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Volumn 10, Issue 1, 2009, Pages 65-74

Web-based applications for building, managing and analysing kinetic models of biological systems

Author keywords

Dynamic simulation; Kinetic modelling; Systems biology; Web based applications

Indexed keywords

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, FACTUAL; HUMANS; INTERNET; MATHEMATICS; MODELS, BIOLOGICAL; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 60749102914     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbn039     Document Type: Article
Times cited : (18)

References (46)
  • 1
    • 0037079054 scopus 로고    scopus 로고
    • Computational systems biology
    • Kitano H. Computational systems biology. Nature 2002;420: 206-10.
    • (2002) Nature , vol.420 , pp. 206-210
    • Kitano, H.1
  • 2
    • 33749506763 scopus 로고    scopus 로고
    • From in vivo to in silico biology and back
    • Di Ventura B, Lemerle C, Michalodimitrakis K, et al. From in vivo to in silico biology and back. Nature 2006;443: 527-533.
    • (2006) Nature , vol.443 , pp. 527-533
    • Di Ventura, B.1    Lemerle, C.2    Michalodimitrakis, K.3
  • 3
    • 33845410054 scopus 로고    scopus 로고
    • Dynamic modelling and analysis of biochemical networks: Mechanism-based models and model-based experiments
    • van Riel NAW. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Brief Bioinform 2006;7(4):364-74.
    • (2006) Brief Bioinform , vol.7 , Issue.4 , pp. 364-374
    • van Riel, N.A.W.1
  • 4
    • 31444442519 scopus 로고    scopus 로고
    • The Blue Brain Project
    • Markram H. The Blue Brain Project. Nat Rev Neurosci 2006; 7 153-60.
    • (2006) Nat Rev Neurosci , vol.7 , pp. 153-160
    • Markram, H.1
  • 5
    • 20444461186 scopus 로고    scopus 로고
    • Simulations of the formation, evolution and clustering of galaxies and quasars
    • Springel V, White SDM, Jenkins A, et al. Simulations of the formation, evolution and clustering of galaxies and quasars. Nature 2005;435:629-36.
    • (2005) Nature , vol.435 , pp. 629-636
    • Springel, V.1    White, S.D.M.2    Jenkins, A.3
  • 6
    • 13444269104 scopus 로고    scopus 로고
    • Uncertainty in predictions of the climate response to rising levels of greenhouse gases
    • Stainforth DA, Aina T, Christensen C, et al. Uncertainty in predictions of the climate response to rising levels of greenhouse gases. Nature 2005;433:403-6.
    • (2005) Nature , vol.433 , pp. 403-406
    • Stainforth, D.A.1    Aina, T.2    Christensen, C.3
  • 7
    • 33845466196 scopus 로고    scopus 로고
    • Computational methodologies for modelling, analysis and simulation of signalling networks
    • Gilbert D, Fuß H, Gu X, et al. Computational methodologies for modelling, analysis and simulation of signalling networks. Brief Bioinform 2006;7(4):339-53.
    • (2006) Brief Bioinform , vol.7 , Issue.4 , pp. 339-353
    • Gilbert, D.1    Fuß, H.2    Gu, X.3
  • 8
    • 20644467467 scopus 로고    scopus 로고
    • Systems biotechnology for strain improvement
    • Lee SY, Lee D-Y, Kim TY. Systems biotechnology for strain improvement. Trends Biotechnol 2005;23:349-58.
    • (2005) Trends Biotechnol , vol.23 , pp. 349-358
    • Lee, S.Y.1    Lee, D.-Y.2    Kim, T.Y.3
  • 9
    • 10644250404 scopus 로고    scopus 로고
    • Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project
    • Hucka M, Finney A, Bornstein BJ, et al. Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project. Syst Biol 2004;1:41-53.
    • (2004) Syst Biol , vol.1 , pp. 41-53
    • Hucka, M.1    Finney, A.2    Bornstein, B.J.3
  • 10
    • 33745075591 scopus 로고    scopus 로고
    • Tools for kinetic modelling of biochemical networks
    • Alves R, Antunes F, Salvador A. Tools for kinetic modelling of biochemical networks. Nat Biotechnol 2006; 24:667-72.
