메뉴 건너뛰기




Volumn 2, Issue 4, 2004, Pages 619-637

Modeling and simulation of molecular biology systems using Petri nets: Modeling goals of various approaches

Author keywords

Biochemical pathways modeling; Petri net; Qualitative analysis; Simulation

Indexed keywords

GLUCOSE; PROTEIN;

EID: 10944244598     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720004000764     Document Type: Review
Times cited : (47)

References (51)
  • 1
    • 0037079054 scopus 로고    scopus 로고
    • Computational systems biology
    • Kitano H, Computational systems biology, Nature 420 206-210, 2002.
    • (2002) Nature , vol.420 , pp. 206-210
    • Kitano, H.1
  • 2
    • 0031824204 scopus 로고    scopus 로고
    • The modelling of metabolic systems. Structure, control and optimality
    • Heinrich R, Schuster S, The modelling of metabolic systems. Structure, control and optimality, Biosystems 47:61-77, 1998.
    • (1998) Biosystems , vol.47 , pp. 61-77
    • Heinrich, R.1    Schuster, S.2
  • 3
    • 0027370376 scopus 로고
    • GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
    • Mendes P, GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems, Comput Appl Biosci 9(5):563-571, 1993.
    • (1993) Comput. Appl. Biosci. , vol.9 , Issue.5 , pp. 563-571
    • Mendes, P.1
  • 6
    • 0035094449 scopus 로고    scopus 로고
    • Cis-regulatory logic in the endo 16 gene: Switching from a specification to a differentiation mode of control
    • Yuh CH, Bolouri H, Davidson EH, Cis-regulatory logic in the endo 16 gene: Switching from a specification to a differentiation mode of control, Development 128:617-629, 2001.
    • (2001) Development , vol.128 , pp. 617-629
    • Yuh, C.H.1    Bolouri, H.2    Davidson, E.H.3
  • 7
    • 0032499741 scopus 로고    scopus 로고
    • Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
    • Goss PJE, Peccoud J, Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets, Proc Natl Acad Sci USA 95:6750-6755, 1998.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6750-6755
    • Goss, P.J.E.1    Peccoud, J.2
  • 8
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
    • Arkin A, Ross J, McAdams HH, Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells, Genetics 149: 1633-1648, 1998.
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 9
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • de Jong H, Modeling and simulation of genetic regulatory systems: A literature review, J Comput Biol 9(1):67-103, 2002.
    • (2002) J. Comput. Biol. , vol.9 , Issue.1 , pp. 67-103
    • de Jong, H.1
  • 10
    • 0035905782 scopus 로고    scopus 로고
    • Modelling cellular behavior
    • Endy D, Brent R, Modelling cellular behavior, Nature 409 391-395, 2001.
    • (2001) Nature , vol.409 , pp. 391-395
    • Endy, D.1    Brent, R.2
  • 14
    • 0042828946 scopus 로고    scopus 로고
    • Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets
    • Bahi-Jaber N, Pontier D, Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets, Math Biosci 185:1-13, 2003.
    • (2003) Math Biosci. , vol.185 , pp. 1-13
    • Bahi-Jaber, N.1    Pontier, D.2
  • 15
    • 0032076167 scopus 로고    scopus 로고
    • Event-based modelling of ecological systems with asynchronous cellular automata
    • Gronewold A, Sonnenschein M, Event-based modelling of ecological systems with asynchronous cellular automata, Ecol Modelling 108:37-52, 1998.
    • (1998) Ecol. Modelling , vol.108 , pp. 37-52
    • Gronewold, A.1    Sonnenschein, M.2
  • 16
    • 0025989454 scopus 로고
    • Self-reproducing systems: Structure, niche relations and evolution
    • Sharov A, Self-reproducing systems: Structure, niche relations and evolution, Biosystems 25(4):237-249, 1991.
    • (1991) Biosystems , vol.25 , Issue.4 , pp. 237-249
    • Sharov, A.1
  • 17
    • 0036300225 scopus 로고    scopus 로고
    • Modelling biological processes using workflow and Petri net models
    • Peleg M, Yeh I, Altman RB, Modelling biological processes using workflow and Petri net models, Bioinformatics 18 6):825-837, 2002.
    • (2002) Bioinformatics , vol.18 , Issue.6 , pp. 825-837
