메뉴 건너뛰기




Volumn 22, Issue 24, 2006, Pages 3075-3081

Design and implementation of a tool for translating SBML into the biochemical stochastic π-calculus

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; BIOLOGICAL MODEL; COMPUTER LANGUAGE; COMPUTER PROGRAM; COMPUTER SIMULATION; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; STOCHASTIC MODEL; SYSTEM ANALYSIS; SYSTEMS BIOLOGY; VALIDATION PROCESS;

EID: 33845352304     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl516     Document Type: Article
Times cited : (5)

References (32)
  • 1
    • 0035106485 scopus 로고    scopus 로고
    • XML, bioinformatics and data integration
    • Achard,F. et al. (2001) XML, bioinformatics and data integration. Bioinformatics, 17, 115-125.
    • (2001) Bioinformatics , vol.17 , pp. 115-125
    • Achard, F.1
  • 2
    • 1342329447 scopus 로고    scopus 로고
    • An overview of CELLML 1.1, a biological model description language
    • Cuellar,A.A. et al. (2003) An overview of CELLML 1.1, a biological model description language. Simulation, 79, 740-747.
    • (2003) Simulation , vol.79 , pp. 740-747
    • Cuellar, A.A.1
  • 4
    • 0030281174 scopus 로고    scopus 로고
    • A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions
    • Edelstein,S.J. et al. (1996) A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions. Biol. Cybern., 75, 361-379.
    • (1996) Biol. Cybern. , vol.75 , pp. 361-379
    • Edelstein, S.J.1
  • 5
    • 0038745251 scopus 로고    scopus 로고
    • Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions
    • Finney,A. and Hucka,M. (2003) Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions.
    • (2003)
    • Finney, A.1    Hucka, M.2
  • 6
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie,D.T. (1977) Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem., 81, 2340-2361.
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 7
    • 0036455918 scopus 로고    scopus 로고
    • ProML - The Protein Markup Language for specification of protein sequences, structures and families
    • Hanisch,D. et al. (2002) ProML - the Protein Markup Language for specification of protein sequences, structures and families. In Silico Biol, 2, 313-324.
    • (2002) In Silico Biol , vol.2 , pp. 313-324
    • Hanisch, D.1
  • 8
    • 0037200091 scopus 로고    scopus 로고
    • Alliance launched to model E. coli
    • Holden,C. (2002) Alliance launched to model E. coli. Science, 297, 1459-1460.
    • (2002) Science , vol.297 , pp. 1459-1460
    • Holden, C.1
  • 9
    • 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
  • 10
    • 10644250404 scopus 로고    scopus 로고
    • Evolving a lingua franca and associated software infrastructure for computational systems biology: The System Biology Markup Language (SBML) project
    • Hucka,M. et al. (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: The System Biology Markup Language (SBML) project. Syst. Biol., 1, 41-53.
    • (2004) Syst. Biol. , vol.1 , pp. 41-53
    • Hucka, M.1
  • 11
    • 0035790856 scopus 로고    scopus 로고
    • The immune system as a reactive system: Modeling t cell activation with statecharts
    • In IEEE Computer Society Press
    • Kam,N. et al. (2001) The immune system as a reactive system: Modeling t cell activation with statecharts. In Proceedings of Symposia on Human-Centric Computing Languages and Environments, IEEE Computer Society Press, pp. 15-22.
    • (2001) Proceedings of Symposia on Human-Centric Computing Languages and Environments , pp. 15-22
    • Kam, N.1
  • 12
    • 1142293035 scopus 로고    scopus 로고
    • A multi-agent system for the quantitative simulation of biological networks
    • In Melbourne, Australia
    • Kahn,S. et al. (2003) A multi-agent system for the quantitative simulation of biological networks. In Proceedings of the AAMAS '03, Melbourne, Australia, pp. 385-392.
    • (2003) Proceedings of the AAMAS '03 , pp. 385-392
    • Kahn, S.1
  • 14
    • 0142042996 scopus 로고    scopus 로고
    • BioSPICE: A computational infrastructure for integrative biology
    • Kumar,S. and Feidler,J.C. (2003) BioSPICE: A computational infrastructure for integrative biology. Omics: A J. Int. Biol., 7, 225.
    • (2003) Omics: A J. Int. Biol. , vol.7 , pp. 225
    • Kumar, S.1    Feidler, J.C.2
  • 15
    • 38149103597 scopus 로고    scopus 로고
    • Gene regulation in the Pi calculus: Simulating cooperativity at the lambda switch
