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Volumn 121, Issue , 2010, Pages 109-138

Modeling languages for biochemical network simulation: Reaction vs equation based approaches

Author keywords

Biochemical network modeling; Modelica; Modeling languages; Object oriented modeling; SBML

Indexed keywords

BIOPOLYMER;

EID: 80053384066     PISSN: 07246145     EISSN: None     Source Type: Book Series    
DOI: 10.1007/10_2009_64     Document Type: Article
Times cited : (8)

References (47)
  • 5
    • 20444411533 scopus 로고    scopus 로고
    • The Silicon Cell initiative: Working towards a detailed kinetic description at the cellular level
    • Snoep JL (2005) The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level. Curr Opin Biotechnol 16:336-343
    • (2005) Curr Opin Biotechnol , vol.16 , pp. 336-343
    • Snoep, J.L.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, Finney A, Sauro HM 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    Finney, A.2    Sauro, H.M.3
  • 13
    • 0037715313 scopus 로고    scopus 로고
    • Modular modeling of cellular systems with ProMoT/Diva
    • Ginkel M, Kremling A, Nutsch T et al (2003) Modular modeling of cellular systems with ProMoT/Diva. Bioinformatics 19:1169-1176
    • (2003) Bioinformatics , vol.19 , pp. 1169-1176
    • Ginkel, M.1    Kremling, A.2    Nutsch, T.3
  • 14
    • 82055180479 scopus 로고
    • Equation formulation and solution methods behind DYNAST-a multipurpose simulation tool
    • In:, Vienna
    • Mann H (1994) Equation formulation and solution methods behind DYNAST-a multipurpose simulation tool. In: IMACS symp. on mathematical modelling MATHMOD, Vienna, pp938-939
    • (1994) IMACS symp. on mathematical modelling MATHMOD , pp. 938-939
    • Mann, H.1
  • 17
    • 9444266171 scopus 로고    scopus 로고
    • CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
    • Funahashi A, Tanimura N, Morohashi M et al (2003) CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1:159-162
    • (2003) BIOSILICO , vol.1 , pp. 159-162
    • Funahashi, A.1    Tanimura, N.2    Morohashi, M.3
  • 18
    • 33845368513 scopus 로고    scopus 로고
    • COPASI-a COmplex PAthway SImulator
    • Hoops S, Sahle S, Gauges R et al (2006) COPASI-a COmplex PAthway SImulator. Bioinformatics 22:3067-3074
    • (2006) Bioinformatics , vol.22 , pp. 3067-3074
    • Hoops, S.1    Sahle, S.2    Gauges, R.3
  • 22
    • 0041485347 scopus 로고
    • Object-oriented modeling and automatic formula manipulation in Dymola
    • In:, Kongsberg, Norway
    • Elmqvist H (1993) Object-oriented modeling and automatic formula manipulation in Dymola. In: SIMS'93, Scandinavian Simulation Society, Kongsberg, Norway
    • (1993) SIMS'93, Scandinavian Simulation Society
    • Elmqvist, H.1
  • 23
    • 0030247158 scopus 로고    scopus 로고
    • Generating efficient computational procedures from declarative models
    • Maffezzoni C, Girelli R, Lluka P (1996) Generating efficient computational procedures from declarative models. Simul Pract Theory 4:303-317
    • (1996) Simul Pract Theory , vol.4 , pp. 303-317
    • Maffezzoni, C.1    Girelli, R.2    Lluka, P.3
  • 25
    • 84901072107 scopus 로고    scopus 로고
    • A multi-scale modeling concept and computational tools for the integrative analysis of stationary metabolic data
    • Lieres E, Petersen S, Wiechert W (2004) A multi-scale modeling concept and computational tools for the integrative analysis of stationary metabolic data, vol 1. J Integr Bioinform
    • (2004) J Integr Bioinform , vol.1
    • Lieres, E.1    Petersen, S.2    Wiechert, W.3
  • 28
    • 0035890418 scopus 로고    scopus 로고
    • Structural solvability analysis of dynamic process models
    • Leitold A, Hangos KM (2001) Structural solvability analysis of dynamic process models. Comput Chem Eng 25:1633-1646
    • (2001) Comput Chem Eng , vol.25 , pp. 1633-1646
    • Leitold, A.1    Hangos, K.M.2
  • 29
    • 0000261734 scopus 로고
    • Index reduction in differential-algebraic equations using dummy derivatives