    • Peleg, M.1    Yeh, I.2    Altman, R.B.3
  • 18
    • 0345170901 scopus 로고    scopus 로고
    • Quantitative Petri net model of gene regulated metabolic networks in the cell
    • Chen M, Hofestädt R, Quantitative Petri net model of gene regulated metabolic networks in the cell, In Silico Biol 3, http://www.bioinfo.de/isb/2003/03/0030/, 2003.
    • (2003) Silico Biol. , vol.3
    • Chen, M.1    Hofestädt, R.2
  • 19
    • 0345170900 scopus 로고    scopus 로고
    • Biopath-ways representation and simulation on hybrid functional Petri net
    • Matsuno H, Tanaka Y, Aoshima H, Doi A, Matsui M, Miyano S, Biopath-ways representation and simulation on hybrid functional Petri net, In Silico Biol 3, http://www.bioinfo.de/isb/2003/03/0032/, 2003.
    • (2003) Silico Biol. , vol.3
    • Matsuno, H.1    Tanaka, Y.2    Aoshima, H.3    Doi, A.4    Matsui, M.5    Miyano, S.6
  • 22
    • 0345096675 scopus 로고    scopus 로고
    • Steady-state analysis of metabolic pathways using Petri nets
    • Voss K, Heiner M, Koch I, Steady-state analysis of metabolic pathways using Petri nets, In Silico Biol 3, http://www.bioinfo.de/isb/2003/03/0031/, 2003.
    • (2003) Silico Biol. , vol.3
    • Voss, K.1    Heiner, M.2    Koch, I.3
  • 23
    • 0345602990 scopus 로고    scopus 로고
    • Topological analysis of metabolic networks based on Petri net theory
    • Zevedei-Oancea I, Schuster S, Topological analysis of metabolic networks based on Petri net theory, In Silico Biol 3, http://www.bioinfo.de/isb/2003/03/0029/, 2003.
    • (2003) Silico Biol. , vol.3
    • Zevedei-Oancea, I.1    Schuster, S.2
  • 24
    • 0035753662 scopus 로고    scopus 로고
    • XML documentation of biopathways and their simulations in Genomic Object Net
    • Matsuno H, Doi A, Hirata Y, Miyano S, XML documentation of biopathways and their simulations in Genomic Object Net, Genome Inform 12 54-62, 2001.
    • (2001) Genome Inform. , vol.12 , pp. 54-62
    • Matsuno, H.1    Doi, A.2    Hirata, Y.3    Miyano, S.4
  • 25
    • 2642533799 scopus 로고    scopus 로고
    • Genomic Object Net: I. A platform for modeling and simulating biopathways
    • Nagasaki M, Doi A, Matsuno H, Miyano S, Genomic Object Net: I. A platform for modeling and simulating biopathways, App Bioinform 2 3):181-184, 2003.
    • (2003) App. Bioinform. , vol.2 , Issue.3 , pp. 181-184
    • Nagasaki, M.1    Doi, A.2    Matsuno, H.3    Miyano, S.4
  • 26
    • 2642527148 scopus 로고    scopus 로고
    • Genomic Object Net: II. Modeling biopathways by hybrid functional Petri net with extension
    • Doi A, Nagasaki M, Fujita S, Matsuno H, Miyano S, Genomic Object Net: II. Modeling biopathways by hybrid functional Petri net with extension, App Bioinform 2(3):185-188, 2003.
    • (2003) App. Bioinform. , vol.2 , Issue.3 , pp. 185-188
    • Doi, A.1    Nagasaki, M.2    Fujita, S.3    Matsuno, H.4    Miyano, S.5
  • 28
    • 0033670135 scopus 로고    scopus 로고
    • Pathway analysis in metabolic databases via differential metabolic display (DMD)
    • Küffner R, Zimmer R, Lengauer T, Pathway analysis in metabolic databases via differential metabolic display (DMD), Bioinformatics 16(9):825-836, 2000.
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 825-836
    • Küffner, R.1    Zimmer, R.2    Lengauer, T.3
  • 29
    • 0004006996 scopus 로고
    • Monographs on Theoretical Computer Science, Springer-Verlag
    • Reisig W, Petri Nets: An Introduction, Monographs on Theoretical Computer Science, Springer-Verlag, 1985.
    • (1985) Petri Nets: an Introduction
    • Reisig, W.1
  • 32
    • 10944241245 scopus 로고    scopus 로고
    • Quantitative modeling of metabolic processes
    • Hofestädt R, Thelen S, Quantitative modeling of metabolic processes, In Silico Biol 1, http://www.bioinfo.de/isb/1998/01/0006/, 1998.
    • (1998) Silico Biol. , vol.1
    • Hofestädt, R.1    Thelen, S.2
  • 33
    • 85034565293 scopus 로고
    • Self-modifying nets, a natural extension of Petri nets
    • ICALP
    • Valk R, Self-modifying nets, a natural extension of Petri nets, Lect Notes Comput Sci 62(ICALP), 464-476, 1978.