    • (2006) Nat Biotechnol , vol.24 , pp. 667-672
    • Alves, R.1    Antunes, F.2    Salvador, A.3
  • 11
    • 34147189103 scopus 로고    scopus 로고
    • Systems biology standards-the community speaks
    • Klipp E, Liebermeister W, Helbig A, et al. Systems biology standards-the community speaks. Nat Biotechnol 2007;25:390-1.
    • (2007) Nat Biotechnol , vol.25 , pp. 390-391
    • Klipp, E.1    Liebermeister, W.2    Helbig, A.3
  • 12
    • 0033031386 scopus 로고    scopus 로고
    • E-Cell: Software environment for computational cell biology
    • Tomita M, Hashimoto K, Takahashi K, et al. E-Cell: Software environment for computational cell biology. Bioinformatics 1999; 15(1):72-84.
    • (1999) Bioinformatics , vol.15 , Issue.1 , pp. 72-84
    • Tomita, M.1    Hashimoto, K.2    Takahashi, K.3
  • 13
    • 0347511691 scopus 로고    scopus 로고
    • Next generation simulation tools: The systems biology workbench and BioSPICE integration
    • Sauro HM, Hucka M, Finney A, et al. Next generation simulation tools: The systems biology workbench and BioSPICE integration. OMICS 2003;7(4):355-72.
    • (2003) OMICS , vol.7 , Issue.4 , pp. 355-372
    • Sauro, H.M.1    Hucka, M.2    Finney, A.3
  • 14
    • 33845368513 scopus 로고    scopus 로고
    • COPASI - a COmplex PAthway SImulator
    • Hoops S, Sahle S, Gauges R, et al. COPASI - a COmplex PAthway SImulator. Bioinformatics 2006;22(24): 3067-74.
    • (2006) Bioinformatics , vol.22 , Issue.24 , pp. 3067-3074
    • Hoops, S.1    Sahle, S.2    Gauges, R.3
  • 15
    • 33644877164 scopus 로고    scopus 로고
    • BioModels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
    • Le Novère N, Bornstein B, Broicher A, et al. BioModels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006;34: D689-91.
    • (2006) Nucleic Acids Res , vol.34
    • Le Novère, N.1    Bornstein, B.2    Broicher, A.3
  • 16
    • 0037433037 scopus 로고    scopus 로고
    • The database of quantitative cellular signalling: Management and analysis of chemical kinetic models of signalling networks
    • Sivakumaran S, Hariharaputran S, Mishra J, et al. The database of quantitative cellular signalling: Management and analysis of chemical kinetic models of signalling networks. Bioinformatics 2003;19 (3):408-15.
    • (2003) Bioinformatics , vol.19 , Issue.3 , pp. 408-415
    • Sivakumaran, S.1    Hariharaputran, S.2    Mishra, J.3
  • 17
    • 4544344218 scopus 로고    scopus 로고
    • Web-based kinetic modelling using JWS online
    • Olivier BG, Snoep JL. Web-based kinetic modelling using JWS online. Bioinformatics 2004;20(13):2143-4.
    • (2004) Bioinformatics , vol.20 , Issue.13 , pp. 2143-2144
    • Olivier, B.G.1    Snoep, J.L.2
  • 18
    • 0035478586 scopus 로고    scopus 로고
    • The virtual cell: A software environment for computational cell biology
    • Loew LM, Schaff JC. The virtual cell: A software environment for computational cell biology. Trends Biotechnol 2001;19:401-6.
    • (2001) Trends Biotechnol , vol.19 , pp. 401-406
    • Loew, L.M.1    Schaff, J.C.2
  • 20
    • 33646203362 scopus 로고    scopus 로고
    • WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks
    • Lee D-Y, Yun C, Cho A, et al. WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics 2006;22(9): 1150-1.
    • (2006) Bioinformatics , vol.22 , Issue.9 , pp. 1150-1151
    • Lee, D.-Y.1    Yun, C.2    Cho, A.3
  • 21
    • 45449110775 scopus 로고    scopus 로고
    • SYCAMORE - a systems biology computational analysis and modelling research environment
    • Weidemann A, Richter S, Stein M, et al. SYCAMORE - a systems biology computational analysis and modelling research environment. Bioinformatics 2008;24(12):1463-4.
