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Volumn 8, Issue , 2007, Pages

Modeling biochemical transformation processes and information processing with Narrator

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL TRANSFORMATION; BIOLOGICAL INFORMATION PROCESSING; GRAPHICAL USER INTERFACE (GUIS); MATHEMATICAL DETAILS; MATHEMATICAL FORMALISM; SIGNAL PROCESSING STRUCTURES; SYSTEMS BIOLOGY MARKUP LANGUAGES; TRANSPORT AND TRANSFORMATION;

EID: 34147140120     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-103     Document Type: Article
Times cited : (10)

References (51)
  • 1
    • 84886764465 scopus 로고    scopus 로고
    • Systems Biology Markup Language http://www.sbml.org
  • 2
    • 84886765907 scopus 로고    scopus 로고
    • SBMLR http://epbi-radivot.cwru.edu/SBMLR/
  • 3
    • 32544443964 scopus 로고    scopus 로고
    • Systems biology toolbox for MATLAB: A computational platform for research in systems biology
    • 10.1093/bioinformatics/bti799 16317076
    • Schmidt H Jirstrand M Systems biology toolbox for MATLAB: A computational platform for research in systems biology Bioinformatics 2006 22 514-515 10.1093/bioinformatics/bti799 16317076
    • (2006) Bioinformatics , vol.22 , pp. 514-515
    • Schmidt, H.1    Jirstrand, M.2
  • 4
    • 84886765681 scopus 로고    scopus 로고
    • MathSBML http://sbml.org/software/mathsbml
  • 5
    • 84886764830 scopus 로고    scopus 로고
    • SBMLmerge Project http://sysbio.molgen.mpg.de/sbmlmerge/index.html
  • 6
    • 4544344218 scopus 로고    scopus 로고
    • Web-based kinetic modelling using JWS online
    • 10.1093/bioinformatics/bth200 15072998
    • Olivier BG Snoep JL Web-based kinetic modelling using JWS online Bioinformatics 2004 20 2143-2144 10.1093/bioinformatics/bth200 15072998
    • (2004) Bioinformatics , vol.20 , pp. 2143-2144
    • Olivier, B.G.1    Snoep, J.L.2
  • 7
    • 33646203362 scopus 로고    scopus 로고
    • WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks
    • 10.1093/bioinformatics/btl091 16543278
    • Lee D Yun C Cho A Hou BK Park S Lee SY WebCell: A web-based environment for kinetic modeling and dynamic simulation of cellular networks Bioinformatics 2006 22 1150-1151 10.1093/bioinformatics/btl091 16543278
    • (2006) Bioinformatics , vol.22 , pp. 1150-1151
    • Lee, D.1    Yun, C.2    Cho, A.3    Hou, B.K.4    Park, S.5    Lee, S.Y.6
  • 10
    • 4644293116 scopus 로고    scopus 로고
    • An introduction to biochemical modeling using JDesigner
    • Claremont, CA: Keck Graduate Institute
    • Sauro HM An introduction to biochemical modeling using JDesigner Claremont, CA: Keck Graduate Institute 2004
    • (2004)
    • Sauro, H.M.1
  • 11
    • 9444266171 scopus 로고    scopus 로고
    • CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
    • 10.1016/S1478-5382(03)02370-9
    • Funahashi A Tanimura N Morohashi M Kitano H CellDesigner: A process diagram editor for gene-regulatory and biochemical networks BIOSILICO 2003 159-162 10.1016/S1478-5382(03)02370-9
    • (2003) BIOSILICO , pp. 159-162
    • Funahashi, A.1    Tanimura, N.2    Morohashi, M.3    Kitano, H.4
  • 13
    • 0347506655 scopus 로고    scopus 로고
    • An overview of data models for the analysis of biochemical pathways
    • 10.1093/bib/4.3.246 14582519
    • Deville Y Gilbert D Helden JV Wodak SJ An overview of data models for the analysis of biochemical pathways Briefings in Bioinformatics 2003 4 246-259 10.1093/bib/4.3.246 14582519
    • (2003) Briefings in Bioinformatics , vol.4 , pp. 246-259
    • Deville, Y.1    Gilbert, D.2    Helden, J.V.3    Wodak, S.J.4
  • 14
    • 34147142580 scopus 로고    scopus 로고
    • Modelling Codependence in Biological Systems
    • 10.1049/iet-syb:20060002 17370426
    • Mandel JJ Palfreyman NM Dubitzky W Modelling Codependence in Biological Systems IET Systems Biology 2007 1 1 18-32 10.1049/iet-syb:20060002 17370426
    • (2007) IET Systems Biology , vol.1 , Issue.1 , pp. 18-32
    • Mandel, J.J.1    Palfreyman, N.M.2    Dubitzky, W.3
  • 16
    • 33747872720 scopus 로고    scopus 로고
    • Bistable Switching and Excitable Behaviour in the Activation of Src at Mitosis
