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Volumn 2, Issue 4, 2014, Pages 246-257

SBMLSimulator: A java tool for model simulation and parameter estimation in systems biology

Author keywords

Ordinary differential equation (ODE) modeling; Parameter estimation; Simulation; Systems Biology Markup Language (SBML)

Indexed keywords


EID: 84966367307     PISSN: None     EISSN: 20793197     Source Type: Journal    
DOI: 10.3390/computation2040246     Document Type: Article
Times cited : (10)

References (42)
  • 1
    • 0036851376 scopus 로고    scopus 로고
    • In Silico Model-Driven Assessment of the Effects of Single Nucleotide Polymorphisms (SNPs) on Human Red Blood Cell Metabolism
    • Jamshidi, N.; Wiback, S.J.; Palsson, B.Ø. In Silico Model-Driven Assessment of the Effects of Single Nucleotide Polymorphisms (SNPs) on Human Red Blood Cell Metabolism. Genome Res. 2002, 12, 1687-1692.
    • (2002) Genome Res. , vol.12 , pp. 1687-1692
    • Jamshidi, N.1    Wiback, S.J.2    Palsson, B.Ø.3
  • 2
    • 84991905414 scopus 로고    scopus 로고
    • Improving collaboration by standardization efforts in systems biology
    • Dräger, A.; Palsson, B.Ø. Improving collaboration by standardization efforts in systems biology. Front. Bioeng. 2014, 2, doi: 10.3389/fbioe.2014.00061.
    • (2014) Front. Bioeng , vol.2
    • Dräger, A.1    Palsson, B.Ø.2
  • 6
    • 79960940147 scopus 로고    scopus 로고
    • Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling
    • Costa, R.; Machado, D.; Rocha, I.; Ferreira, E. Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling. IET Syst. Biol. 2011, 5, 157-163.
    • (2011) IET Syst. Biol , vol.5 , pp. 157-163
    • Costa, R.1    Machado, D.2    Rocha, I.3    Ferreira, E.4
  • 7
    • 84856433620 scopus 로고    scopus 로고
    • Metabolic network reconstruction: Advances in in silico interpretation of analytical information
    • Chen, N.; Del, V.I.; Kyriakopoulos, S.; Polizzi, K.; Kontoravdi, C. Metabolic network reconstruction: Advances in in silico interpretation of analytical information. Curr. Opin. Biotechnol. 2012, 23, 77-82.
    • (2012) Curr. Opin. Biotechnol , vol.23 , pp. 77-82
    • Chen, N.1    Del, V.I.2    Kyriakopoulos, S.3    Polizzi, K.4    Kontoravdi, C.5
  • 10
    • 84908387275 scopus 로고    scopus 로고
    • KiMoSys: A web-based repository of experimental data for KInetic MOdels of biological SYStems
    • Costa, R.S.; Veríssimo, A.; Vinga, S. KiMoSys: A web-based repository of experimental data for KInetic MOdels of biological SYStems. BMC Syst. Biol. 2014, 8, 85.
    • (2014) BMC Syst. Biol , vol.8 , pp. 85
    • Costa, R.S.1    Veríssimo, A.2    Vinga, S.3
  • 13
    • 44949195709 scopus 로고    scopus 로고
    • Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in Corynebacterium glutamicum
    • Singapore, 25-28 September
    • Dräger, A.; Supper, J.; Planatscher, H.; Magnus, J.B.; Oldiges, M.; Zell, A. Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in Corynebacterium glutamicum. In Proceedings of the 2007 IEEE Congress on Evolutionary Computation, Singapore, 25-28 September 2007; pp. 620-627.
    • (2007) In Proceedings of the 2007 IEEE Congress on Evolutionary Computation , pp. 620-627
    • Dräger, A.1    Supper, J.2    Planatscher, H.3    Magnus, J.B.4    Oldiges, M.5    Zell, A.6
  • 17
    • 79961185589 scopus 로고    scopus 로고
    • AMIGO, a toolbox for advanced model identification in systems biology using global optimization
    • Balsa-Canto, E.; Banga, J.R. AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Bioinformatics 2011, 27, 2311-2313.
    • (2011) Bioinformatics , vol.27 , pp. 2311-2313
    • Balsa-Canto, E.1    Banga, J.R.2
  • 18
    • 32544443964 scopus 로고    scopus 로고
    • Systems Biology Toolbox for MATLAB: A computational platform for research in systems biology
    • Schmidt, H.; Jirstrand, M. Systems Biology Toolbox for MATLAB: A computational platform for research in systems biology. Bioinformatics 2006, 22, 514-515.
    • (2006) Bioinformatics , vol.22 , pp. 514-515
    • Schmidt, H.1    Jirstrand, M.2
  • 19
    • 33750415038 scopus 로고    scopus 로고
    • SBML-PET: A Systems Biology Markup Language-based parameter estimation tool
    • Zi, Z.; Klipp, E. SBML-PET: A Systems Biology Markup Language-based parameter estimation tool. Bioinformatics 2006, 22, 2704-2705.
