
    • (1996) Biothermokinetics of the Living Cell: 1996; Amsterdam , pp. 252-254
    • Goryanin, I.1
  • 24
    • 70449720998 scopus 로고    scopus 로고
    • Modeling of ATP-ADP steady-state exchange rate mediated by the adenine nucleotide translocase in isolated mitochondria
    • 10.1111/j.1742-4658.2009.07394.x, 19860824
    • 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, 19860824.
    • (2009) FEBS J , vol.276 , pp. 6942-6955
    • Metelkin, E.1    Demin, O.2    Kovecs, Z.3    Christos, C.4
  • 25
    • 0037039289 scopus 로고    scopus 로고
    • Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model
    • 10.1021/bi011506c, 11772030
    • 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, 11772030.
    • (2002) Biochemistry , vol.41 , pp. 306-320
    • Moehren, G.1    Markevic, N.2    Demin, O.V.3    Kiyatkin, A.4    Goryain, I.5    Kholodenko, B.N.6
  • 26
    • 23244446113 scopus 로고    scopus 로고
    • Signal processing at the ras circuit: what shapes ras activation patterns?
    • 10.1049/sb:20045003, 17052120
    • 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, 17052120.
    • (2004) Systems Biology , vol.1 , pp. 104-113
    • Markevich, N.I.1    Moehren, G.2    Demin, O.V.3    Kiyatkin, A.4    Hoek, J.B.5    Kholodenko, B.N.6
  • 31
    • 77956169907 scopus 로고    scopus 로고
    • Applications of Whole Cell and Large Pathway Mathematical Models in the Pharmaceutical Industry
    • Horison Bioscience, Kholodenko B, Westerhoff H
    • 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 2003, 103-129. Horison Bioscience, Kholodenko B, Westerhoff H.
    • (2003) Metabolic Engineering in the Post Genomic Era: 2003; UK , pp. 103-129
    • Goryanin, I.I.1    Demin, O.V.2    Tobin, F.3
  • 34
    • 58049195553 scopus 로고    scopus 로고
    • Optimization of antimicrobial drug gramicidin S dosing regime using biosimulations
    • Smirnov S, Belashov A, Demin O. Optimization of antimicrobial drug gramicidin S dosing regime using biosimulations. Europ J Pharmac Sciences 2009, 36:105-109.
    • (2009) Europ J Pharmac Sciences , vol.36 , pp. 105-109
    • Smirnov, S.1    Belashov, A.2    Demin, O.3
  • 35
    • 34548864752 scopus 로고    scopus 로고
    • Kinetic Model of Mitochondrial Krebs Cycle: Unraveling the Mechanism of Salicylate Hepatotoxic Effects
    • 10.1007/s10867-006-9015-y, 2651525, 19669466
    • 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, 2651525, 19669466.
    • (2006) Journal of Biological Physics , vol.32 , pp. 245-271
    • Mogilevskaya, E.1    Demin, O.2    Goryanin, I.3
  • 36
    • 84872261630 scopus 로고    scopus 로고
    • The systems biology markup language site
    • The systems biology markup language site. , http://www.sbml.org
  • 37
    • 33646172301 scopus 로고    scopus 로고
    • Mathematical modeling of mitochondrial adenine nucleotide translocase
    • 10.1529/biophysj.105.061986, 1367049, 16239329
    • Metelkin E, Goryanin I, Demin O. Mathematical modeling of mitochondrial adenine nucleotide translocase. Biophys J 2006, 90:423-432. 10.1529/biophysj.105.061986, 1367049, 16239329.
    • (2006) Biophys J , vol.90 , pp. 423-432
    • Metelkin, E.1    Goryanin, I.2    Demin, O.3
  • 38
    • 51749105256 scopus 로고    scopus 로고
    • Kinetic Model of Phosphofructokinase-1 from Escherichia coli
    • 10.1142/S0219720008003643, 18763746
    • 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, 18763746.
    • (2008) J Bioinform Comput Biol , vol.6 , pp. 843-867
    • Peskov, K.1    Goryanin, I.2    Demin, O.3
  • 40
    • 77956177783 scopus 로고    scopus 로고
    • 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\"
    • 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
  • 41
    • 77956179119 scopus 로고    scopus 로고
    • Free software application allow to run Windows applications on Unix-like computers
    • Free software application allow to run Windows applications on Unix-like computers. , http://www.winehq.org/
  • 42
    • 77956177465 scopus 로고    scopus 로고
    • 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
    • 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
  • 43
    • 77956173611 scopus 로고    scopus 로고
    • DBSolve Optimum license
    • DBSolve Optimum license. , http://biokinetics.ru/images/dbsolve/license/license


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.