메뉴 건너뛰기




Volumn 6, Issue , 2012, Pages

A specialized ODE integrator for the efficient computation of parameter sensitivities

Author keywords

Dynamical models; Integration; Ordinary differential equations; Parameter sensitivities

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER LANGUAGE; METHODOLOGY; SYSTEMS BIOLOGY;

EID: 84861147460     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-46     Document Type: Article
Times cited : (14)

References (48)
  • 1
    • 77956289955 scopus 로고    scopus 로고
    • Classic and contemporary approaches to modeling biochemical reactions
    • 10.1101/gad.1945410, 2932968, 20810646
    • Chen WW, Niepel M, Sorger PK. Classic and contemporary approaches to modeling biochemical reactions. Genes Dev 2010, 24(17):1861-1875. http://dx.doi.org/10.1101/gad.1945410, 10.1101/gad.1945410, 2932968, 20810646.
    • (2010) Genes Dev , vol.24 , Issue.17 , pp. 1861-1875
    • Chen, W.W.1    Niepel, M.2    Sorger, P.K.3
  • 2
    • 35748977901 scopus 로고    scopus 로고
    • Universally sloppy parameter sensitivities in systems biology models
    • 2000971, 17922568
    • Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, Sethna JP. Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol 2007, 3(10):1871-1878. http://dx.doi.org/10.1371/journal.pcbi.0030189, 2000971, 17922568.
    • (2007) PLoS Comput Biol , vol.3 , Issue.10 , pp. 1871-1878
    • Gutenkunst, R.N.1    Waterfall, J.J.2    Casey, F.P.3    Brown, K.S.4    Myers, C.R.5    Sethna, J.P.6
  • 3
    • 0038606184 scopus 로고    scopus 로고
    • Local methods
    • Chichester, UK: John Wiley & Sons, Ltd., Saltelli A, Chan K, Scott E
    • Turányi T, Rabitz H. Local methods. Sensitivity analysis 2000, 81-100. Chichester, UK: John Wiley & Sons, Ltd., Saltelli A, Chan K, Scott E.
    • (2000) Sensitivity analysis , pp. 81-100
    • Turányi, T.1    Rabitz, H.2
  • 4
    • 58149232578 scopus 로고    scopus 로고
    • Parameter estimation and optimal experimental design
    • Banga JR, Balsa-Canto E. Parameter estimation and optimal experimental design. Essays in Biochem: Syst Biol 2008, 45:195-209.
    • (2008) Essays in Biochem: Syst Biol , vol.45 , pp. 195-209
    • Banga, J.R.1    Balsa-Canto, E.2
  • 5
    • 67649418422 scopus 로고    scopus 로고
    • Efficient uncertainty quantification with the polynomial chaos method for stiff systems
    • Cheng H, Sandu A. Efficient uncertainty quantification with the polynomial chaos method for stiff systems. Math Comput Simul 2009, 79(11):3278-3295.
    • (2009) Math Comput Simul , vol.79 , Issue.11 , pp. 3278-3295
    • Cheng, H.1    Sandu, A.2
  • 6
    • 33750628424 scopus 로고    scopus 로고
    • Systems interface biology
    • 10.1098/rsif.2006.0143, 1664650, 16971329
    • Doyle FJ, Stelling J. Systems interface biology. J R Soc Interface 2006, 3(10):603-616. 10.1098/rsif.2006.0143, 1664650, 16971329.
    • (2006) J R Soc Interface , vol.3 , Issue.10 , pp. 603-616
    • Doyle, F.J.1    Stelling, J.2
  • 7
    • 0038070188 scopus 로고    scopus 로고
    • Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution
    • Cao Y, Li S, Petzold L, Serban R. Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution. SIAM J Sci Comput 2003, 24(3):1076-1089.
    • (2003) SIAM J Sci Comput , vol.24 , Issue.3 , pp. 1076-1089
    • Cao, Y.1    Li, S.2    Petzold, L.3    Serban, R.4
  • 8
    • 68149178255 scopus 로고    scopus 로고
    • Sensitivity Analysis for Oscillating Dynamical Systems
    • Wilkins AK, Tidor B, White J, Barton PI. Sensitivity Analysis for Oscillating Dynamical Systems. SIAM J Sci Comput 2009, 31(4):2706-2732.
    • (2009) SIAM J Sci Comput , vol.31 , Issue.4 , pp. 2706-2732
    • Wilkins, A.K.1    Tidor, B.2    White, J.3    Barton, P.I.4
  • 9
    • 0033522751 scopus 로고    scopus 로고