    • (1978) Lect. Notes Comput. Sci. , vol.62 , pp. 464-476
    • Valk, R.1
  • 35
    • 0032605507 scopus 로고    scopus 로고
    • Analysis of the stabilizing effect of Rom on the genetic network controllin ColE1 plasmid replication
    • Goss PJE, Peccoud J, Analysis of the stabilizing effect of Rom on the genetic network controllin ColE1 plasmid replication, Pac Symp Biocomput 4:65-76, 1999.
    • (1999) Pac. Symp. Biocomput. , vol.4 , pp. 65-76
    • Goss, P.J.E.1    Peccoud, J.2
  • 37
    • 0036400749 scopus 로고    scopus 로고
    • Stochastic versus deterministic modeling of intracellular viral kinetics
    • Srivastava R, You L, Summers J, Yin J, Stochastic versus deterministic modeling of intracellular viral kinetics, J Theor Biol 218 309-321, 2002.
    • (2002) J. Theor. Biol. , vol.218 , pp. 309-321
    • Srivastava, R.1    You, L.2    Summers, J.3    Yin, J.4
  • 38
    • 10944249851 scopus 로고    scopus 로고
    • Möbius UltraSAN
    • Möbius and UltraSAN, http://www.crhc.uiuc.edu/PER.FORM/.
  • 40
    • 10944256983 scopus 로고    scopus 로고
    • Design/CPN
    • Design/CPN, http://daimi.au.uk/designCPN/.
  • 41
    • 84896689115 scopus 로고    scopus 로고
    • Executable Petri net models for the analysis of metabolic pathways
    • Genrich H, Küffner R, Voss K, Executable Petri net models for the analysis of metabolic pathways, Int J STTT 3(4):394-404, 2001.
    • (2001) Int. J. STTT , vol.3 , Issue.4 , pp. 394-404
    • Genrich, H.1    Küffner, R.2    Voss, K.3
  • 42
    • 10944265629 scopus 로고    scopus 로고
    • BRENDA
    • BRENDA, http://www.brenda.uni-koeln.de:80/.
  • 44
    • 3042996554 scopus 로고    scopus 로고
    • Continuous and hybrid Petri nets
    • Alla H, David R, Continuous and hybrid Petri nets, J Circuits Syst Comp 8(1):159-188, 1998.
    • (1998) J. Circuits Syst. Comp. , vol.8 , Issue.1 , pp. 159-188
    • Alla, H.1    David, R.2
  • 46
    • 10944272299 scopus 로고    scopus 로고
    • Visual Object Net++
    • Visual Object Net++, http://www.systemtechnik.tu-ilmenau.de/~drath/visual.htm.
  • 47
    • 10944269855 scopus 로고    scopus 로고
    • Genomic Object Net
    • Genomic Object Net, http://genomicobject.net.
  • 48
    • 0041627864 scopus 로고    scopus 로고
    • Boundary formation by Notch signaling in Drosophila multicellular systems: Experimental observations and gene network modeling by Genomic Object Net
    • Matsuno H, Murakani R, Yamane R, Yamasaki N, Fujita S, Yoshimori H, Miyano S, Boundary formation by Notch signaling in Drosophila multicellular systems: Experimental observations and gene network modeling by Genomic Object Net, Pac Symp Biocomput 8:152-163, 2003.
    • (2003) Pac. Symp. Biocomput. , vol.8 , pp. 152-163
    • Matsuno, H.1    Murakani, R.2    Yamane, R.3    Yamasaki, N.4    Fujita, S.5    Yoshimori, H.6    Miyano, S.7
  • 49
    • 10944235258 scopus 로고    scopus 로고
    • Biopathways model conversion from E-CELL to Genomic Object Net
    • Matsui M, Doi A, Matsuno H, Hirata Y, Miyano S, Biopathways model conversion from E-CELL to Genomic Object Net, Genome Inform 12 290-291, 2001.
    • (2001) Genome Inform. , vol.12 , pp. 290-291
    • Matsui, M.1    Doi, A.2    Matsuno, H.3    Hirata, Y.4    Miyano, S.5
  • 50
    • 0035169963 scopus 로고    scopus 로고
    • An algebraic-combinatorial model for the identification and mapping of biochemical pathways
    • Oliveira JS, Bailey CG, Jones-Oliveira JB, Dixon DA, An algebraic-combinatorial model for the identification and mapping of biochemical pathways, Bull Math Biol 63:1163-1196, 2001.
    • (2001) Bull. Math. Biol. , vol.63 , pp. 1163-1196
    • Oliveira, J.S.1    Bailey, C.G.2    Jones-Oliveira, J.B.3    Dixon, D.A.4
  • 51
    • 0345653653 scopus 로고    scopus 로고
    • Modelling and simulation of metabolic networks: Petri net approach and perspective
    • Chen M, Modelling and simulation of metabolic networks: Petri net approach and perspective, Proc ESM 2002, 441-444, 2002.
    • (2002) Proc. ESM 2002 , pp. 441-444
    • Chen, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.