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Volumn 27, Issue 7, 2011, Pages 1028-1029

SBML-PET-MPI: A parallel parameter estimation tool for Systems Biology Markup Language based models

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER LANGUAGE; COMPUTER PROGRAM; METHODOLOGY; SYSTEMS BIOLOGY;

EID: 79953317637     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr038     Document Type: Article
Times cited : (16)

References (16)
  • 1
    • 77953582302 scopus 로고    scopus 로고
    • Covering a broad dynamic range: information processing at the erythropoietin receptor
    • Becker,V. et al. (2010) Covering a broad dynamic range: information processing at the erythropoietin receptor. Science, 328, 1404-1408.
    • (2010) Science , vol.328 , pp. 1404-1408
    • Becker, V.1
  • 2
    • 40749162829 scopus 로고    scopus 로고
    • LibSBML: an API library for SBML
    • Bornstein,B.J. et al. (2008) LibSBML: an API library for SBML. Bioinformatics, 24, 880-881.
    • (2008) Bioinformatics , vol.24 , pp. 880-881
    • Bornstein, B.J.1
  • 3
    • 0030243005 scopus 로고    scopus 로고
    • A high-performance, portable implementation of the MPI message passing interface standard
    • Gropp,W. et al. (1996) A high-performance, portable implementation of the MPI message passing interface standard. Parallel Comput., 22, 789-828.
    • (1996) Parallel Comput. , vol.22 , pp. 789-828
    • Gropp, W.1
  • 4
    • 0001811061 scopus 로고
    • ODEPACK, a systematized collection of ODE solvers
    • Stepleman,R.S. et al. (eds), North-Holland, Amsterdam
    • Hindmarsh, A.C. (1983) ODEPACK, a systematized collection of ODE solvers. In Stepleman,R.S. et al. (eds), Scientific Computing. North-Holland, Amsterdam, pp. 55-64.
    • (1983) Scientific Computing , pp. 55-64
    • Hindmarsh, A.C.1
  • 5
    • 68349101376 scopus 로고    scopus 로고
    • DOTcvpSB, a software toolbox for dynamic optimization in systems biology
    • Hirmajer,T. et al. (2009) DOTcvpSB, a software toolbox for dynamic optimization in systems biology. BMC Bioinformatics, 10, 199.
    • (2009) BMC Bioinformatics , vol.10 , pp. 199
    • Hirmajer, T.1
  • 6
    • 33845368513 scopus 로고    scopus 로고
    • COPASI-a COmplex PAthway Simulator
    • Hoops,S. et al. (2006) COPASI-a COmplex PAthway Simulator. Bioinformatics, 22, 3067-3074.
    • (2006) Bioinformatics , vol.22 , pp. 3067-3074
    • Hoops, S.1
  • 7
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    • Hucka,M. et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1
  • 8
    • 30344470205 scopus 로고    scopus 로고
    • libSRES: a C library for stochastic ranking evolution strategy for parameter estimation
    • Ji,X. and Xu,Y. (2006) libSRES: a C library for stochastic ranking evolution strategy for parameter estimation. Bioinformatics, 22, 124-126.
    • (2006) Bioinformatics , vol.22 , pp. 124-126
    • Ji, X.1    Xu, Y.2
  • 9
    • 77954498298 scopus 로고    scopus 로고
    • DA 1.0: parameter estimation of biological pathways using data assimilation approach
    • Koh,C.H. et al. (2010) DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics, 26, 1794-1796.
    • (2010) Bioinformatics , vol.26 , pp. 1794-1796
    • Koh, C.H.1
  • 10
    • 51749122228 scopus 로고    scopus 로고
    • Dynamical modeling and multi-experiment fitting with PottersWheel
    • Maiwald,T. and Timmer,J. (2008) Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinformatics, 24, 2037-2043.
    • (2008) Bioinformatics , vol.24 , pp. 2037-2043
    • Maiwald, T.1    Timmer, J.2
  • 11
    • 0000169232 scopus 로고
    • An algorithm for least-squares estimation of nonlinear parameters
    • Marquardt,D.W. (1963) An algorithm for least-squares estimation of nonlinear parameters. J. Soc. Ind. Appl. Math., 11, 431-441.
    • (1963) J. Soc. Ind. Appl. Math. , vol.11 , pp. 431-441
    • Marquardt, D.W.1
  • 13
    • 36549012683 scopus 로고    scopus 로고
    • Estimating parameters and hidden variables in non-linear statespace models based on ODEs for biological networks inference
    • Quach,M. et al. (2007) Estimating parameters and hidden variables in non-linear statespace models based on ODEs for biological networks inference. Bioinformatics, 23, 3209-3216.
    • (2007) Bioinformatics , vol.23 , pp. 3209-3216
    • Quach, M.1
  • 14
    • 67650760503 scopus 로고    scopus 로고
    • Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
    • Raue,A. et al. (2009) Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics, 25, 1923-1929.
    • (2009) Bioinformatics , vol.25 , pp. 1923-1929
    • Raue, A.1
  • 15
    • 0034266683 scopus 로고    scopus 로고
    • Stochastic ranking for constrained evolutionary optimization
    • Runarsson,T.P. and Yao,X. (2000) Stochastic ranking for constrained evolutionary optimization. IEEE Trans. Evol. Comput., 4, 284-294.
    • (2000) IEEE Trans. Evol. Comput. , vol.4 , pp. 284-294
    • Runarsson, T.P.1    Yao, X.2
  • 16
    • 33750415038 scopus 로고    scopus 로고
    • SBML-PET: a Systems Biology Markup Language-based parameter estimation tool
    • Zi,Z. and Klipp,E. (2006) SBML-PET: a Systems Biology Markup Language-based parameter estimation tool. Bioinformatics, 22, 2704-2705.
    • (2006) Bioinformatics , vol.22 , pp. 2704-2705
    • Zi, Z.1    Klipp, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.