    • 10.1093/bioinformatics/btl201 16873466
    • Fuß H Dubitzky W Downes CS Kurth MJ Bistable Switching and Excitable Behaviour in the Activation of Src at Mitosis Bioinformatics 2006 22 14 e158-e164 10.1093/bioinformatics/btl201 16873466
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Fuß, H.1    Dubitzky, W.2    Downes, C.S.3    Kurth, M.J.4
  • 17
    • 0042665800 scopus 로고    scopus 로고
    • A kinetic model of the cyclin e/cdk2 developmental timer in xenopus laevis embryos
    • 10.1016/S0301-4622(03)00060-7 12914904
    • Ciliberto A Petrus MJ Tyson JJ Sible JC A kinetic model of the cyclin e/ cdk2 developmental timer in xenopus laevis embryos Biophys Chem 2003 104 573-589 10.1016/S0301-4622(03)00060-7 12914904
    • (2003) Biophys Chem , vol.104 , pp. 573-589
    • Ciliberto, A.1    Petrus, M.J.2    Tyson, J.J.3    Sible, J.C.4
  • 22
    • 84886757395 scopus 로고    scopus 로고
    • Java Compiler Compiler https://javacc.dev.java.net/
  • 23
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • 10.1016/0021-9991(76)90041-3
    • Gillespie D A general method for numerically simulating the stochastic time evolution of coupled chemical reactions J Comp Phys 1976 22 403-434 10.1016/0021-9991(76)90041-3
    • (1976) J Comp Phys , vol.22 , pp. 403-434
    • Gillespie, D.1
  • 24
    • 84886760280 scopus 로고    scopus 로고
    • JFreeChart http://www.jfree.org/jfreechart/
  • 25
    • 84886760302 scopus 로고    scopus 로고
    • Jeks http://www.eteks.com/jeks/
  • 27
    • 34147180141 scopus 로고    scopus 로고
    • Simulation study of differential equation model for protein kinase C signaling
    • Report 3 Institute of Signal Processing and Institute of Mathematics, Tampere, Finland
    • Manninen T Saarinen A and Linne ML Simulation study of differential equation model for protein kinase C signaling Report 3 Institute of Signal Processing and Institute of Mathematics, Tampere, Finland 2004
    • (2004)
    • Manninen, T.1    Saarinen, A.2    Linne, M.L.3
  • 28
    • 84886758977 scopus 로고    scopus 로고
    • Octave http://www.gnu.org/software/octave/
  • 29
    • 0003588772 scopus 로고
    • Description and Use of LSODE, the Livermore Solver for Ordinary Differential Equations
    • Lawrence Livermore Laboratory, Livermore CAUCRL-ID-113855
    • Radhakrishnan K Hindmarsh AC Description and Use of LSODE, the Livermore Solver for Ordinary Differential Equations Lawrence Livermore Laboratory, Livermore 1993 CAUCRL-ID-113855
    • (1993)
    • Radhakrishnan, K.1    Hindmarsh, A.C.2
  • 30
    • 84886755053 scopus 로고    scopus 로고
    • SBML Validator http://sbml.org/validator/validate.php
  • 31
    • 84886756519 scopus 로고    scopus 로고
    • Narrator Project
    • Narrator Project http://www.narrator-tool.org
  • 33
    • 23444439817 scopus 로고    scopus 로고
    • Using process diagrams for the graphical representation of biological networks
    • 10.1038/nbt1111 16082367
    • Kitano H Funahasi A Matsuoka Y Oda Using process diagrams for the graphical representation of biological networks Nature Biotechnology 2005 23 961-966 10.1038/nbt1111 16082367
    • (2005) Nature Biotechnology , vol.23 , pp. 961-966
    • Kitano, H.1    Funahasi, A.2    Matsuoka, Y.3    Oda4
  • 36
    • 30044440098 scopus 로고    scopus 로고
    • Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology
    • 1345641 16267266 10.1091/mbc.E05-09-0824
    • Kohn KW Aladjem MI Weinstein JN Pommier Y Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology Mol Biol Cell 2006 17 1-13 1345641 16267266 10.1091/mbc.E05-09-0824
    • (2006) Mol Biol Cell , vol.17 , pp. 1-13
    • Kohn, K.W.1    Aladjem, M.I.2    Weinstein, J.N.3    Pommier, Y.4
  • 37
    • 34147189208 scopus 로고    scopus 로고
    • A Graphical Notation to describe the Logical Interactions of Biological Pathways
    • Moodie SL Sorokin A Groyanin I Ghazal P A Graphical Notation to describe the Logical Interactions of Biological Pathways Journal of Integrative Bioinformatics 2006 3 2 36 http://journal.imbio.de/index.php?paper_id=36
    • (2006) Journal of Integrative Bioinformatics , vol.3 , Issue.2 , pp. 36