    • Second-order sensitivities of general dynamic systems with application to optimal control problems
    • Vassiliadis VS, Canto EB, Banga JR. Second-order sensitivities of general dynamic systems with application to optimal control problems. Chem Eng Sci 1999, 54(17):3851-3860.
    • (1999) Chem Eng Sci , vol.54 , Issue.17 , pp. 3851-3860
    • Vassiliadis, V.S.1    Canto, E.B.2    Banga, J.R.3
  • 10
    • 0034332746 scopus 로고    scopus 로고
    • Efficient Optimal Control of Bioprocesses Using Second-Order Information
    • Balsa-Canto E, Banga JR, Alonso AA, Vassiliadis VS. Efficient Optimal Control of Bioprocesses Using Second-Order Information. Ind Eng Chem Res 2000, 39(11):4287-4295.
    • (2000) Ind Eng Chem Res , vol.39 , Issue.11 , pp. 4287-4295
    • Balsa-Canto, E.1    Banga, J.R.2    Alonso, A.A.3    Vassiliadis, V.S.4
  • 11
    • 79951823001 scopus 로고    scopus 로고
    • A Local Sensitivity Analysis Method for Developing Biological Models with Identifiable Parameters: Application to L-type Calcium Channel Modelling
    • Sher A, Wang K, Wathen A, Mirams G, Abramson D, Gavaghan D. A Local Sensitivity Analysis Method for Developing Biological Models with Identifiable Parameters: Application to L-type Calcium Channel Modelling. IEEE Sixth International Conference on e-Science 2010, 176-181.
    • (2010) IEEE Sixth International Conference on e-Science , pp. 176-181
    • Sher, A.1    Wang, K.2    Wathen, A.3    Mirams, G.4    Abramson, D.5    Gavaghan, D.6
  • 12
    • 16344394782 scopus 로고    scopus 로고
    • Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling
    • 10.1093/bioinformatics/bti118, 15531606
    • Liu G, Swihart MT, Neelamegham S. Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling. Bioinformatics 2005, 21(7):1194-1202. 10.1093/bioinformatics/bti118, 15531606.
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 1194-1202
    • Liu, G.1    Swihart, M.T.2    Neelamegham, S.3
  • 14
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • 10.1038/nrg1272, 14735121
    • Barabási AL, Oltvai Z. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-13. 10.1038/nrg1272, 14735121.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabási, A.L.1    Oltvai, Z.2
  • 17
    • 1542722129 scopus 로고    scopus 로고
    • Efficient numerical methods for the solution of stiff initial-value problems and differential algebraic equations
    • Cash JR. Efficient numerical methods for the solution of stiff initial-value problems and differential algebraic equations. Proc R Soc London Series a-Math Phys Eng Sci 2002, 459(2032):797-815.
    • (2002) Proc R Soc London Series a-Math Phys Eng Sci , vol.459 , Issue.2032 , pp. 797-815
    • Cash, J.R.1
  • 19
    • 0030105583 scopus 로고    scopus 로고
    • CVODE, a stiff/nonstiff ODE solver in C
    • Cohen SD, Hindmarsh AC. CVODE, a stiff/nonstiff ODE solver in C. Comput Phys 1996, 10(2):138-143.
    • (1996) Comput Phys , vol.10 , Issue.2 , pp. 138-143
    • Cohen, S.D.1    Hindmarsh, A.C.2
  • 22
    • 32544443964 scopus 로고    scopus 로고
    • Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
    • [Schmidt, Henning Jirstrand, Mats Research Support, Non-U.S. Gov't England Bioinformatics (Oxford, England) Bioinformatics. 2006 Feb 15;22(4):514-5. Epub 2005 Nov 29.]., 10.1093/bioinformatics/bti799, 16317076
    • Schmidt H, Jirstrand M. Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics 2006, 22(4):514-5. [Schmidt, Henning Jirstrand, Mats Research Support, Non-U.S. Gov't England Bioinformatics (Oxford, England) Bioinformatics. 2006 Feb 15;22(4):514-5. Epub 2005 Nov 29.]., 10.1093/bioinformatics/bti799, 16317076.
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 514-515
    • Schmidt, H.1    Jirstrand, M.2