    • In Priami,C., Ingolfsdottir,A., Mishra,B., Nielson,H.R. (eds), Springer
    • Kuttler,C. et al. (2006) Gene regulation in the Pi calculus: Simulating cooperativity at the lambda switch. In Priami,C., Ingolfsdottir,A., Mishra,B., Nielson,H.R. (eds), TCSB VII, Lecture Notes in Computer Science (LNCS) 4230, Springer, pp. 29-59.
    • (2006) TCSB VII, Lecture Notes in Computer Science (LNCS) 4230 , pp. 29-59
    • Kuttler, C.1
  • 17
    • 4043167812 scopus 로고    scopus 로고
    • A stochastic process algebra approach to simulation of autoreactive lymphocyte recruitment
    • Lecca,P. et al. (2004) A stochastic process algebra approach to simulation of autoreactive lymphocyte recruitment. Simulation, 80, 273-288.
    • (2004) Simulation , vol.80 , pp. 273-288
    • Lecca, P.1
  • 18
    • 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. et al. (2006) BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res., 34, D689-D691.
    • (2006) Nucleic Acids Res. , vol.34
    • Le Novère, N.1
  • 19
    • 0036646530 scopus 로고    scopus 로고
    • The chemical markup language
    • Liao,Y.M. and Ghanadan,H. (2002) The chemical markup language. Anal. Chem., 74, 389A-390A.
    • (2002) Anal. Chem. , vol.74
    • Liao, Y.M.1    Ghanadan, H.2
  • 20
    • 0345170900 scopus 로고    scopus 로고
    • Biopathways representation and simulation on hybrid functional Petri net
    • Matsuno,H. et al. (2003) Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol, 3, 389-404.
    • (2003) In Silico Biol , vol.3 , pp. 389-404
    • Matsuno, H.1
  • 21
    • 0028844979 scopus 로고
    • A mathematical framework for describing and analyzing gene regulatory networks
    • Mestl,T. et al. (1995) A mathematical framework for describing and analyzing gene regulatory networks. J. Theor. Biol., 176, 291-300.
    • (1995) J. Theor. Biol. , vol.176 , pp. 291-300
    • Mestl, T.1
  • 22
    • 0031029852 scopus 로고    scopus 로고
    • Stochastic mechanism in gene expression
    • McAdams,H.H. and Arkin,A. (1997) Stochastic mechanism in gene expression. Proc. Natl Acad. Sci. USA, 94, 814-819.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 814-819
    • McAdams, H.H.1    Arkin, A.2
  • 23
  • 26
    • 0035888407 scopus 로고    scopus 로고
    • Application of a stochastic name-passing calculus to representation and simulation of molecular processes
    • Priami,C. et al. (2001) Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf. Proc. Lett, 80, 25-31.
    • (2001) Inf. Proc. Lett , vol.80 , pp. 25-31
    • Priami, C.1
  • 27
    • 0035235039 scopus 로고    scopus 로고
    • Representation and simulation of biological processes using the π-calculus process algebra
    • Regev,A. et al. (2001) Representation and simulation of biological processes using the π-calculus process algebra. In Proceedings of the 6th Pacific Symposium on Biocomputing, pp. 459-470.
    • (2001) Proceedings of the 6th Pacific Symposium on Biocomputing , pp. 459-470
    • Regev, A.1
  • 28
    • 0037163144 scopus 로고    scopus 로고
    • Design and implementation of Microarray Gene Expression Markup Language
    • Spellman,P.T. et al. (2002) Design and implementation of Microarray Gene Expression Markup Language. Genome Biol, 3, 0046.0041-0046.0049.
    • (2002) Genome Biol , vol.3
    • Spellman, P.T.1
  • 29
    • 0037337307 scopus 로고    scopus 로고
    • A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    • Taylor,C.F. et al. (2003) A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat. Biotechnol., 21, 247-254.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 247-254
    • Taylor, C.F.1
  • 30
    • 0025826876 scopus 로고
    • Modeling the cell division cycle: Cdc2 and cyclin interactions
    • Tyson,J.J. (1991) Modeling the cell division cycle: Cdc2 and cyclin interactions. Cell Biol., 88, 7328-7332.
    • (1991) Cell Biol. , vol.88 , pp. 7328-7332
    • Tyson, J.J.1
  • 31
    • 33845351460 scopus 로고    scopus 로고
    • The BioSpi project
    • Web site
    • The BioSpi project (200) Web site.
    • (2000)
  • 32
    • 18444386491 scopus 로고    scopus 로고
    • RNAML: A standard syntax for exchanging RNA information
    • Waugh,A. et al. (2002) RNAML: A standard syntax for exchanging RNA information. RNA, 8, 707-717.
    • (2002) RNA , vol.8 , pp. 707-717
    • Waugh, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.