    • Moodie, S.L.1    Sorokin, A.2    Groyanin, I.3    Ghazal, P.4
  • 38
    • 84886767100 scopus 로고    scopus 로고
    • CellML language http://www.cellml.org/tutorial/notation/
  • 39
    • 84886755249 scopus 로고    scopus 로고
    • Systems Biology Graphical Notation http://www.sbgn.org/
  • 40
    • 33747825750 scopus 로고    scopus 로고
    • A model diagram layout extension for SBML
    • 10.1093/bioinformatics/btl195 16709586
    • Gauges R Rost U Sahle S Wegner K A model diagram layout extension for SBML Bioinformatics 2006 22 15 1879-1885 10.1093/bioinformatics/btl195 16709586
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1879-1885
    • Gauges, R.1    Rost, U.2    Sahle, S.3    Wegner, K.4
  • 41
    • 84886759856 scopus 로고    scopus 로고
    • Systems Biology Ontology http://www.ebi.ac.uk/sbo/
  • 42
    • 33745075591 scopus 로고    scopus 로고
    • Tools for kinetic modeling of biochemical networks
    • 10.1038/nbt0606-667 16763599
    • Alves R Antunes F Salvador A Tools for kinetic modeling of biochemical networks Nature Biotechnology 2006 24 667-672 10.1038/nbt0606-667 16763599
    • (2006) Nature Biotechnology , vol.24 , pp. 667-672
    • Alves, R.1    Antunes, F.2    Salvador, A.3
  • 43
    • 23444446572 scopus 로고    scopus 로고
    • Closing the circle of osmoregulation
    • 10.1038/nbt0805-941 16082361
    • D'haeseleer P Closing the circle of osmoregulation Nature Biotechnology 2005 23 941-942 10.1038/nbt0805-941 16082361
    • (2005) Nature Biotechnology , vol.23 , pp. 941-942
    • D'haeseleer, P.1
  • 44
    • 33749450882 scopus 로고    scopus 로고
    • A simple mathematical model of adaptation to high osmolarity in yeast
    • Gennemark P Nordlander B Hohmann S Wedelin D A simple mathematical model of adaptation to high osmolarity in yeast In Silico Biology 2006 6 0018
    • (2006) Silico Biology , vol.6 , pp. 0018
    • Gennemark, P.1    Nordlander, B.2    Hohmann, S.3    Wedelin, D.4
  • 45
    • 33745658975 scopus 로고    scopus 로고
    • Model-View-Controller
    • Sun Microsystems, Java BluePrints
    • Sun Microsystems, Java BluePrints Model-View-Controller 2002 http://java.sun.com/blueprints/patterns/MVC-detailed.html
    • (2002)
  • 47
    • 0003905225 scopus 로고
    • Chaos and integrability in nonlinear dynamics: An introduction
    • Wiley New York
    • Tabor M Chaos and integrability in nonlinear dynamics: An introduction Wiley New York 1989
    • (1989)
    • Tabor, M.1
  • 49
    • 0002203999 scopus 로고    scopus 로고
    • JARNAC: A system for interactive metabolic analysis
    • Stellenbosch, University Press Stellenbosch Hofmeyr J-HS, Rohwer JM, Snoep JL
    • Sauro HM JARNAC: A system for interactive metabolic analysis Animating the Cellular Map Stellenbosch, University Press Stellenbosch Hofmeyr J-HS, Rohwer JM, Snoep JL 2001 221-228
    • (2001) Animating the Cellular Map , pp. 221-228
    • Sauro, H.M.1
  • 50
    • 0347511691 scopus 로고    scopus 로고
    • Next generation simulation tools: The Systems BiologyWorkbench and BioSPICE integration
    • 10.1089/153623103322637670 14683609
    • Sauro HM Hucka M Finney A Wellock C Bolouri H Doyle J Kitano H Next generation simulation tools: The Systems BiologyWorkbench and BioSPICE integration OMICS 2003 7 4 355-72 10.1089/153623103322637670 14683609
    • (2003) OMICS , vol.7 , Issue.4 , pp. 355-372
    • Sauro, H.M.1    Hucka, M.2    Finney, A.3    Wellock, C.4    Bolouri, H.5    Doyle, J.6    Kitano, H.7
  • 51
    • 3042595010 scopus 로고    scopus 로고
    • Cellware - A multi-algorithmic software for computational systems biology
    • 10.1093/bioinformatics/bth067 14871872
    • Dhar P Meng TC Somani S Ye L Sairam A Chitre M Hao Z Sakharkar K Cellware - a multi-algorithmic software for computational systems biology Bioinformatics 2004 20 8 1319-1321 10.1093/bioinformatics/bth067 14871872
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1319-1321
    • Dhar, P.1    Meng, T.C.2    Somani, S.3    Ye, L.4    Sairam, A.5    Chitre, M.6    Hao, Z.7    Sakharkar, K.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.