    • (2008) Bioinformatics , vol.24 , Issue.12 , pp. 1463-1464
    • Weidemann, A.1    Richter, S.2    Stein, M.3
  • 22
    • 0037337990 scopus 로고    scopus 로고
    • Towards an e-biology of ageing: Integrating theory and data
    • Kirkwood TB, Boys RJ, Gillespie CS, et al. Towards an e-biology of ageing: Integrating theory and data. Nat Rev Mol Cell Biol 2003; 4:243-9.
    • (2003) Nat Rev Mol Cell Biol , vol.4 , pp. 243-249
    • Kirkwood, T.B.1    Boys, R.J.2    Gillespie, C.S.3
  • 23
    • 0242380634 scopus 로고    scopus 로고
    • CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
    • Kurata H, Matoba N, Shimizu N. CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res 2003;31 (14):4071-84.
    • (2003) Nucleic Acids Res , vol.31 , Issue.14 , pp. 4071-4084
    • Kurata, H.1    Matoba, N.2    Shimizu, N.3
  • 24
    • 17844397967 scopus 로고    scopus 로고
    • CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models
    • Kurata H, Masaki K, Sumida Y, et al. CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models. Genome Res 2005;15:590-600.
    • (2005) Genome Res , vol.15 , pp. 590-600
    • Kurata, H.1    Masaki, K.2    Sumida, Y.3
  • 25
    • 13844266102 scopus 로고    scopus 로고
    • Simulation tools for biochemical networks: Evaluation of performance and usability
    • Pettinen A, Aho T, Smolander O-P, et al. Simulation tools for biochemical networks: Evaluation of performance and usability. Bioinformatics 2005;21:357-63.
    • (2005) Bioinformatics , vol.21 , pp. 357-363
    • Pettinen, A.1    Aho, T.2    Smolander, O.-P.3
  • 26
    • 33646746237 scopus 로고    scopus 로고
    • The JigCell model builder: A spreadsheet interface for creating biochemical reaction network models
    • Vass MT, Shaffer CA, Ramakrishnan N, et al., The JigCell model builder: A spreadsheet interface for creating biochemical reaction network models. IEEE/ACM Trans. Comput Biol Bioinform 2006;3 155-64.
    • (2006) IEEE/ACM Trans. Comput Biol Bioinform , vol.3 , pp. 155-164
    • Vass, M.T.1    Shaffer, C.A.2    Ramakrishnan, N.3
  • 27
    • 33746675631 scopus 로고    scopus 로고
    • SABIO-RK: Integration and curation of reaction kinetics data
    • Proceedings of the 3rd International workshop on Data Integration in the Life Sciences DILS'06, Springer, Hinxton, UK
    • Wittig U, Golebiewski M, Kania R, et al. SABIO-RK: Integration and curation of reaction kinetics data. In: Proceedings of the 3rd International workshop on Data Integration in the Life Sciences (DILS'06), 2006, Lecture Notes in Bioinformatics, Vol. 4075, pp. 94-103, Springer, Hinxton, UK.
    • (2006) Lecture Notes in Bioinformatics , vol.4075 , pp. 94-103
    • Wittig, U.1    Golebiewski, M.2    Kania, R.3
  • 28
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: A comparison of global optimization methods
    • Moles CG, Mendes P, Banga JR. Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Res 2003;13:2467-74.
    • (2003) Genome Res , vol.13 , pp. 2467-2474
    • Moles, C.G.1    Mendes, P.2    Banga, J.R.3
  • 29
    • 38049052406 scopus 로고    scopus 로고
    • Gabdoulline RR, Stein M, Wade RC. qPIPSA: Relating enzymatic kinetic parameters and interaction fields. BMC Bioinformatics 2007;8 373.
    • Gabdoulline RR, Stein M, Wade RC. qPIPSA: Relating enzymatic kinetic parameters and interaction fields. BMC Bioinformatics 2007;8 373.
  • 31
    • 3342925846 scopus 로고    scopus 로고
    • Comparison of network-based pathway analysis methods
    • Papin JA, Stelling J, Price ND, et al. Comparison of network-based pathway analysis methods. Trends Biotechnol 2004;22:400-5.