  • 23
    • 25444433053 scopus 로고    scopus 로고
    • Cheap second order directional derivatives of stiff ODE embedded functionals
    • Özyurt DB, Barton PI. Cheap second order directional derivatives of stiff ODE embedded functionals. SIAM J Sci Comput 2005, 26(5):1725-1743.
    • (2005) SIAM J Sci Comput , vol.26 , Issue.5 , pp. 1725-1743
    • Özyurt, D.B.1    Barton, P.I.2
  • 24
    • 0013441423 scopus 로고
    • Sur les quadrature mecaniques
    • [Reviewed in Mat. Rev. 10:70]
    • Obrechkoff N. Sur les quadrature mecaniques. Spisanic Bulgar Akad Nauk 1942, 65:191-289. [Reviewed in Mat. Rev. 10:70].
    • (1942) Spisanic Bulgar Akad Nauk , vol.65 , pp. 191-289
    • Obrechkoff, N.1
  • 25
    • 0016047307 scopus 로고
    • Second derivative multistep methods for stiff ordinary differential equations
    • Enright WH. Second derivative multistep methods for stiff ordinary differential equations. SIAM J Numer Anal 1974, 11(2):321-331.
    • (1974) SIAM J Numer Anal , vol.11 , Issue.2 , pp. 321-331
    • Enright, W.H.1
  • 27
    • 0021455519 scopus 로고
    • Second derivative methods applied to implicit first- and second-order systems
    • Addison CA, Gladwell I. Second derivative methods applied to implicit first- and second-order systems. Int J Numer Methods Eng 1984, 20(7):1211-1231.
    • (1984) Int J Numer Methods Eng , vol.20 , Issue.7 , pp. 1211-1231
    • Addison, C.A.1    Gladwell, I.2
  • 29
    • 0021940614 scopus 로고
    • Sensitivity analysis of initial value problems with mixed ODEs and algebraic equations
    • Caracotsios M, Stewart WE. Sensitivity analysis of initial value problems with mixed ODEs and algebraic equations. Comput Chem Eng 1985, 9(4):359-365.
    • (1985) Comput Chem Eng , vol.9 , Issue.4 , pp. 359-365
    • Caracotsios, M.1    Stewart, W.E.2
  • 30
    • 0031257067 scopus 로고    scopus 로고
    • Efficient sensitivity analysis of large-scale differential-algebraic systems
    • Feehery WF, Tolsma JE, Barton PI. Efficient sensitivity analysis of large-scale differential-algebraic systems. Appl Numer Math 1997, 25:41-54.
    • (1997) Appl Numer Math , vol.25 , pp. 41-54
    • Feehery, W.F.1    Tolsma, J.E.2    Barton, P.I.3
  • 32
    • 33745631242 scopus 로고    scopus 로고
    • The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
    • 10.1093/bioinformatics/btl086, 16527832
    • Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C. The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics 2006, 22(11):1406-1407. 10.1093/bioinformatics/btl086, 16527832.
    • (2006) Bioinformatics , vol.22 , Issue.11 , pp. 1406-1407
    • Machné, R.1    Finney, A.2    Müller, S.3    Lu, J.4    Widder, S.5    Flamm, C.6
  • 34
    • 84871173406 scopus 로고    scopus 로고
    • Matlab implementation of the Radau IIA method of order5 by Ch. Engstler after the Fortran Code RADAU5 of Hairer/Wanner
    • Engstler C. Matlab implementation of the Radau IIA method of order5 by Ch. Engstler after the Fortran Code RADAU5 of Hairer/Wanner. 1999, http://na.uni-tuebingen.de/projects.shtml.
    • (1999)
    • Engstler, C.1
  • 38
    • 0033570090 scopus 로고    scopus 로고
    • Quantification of short term signaling by the epidermal growth factor receptor
    • 10.1074/jbc.274.42.30169, 10514507
    • Kholodenko BN, Demin OV, Moehren G, Hoek JB. Quantification of short term signaling by the epidermal growth factor receptor. J Biol Chem 1999, 274(42):30169-30181. 10.1074/jbc.274.42.30169, 10514507.
    • (1999) J Biol Chem , vol.274 , Issue.42 , pp. 30169-30181
    • Kholodenko, B.N.1    Demin, O.V.2    Moehren, G.3    Hoek, J.B.4
  • 39
    • 33751543926 scopus 로고    scopus 로고
    • Modeling regulatory mechanisms in IL-6 signal transduction in hepatocytes
    • 10.1002/bit.21026, 16752369