    • (2006) Bioinformatics , vol.22 , pp. 2704-2705
    • Zi, Z.1    Klipp, E.2
  • 21
    • 51749122228 scopus 로고    scopus 로고
    • Dynamical modeling and multi-experiment fitting with PottersWheel
    • Maiwald, T.; Timmer, J. Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinformatics 2008, 24, 2037-2043.
    • (2008) Bioinformatics , vol.24 , pp. 2037-2043
    • Maiwald, T.1    Timmer, J.2
  • 25
    • 0142000477 scopus 로고    scopus 로고
    • Differential evolution-A simple and efficient heuristic for global optimization over continuous spaces
    • Storn, R.; Price, K. Differential evolution-A simple and efficient heuristic for global optimization over continuous spaces. J. Glob. Opt. 1997, 11, 341-359.
    • (1997) J. Glob. Opt , vol.11 , pp. 341-359
    • Storn, R.1    Price, K.2
  • 26
    • 0029535737 scopus 로고
    • In Proceedings of the IEEE International Conference on Neural Networks, Perth, Australia, 27 November-1 December
    • Kennedy, J.; Eberhart, R. Particle swarm optimization. In Proceedings of the IEEE International Conference on Neural Networks, Perth, Australia, 27 November-1 December 1995; Volume 4, pp. 1942-1948.
    • (1995) Particle swarm optimization , vol.4 , pp. 1942-1948
    • Kennedy, J.1    Eberhart, R.2
  • 29
    • 0011434347 scopus 로고
    • Hill climbing with multiple local optima
    • Tovey, C.A. Hill climbing with multiple local optima. SIAM J. Algebr. Discret. Methods 1985, 6, 384-393.
    • (1985) SIAM J. Algebr. Discret. Methods , vol.6 , pp. 384-393
    • Tovey, C.A.1
  • 30
    • 26444479778 scopus 로고
    • Optimization by Simulated Annealing
    • Kirkpatrick, S.; Gelatt, C.D.; Vecchi, M.P. Optimization by Simulated Annealing. Science 1983, 220, 671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 31
    • 0003904118 scopus 로고
    • Ph.D. Thesis, Department of Process Engineering, Technical University of Berlin, Berlin, Germany, (In German)
    • Schwefel, H.P. Evolutionsstrategie und Numerische Optimierung. Ph.D. Thesis, Department of Process Engineering, Technical University of Berlin, Berlin, Germany, 1975. (In German)
    • (1975) Evolutionsstrategie und Numerische Optimierung
    • Schwefel, H.P.1
  • 32
    • 0035377566 scopus 로고    scopus 로고
    • Completely Derandomized Self-Adaptation in Evolution Strategies
    • Hansen, N.; Ostermeier, A. Completely Derandomized Self-Adaptation in Evolution Strategies. Evolut. Comput. 2001, 9, 159-195.
    • (2001) Evolut. Comput , vol.9 , pp. 159-195
    • Hansen, N.1    Ostermeier, A.2
  • 34
    • 0036464756 scopus 로고    scopus 로고
    • The Particle Swarm-Explosion, Stability, and Convergence in a Multidimensional Complex Space
    • Clerc, M.; Kennedy, J. The Particle Swarm-Explosion, Stability, and Convergence in a Multidimensional Complex Space. IEEE Trans. Evolut. Comput. 2002, 6, 58-73.
    • (2002) IEEE Trans. Evolut. Comput , vol.6 , pp. 58-73
    • Clerc, M.1    Kennedy, J.2
  • 36
    • 84883221825 scopus 로고    scopus 로고
    • BioModels Database: A Repository of Mathematical Models of Biological Processes
    • Schneider, M.V.; Ed.; Springer: New York, NY, USA
    • Chelliah, V.; Laibe, C.; le Novère, N. BioModels Database: A Repository of Mathematical Models of Biological Processes. In In Silico Systems Biology; Schneider, M.V.; Ed.; Springer: New York, NY, USA, 2013; Volume 1021, pp. 189-199.
    • (2013) In In Silico Systems Biology , vol.1021 , pp. 189-199
    • Chelliah, V.1    Laibe, C.2    le Novère, N.3
  • 40
  • 41
    • 85043541313 scopus 로고    scopus 로고
    • A Primer on Modular Mass-Action Modelling with CellML
    • Choi, S.; Ed.; Springer: New York, NY, USA
    • Cooling, M.T. A Primer on Modular Mass-Action Modelling with CellML. In Systems Biology for Signaling Networks; Choi, S.; Ed.; Springer: New York, NY, USA, 2010; Volume 1, pp. 721-750.
    • (2010) In Systems Biology for Signaling Networks , vol.1 , pp. 721-750
    • Cooling, M.T.1
  • 42
    • 41949113538 scopus 로고    scopus 로고
    • Reference descriptions of cellular electrophysiology models
    • Nickerson, D.P.; Corrias, A.; Buist, M.L. Reference descriptions of cellular electrophysiology models. Bioinformatics 2008, 24, 1112-1114.
    • (2008) Bioinformatics , vol.24 , pp. 1112-1114
    • Nickerson, D.P.1    Corrias, A.2    Buist, M.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.