    • (2004) Trends Biotechnol , vol.22 , pp. 400-405
    • Papin, J.A.1    Stelling, J.2    Price, N.D.3
  • 32
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977;81:2340-61.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 34
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
    • Hucka M, Finney A, Sauro HM, et al. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 2003;19:524-31.
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3
  • 35
    • 38949183929 scopus 로고    scopus 로고
    • Web and grid technologies in bioinformatics, computational and systems biology: A review
    • Shah AA, Barthel D, Lukasiak P, et al. Web and grid technologies in bioinformatics, computational and systems biology: A review. Curr Bioinformatics 2008;3:10-31.
    • (2008) Curr Bioinformatics , vol.3 , pp. 10-31
    • Shah, A.A.1    Barthel, D.2    Lukasiak, P.3
  • 37
    • 60749127161 scopus 로고    scopus 로고
    • Bruno EJ. Ajax: Asynchronous JavaScript and XML, creating dynamic web pages. Dr. Dobb's Journal. http://www.ddj.com/web-development/ 184406430 (22 April 2008, date last accessed).
    • Bruno EJ. Ajax: Asynchronous JavaScript and XML, creating dynamic web pages. Dr. Dobb's Journal. http://www.ddj.com/web-development/ 184406430 (22 April 2008, date last accessed).
  • 38
    • 33744744785 scopus 로고    scopus 로고
    • Understanding bistability in complex enzyme-driven reaction networks
    • Craciun G, Tang Y, Feinberg M. Understanding bistability in complex enzyme-driven reaction networks. Proc Natl Acad Sci USA 2006; 103:8697-702.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 8697-8702
    • Craciun, G.1    Tang, Y.2    Feinberg, M.3
  • 39
    • 45749107153 scopus 로고    scopus 로고
    • Discrete event modelling and simulation in systems biology
    • Ewald R, Maus C, Rolfs A, et al. Discrete event modelling and simulation in systems biology. J Simulation 2007;1:81-96.
    • (2007) J Simulation , vol.1 , pp. 81-96
    • Ewald, R.1    Maus, C.2    Rolfs, A.3
  • 40
    • 34248173350 scopus 로고    scopus 로고
    • Addressing the challenges of multiscale model management in systems biology
    • Hetherington J, Bogle IDL, Saffrey P, et al. Addressing the challenges of multiscale model management in systems biology. Comput Chem Eng 2007;31:962-79.
    • (2007) Comput Chem Eng , vol.31 , pp. 962-979
    • Hetherington, J.1    Bogle, I.D.L.2    Saffrey, P.3
  • 41
    • 0242475329 scopus 로고    scopus 로고
    • MetaFluxNet: The management of metabolic reaction information and quantitative metabolic flux analysis
    • Lee D-Y, Yun H, Park S, et al. MetaFluxNet: The management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics 2003;19: 2144-6.
    • (2003) Bioinformatics , vol.19 , pp. 2144-2146
    • Lee, D.-Y.1    Yun, H.2    Park, S.3
  • 43
    • 20444396593 scopus 로고    scopus 로고
    • All systems go: Launching cell simulation fueled by integrated experimental biology data
    • Arita M, Robert M, Tomita M. All systems go: Launching cell simulation fueled by integrated experimental biology data. Curr Opin Biotechnol 2005;16:344-9.
    • (2005) Curr Opin Biotechnol , vol.16 , pp. 344-349
    • Arita, M.1    Robert, M.2    Tomita, M.3
  • 44
    • 24044469341 scopus 로고    scopus 로고
    • Application of metabolome data in functional genomics: A conceptual strategy
    • Wu L, van Winden WA, van Gulik WM, et al. Application of metabolome data in functional genomics: A conceptual strategy. Metab Eng 2005;7:302-10.
    • (2005) Metab Eng , vol.7 , pp. 302-310
    • Wu, L.1    van Winden, W.A.2    van Gulik, W.M.3
  • 46
    • 27144497798 scopus 로고    scopus 로고
    • From XML to RDF: How semantic web technologies will change the design of 'omic' standards
    • Wang X, Gorlitsky R, Almeida JS. From XML to RDF: How semantic web technologies will change the design of 'omic' standards. Nat Biotechnol 2005;9: 1099-103.
    • (2005) Nat Biotechnol , vol.9 , pp. 1099-1103
    • Wang, X.1    Gorlitsky, R.2    Almeida, J.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.