    • Singh A, Jayaraman A, Hahn J. Modeling regulatory mechanisms in IL-6 signal transduction in hepatocytes. Biotechnol Bioeng 2006, 95(5):850-862. 10.1002/bit.21026, 16752369.
    • (2006) Biotechnol Bioeng , vol.95 , Issue.5 , pp. 850-862
    • Singh, A.1    Jayaraman, A.2    Hahn, J.3
  • 41
    • 46549089054 scopus 로고    scopus 로고
    • Simulation of the regulation of EGFR endocytosis and EGFR-ERK signaling by endophilin-mediated RhoA-EGFR crosstalk
    • 10.1016/j.febslet.2008.05.026, 18505685
    • Ung CY, Li H, Ma XH, Jia J, Li BW, Low BC, Chen YZ. Simulation of the regulation of EGFR endocytosis and EGFR-ERK signaling by endophilin-mediated RhoA-EGFR crosstalk. FEBS Lett 2008, 582(15):2283-2290. 10.1016/j.febslet.2008.05.026, 18505685.
    • (2008) FEBS Lett , vol.582 , Issue.15 , pp. 2283-2290
    • Ung, C.Y.1    Li, H.2    Ma, X.H.3    Jia, J.4    Li, B.W.5    Low, B.C.6    Chen, Y.Z.7
  • 42
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • 10.1038/35002125, 10659856
    • Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403(6767):335-338. 10.1038/35002125, 10659856.
    • (2000) Nature , vol.403 , Issue.6767 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 43
    • 0033532569 scopus 로고    scopus 로고
    • Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in Drosophila
    • 10.1006/jtbi.1999.0924, 10366496
    • Leloup G. Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in Drosophila. J Theor Biol 1999, 198(3):445-459. 10.1006/jtbi.1999.0924, 10366496.
    • (1999) J Theor Biol , vol.198 , Issue.3 , pp. 445-459
    • Leloup, G.1
  • 44
    • 0035933603 scopus 로고    scopus 로고
    • Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae
    • 10.1016/S0014-5793(01)02562-5, 11423122
    • Wolf J, Sohn H, Heinrich R, Kuriyama H. Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae. FEBS Lett 2001, 499(3):230-234. 10.1016/S0014-5793(01)02562-5, 11423122.
    • (2001) FEBS Lett , vol.499 , Issue.3 , pp. 230-234
    • Wolf, J.1    Sohn, H.2    Heinrich, R.3    Kuriyama, H.4
  • 45
    • 42449157505 scopus 로고    scopus 로고
    • Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways
    • 10.1016/j.jtbi.2008.01.006, 18308339
    • Goldbeter A, Pourquié O. Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. J Theor Biol 2008, 252(3):574-585. 10.1016/j.jtbi.2008.01.006, 18308339.
    • (2008) J Theor Biol , vol.252 , Issue.3 , pp. 574-585
    • Goldbeter, A.1    Pourquié, O.2
  • 46
    • 33847070037 scopus 로고    scopus 로고
    • Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops
    • 10.1016/j.jtbi.2006.10.028, 17157878
    • Xie Z, Kulasiri D. Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops. J Theor Biol 2007, 245(2):290-304. 10.1016/j.jtbi.2006.10.028, 17157878.
    • (2007) J Theor Biol , vol.245 , Issue.2 , pp. 290-304
    • Xie, Z.1    Kulasiri, D.2
  • 47
    • 0030083833 scopus 로고    scopus 로고
    • Numerical methods and software for sensitivity analysis of differential-algebraic systems
    • Maly T, Petzold LR. Numerical methods and software for sensitivity analysis of differential-algebraic systems. Appl Numer Math 1996, 20(1-2):57-79.
    • (1996) Appl Numer Math , vol.20 , Issue.1-2 , pp. 57-79
    • Maly, T.1    Petzold, L.R.2
  • 48
    • 65649138437 scopus 로고    scopus 로고
    • Computational modeling of biochemical networks using COPASI
    • 10.1007/978-1-59745-525-1_2, 19399433
    • Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. Methods Mol Biol 2009, 500:17-59. http://dx.doi.org/10.1007/978-1-59745-525-1_2, 10.1007/978-1-59745-525-1_2, 19399433.
    • (2009) Methods Mol Biol , vol.500 , pp. 17-59
    • Mendes, P.1    Hoops, S.2    Sahle, S.3    Gauges, R.4    Dada, J.5    Kummer, U.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.