    • Mattsson SE, Söderlind G (1993) Index reduction in differential-algebraic equations using dummy derivatives. SIAM J Sci Comput 14:677-692
    • (1993) SIAM J Sci Comput , vol.14 , pp. 677-692
    • Mattsson, S.E.1    Söderlind, G.2
  • 30
    • 0000353268 scopus 로고
    • The consistent initialization of differential-algebraic systems
    • Pantelides CC (1988) The consistent initialization of differential-algebraic systems. SIAM J Sci Stat Comput 9:213-231
    • (1988) SIAM J Sci Stat Comput , vol.9 , pp. 213-231
    • Pantelides, C.C.1
  • 31
    • 0033662287 scopus 로고    scopus 로고
    • The organization of metabolic reaction networks: A signal-oriented approach to cellular models
    • Kremling A, Jahreis K, Lengeler JW et al (2000) The organization of metabolic reaction networks: a signal-oriented approach to cellular models. Metab Eng 2:190-200
    • (2000) Metab Eng , vol.2 , pp. 190-200
    • Kremling, A.1    Jahreis, K.2    Lengeler, J.W.3
  • 32
    • 0034805944 scopus 로고    scopus 로고
    • The organization of metabolic reaction networks. II. Signal processing in hierarchical structured functional units
    • Kremling A, Gilles ED (2001) The organization of metabolic reaction networks. II. Signal processing in hierarchical structured functional units. Metab Eng 3:138-150
    • (2001) Metab Eng , vol.3 , pp. 138-150
    • Kremling, A.1    Gilles, E.D.2
  • 33
    • 40849084585 scopus 로고    scopus 로고
    • Using automatic differentiation for partial derivatives of functions in Modelica
    • In:, Hamburg, Germany
    • Olsson H, Tummescheit H, Elmqvist H (2005) Using automatic differentiation for partial derivatives of functions in Modelica. In: Modelica 2005, Hamburg, Germany, pp 105-112
    • (2005) Modelica 2005 , pp. 105-112
    • Olsson, H.1    Tummescheit, H.2    Elmqvist, H.3
  • 34
    • 82055180470 scopus 로고    scopus 로고
    • A framework for describing and solving PDE models in Modelica
    • In:, Hamburg, Germany
    • Saldamli L, Bachmann B, Fritzson P (2005) A framework for describing and solving PDE models in Modelica. In: Modelica 2005, Hamburg, Germany, pp 113-122
    • (2005) Modelica 2005 , pp. 113-122
    • Saldamli, L.1    Bachmann, B.2    Fritzson, P.3
  • 36
    • 82055182225 scopus 로고    scopus 로고
    • Teaching finite elements: An alternative approach using Modelica
    • In:, Lubljana
    • Wiechert W, Treude M (2007) Teaching finite elements: an alternative approach using Modelica. In: EUROSIM, Lubljana
    • (2007) EUROSIM
    • Wiechert, W.1    Treude, M.2
  • 37
    • 82055180477 scopus 로고    scopus 로고
    • State events in continuous modelling and simulation-concepts, implementation and new methodology
    • In:, (ed) Advances in simulation
    • Plank J (1997) State events in continuous modelling and simulation-concepts, implementation and new methodology. In: ASIM/ARGESIM/SCS (ed) Advances in simulation
    • (1997) ASIM/ARGESIM/SCS
    • Plank, J.1
  • 39
    • 0036937351 scopus 로고    scopus 로고
    • MMT-a pathway modeling tool for data from rapid sampling experiments
    • Hurlebaus J, Buchholz A, Alt W et al (2002) MMT-a pathway modeling tool for data from rapid sampling experiments. In Silico Biol 2:467-484
    • (2002) In Silico Biol , vol.2 , pp. 467-484
    • Hurlebaus, J.1    Buchholz, A.2    Alt, W.3
  • 42
    • 78651551499 scopus 로고    scopus 로고
    • Sensitivity analysis of Modelica applications via automatic differentiation
    • In:, Bielefeld, Germany
    • Elsheikh A, Noack S, Wiechert W (2008) Sensitivity analysis of Modelica applications via automatic differentiation. In: 6th international Modelica conference, Bielefeld, Germany
    • (2008) 6th international Modelica conference
    • Elsheikh, A.1    Noack, S.2    Wiechert, W.3
  • 46
    • 84901136572 scopus 로고    scopus 로고
    • Biochemical and metabolic modeling and simulation with Modelica
    • In:, Linköping, Sweden
    • Nilsson EL, Fritzson P (2005) Biochemical and metabolic modeling and simulation with Modelica. In: BioMedSim. Linköping, Sweden
    • (2005) BioMedSim
    • Nilsson, E.L.1    Fritzson, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.