메뉴 건너뛰기




Volumn 90, Issue 1-3, 2006, Pages 360-377

simBio: A Java package for the development of detailed cell models

Author keywords

Computational cell biology; Detailed cell model; Mathematical modeling

Indexed keywords

ALGORITHM; ANIMAL; BIOLOGICAL MODEL; COMPUTER LANGUAGE; COMPUTER PROGRAM; CONFERENCE PAPER; HEART MUSCLE CELL; HUMAN;

EID: 28344450017     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2005.05.008     Document Type: Conference Paper
Times cited : (38)

References (38)
  • 1
    • 1342265599 scopus 로고    scopus 로고
    • Improving the development process for eukaryotic cell cycle models with a modeling support environment
    • N.A. Allen, C.A. Shaffer, M.T. Vass, N. Ramakrishnan, and L.T. Watson Improving the development process for eukaryotic cell cycle models with a modeling support environment Simulation 79 12 2003 674 688
    • (2003) Simulation , vol.79 , Issue.12 , pp. 674-688
    • Allen, N.A.1    Shaffer, C.A.2    Vass, M.T.3    Ramakrishnan, N.4    Watson, L.T.5
  • 2
    • 0036326896 scopus 로고    scopus 로고
    • PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways
    • E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, and M. Ozturk PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways Bioinformatics 18 2002 996 1003
    • (2002) Bioinformatics , vol.18 , pp. 996-1003
    • Demir, E.1    Babur, O.2    Dogrusoz, U.3    Gursoy, A.4    Nisanci, G.5    Cetin-Atalay, R.6    Ozturk, M.7
  • 3
    • 0034026881 scopus 로고    scopus 로고
    • i overloaded cardiac myocytes: A simulation study
    • i overloaded cardiac myocytes: a simulation study Biophys. J. 78 2000 2392 2404
    • (2000) Biophys. J. , vol.78 , pp. 2392-2404
    • Faber, G.M.1    Rudy, Y.2
  • 4
    • 0348049802 scopus 로고    scopus 로고
    • Systems biology markup language: Level 2 and beyond
    • A. Finney, and M. Hucka Systems biology markup language: level 2 and beyond Biochem. Soc. Trans. 31 2003 1472 1473
    • (2003) Biochem. Soc. Trans. , vol.31 , pp. 1472-1473
    • Finney, A.1    Hucka, M.2
  • 5
    • 9444266171 scopus 로고    scopus 로고
    • CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
    • A. Funahashi, N. Tanimura, M. Morohashi, and H. Kitano CellDesigner: a process diagram editor for gene-regulatory and biochemical networks BIOSILICO 1 2003 159 162
    • (2003) BIOSILICO , vol.1 , pp. 159-162
    • Funahashi, A.1    Tanimura, N.2    Morohashi, M.3    Kitano, H.4
  • 6
    • 1642276819 scopus 로고    scopus 로고
    • Cellular open resource (COR): A public CellML based environment for modelling biological function
    • A. Garny, P. Kohl, and D. Noble Cellular open resource (COR): a public CellML based environment for modelling biological function Int. J. Bifurcat. Chaos 13 2003 3579 3590
    • (2003) Int. J. Bifurcat. Chaos , vol.13 , pp. 3579-3590
    • Garny, A.1    Kohl, P.2    Noble, D.3
  • 7
    • 0346250869 scopus 로고    scopus 로고
    • BioSPICE: Access to the most current computational tools for biologists
    • T.D. Garvey, P. Lincoln, C.J. Pedersen, D. Martin, and M. Johnson BioSPICE: access to the most current computational tools for biologists OMICS 7 2003 411 420
    • (2003) OMICS , vol.7 , pp. 411-420
    • Garvey, T.D.1    Lincoln, P.2    Pedersen, C.J.3    Martin, D.4    Johnson, M.5
  • 8
    • 0032825010 scopus 로고    scopus 로고
    • Mathematical simulation and analysis of cellular metabolism and regulation
    • I. Goryanin, T.C. Hodgman, and E. Selkov Mathematical simulation and analysis of cellular metabolism and regulation Bioinformatics 15 1999 749 758
    • (1999) Bioinformatics , vol.15 , pp. 749-758
    • Goryanin, I.1    Hodgman, T.C.2    Selkov, E.3
  • 9
    • 0037370478 scopus 로고    scopus 로고
    • Bioinformatics in the post-sequence era
    • M. Kanehisa, and P. Bork Bioinformatics in the post-sequence era Nat. Genet. Suppl 2003 305 310
    • (2003) Nat. Genet. , Issue.SUPPL. , pp. 305-310
    • Kanehisa, M.1    Bork, P.2
  • 10
    • 0037079054 scopus 로고    scopus 로고
    • Computational systems biology
    • H. Kitano Computational systems biology Nature 420 2002 206 210
    • (2002) Nature , vol.420 , pp. 206-210
    • Kitano, H.1
  • 12
    • 0035975695 scopus 로고    scopus 로고
    • A model of oxidative phosphorylation in mammalian skeletal muscle
    • B. Korzeniewski, and J.A. Zoladz A model of oxidative phosphorylation in mammalian skeletal muscle Biophys. Chem. 92 2001 17 34
    • (2001) Biophys. Chem. , vol.92 , pp. 17-34
    • Korzeniewski, B.1    Zoladz, J.A.2
  • 13
    • 0242380634 scopus 로고    scopus 로고
    • CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
    • H. Kurata, N. Matoba, and N. Shimizu CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle Nucleic Acids Res. 31-14 2003 4071 4084
    • (2003) Nucleic Acids Res. , vol.31 , Issue.14 , pp. 4071-4084
    • Kurata, H.1    Matoba, N.2    Shimizu, N.3
  • 14
    • 0034961694 scopus 로고    scopus 로고
    • STOCHSIM: Modelling of stochastic biomolecular processes
    • N. Le Novere, and T.S. Shimizu STOCHSIM: modelling of stochastic biomolecular processes Bioinformatics 17 2001 575 576
    • (2001) Bioinformatics , vol.17 , pp. 575-576
    • Le Novere, N.1    Shimizu, T.S.2
  • 16
    • 0035478586 scopus 로고    scopus 로고
    • The Virtual Cell: A software environment for computational cell biology
    • L.M. Loew, and J.C. Schaff The Virtual Cell: a software environment for computational cell biology Trends Biotechnol. 19 2001 401 406
    • (2001) Trends Biotechnol. , vol.19 , pp. 401-406
    • Loew, L.M.1    Schaff, J.C.2
  • 17
    • 8844222709 scopus 로고    scopus 로고
    • PaVESy: Pathway visualization and editing system
    • A. Ludemann, D. Weicht, J. Selbig, and J. Kopka PaVESy: pathway visualization and editing system Bioinformatics 20 2004 2841 2844
    • (2004) Bioinformatics , vol.20 , pp. 2841-2844
    • Ludemann, A.1    Weicht, D.2    Selbig, J.3    Kopka, J.4
  • 18
    • 0031958402 scopus 로고    scopus 로고
    • Model of beta-cell mitochondrial calcium handling and electrical activity. I. Cytoplasmic variables
    • G. Magnus, and J. Keizer Model of beta-cell mitochondrial calcium handling and electrical activity. I. Cytoplasmic variables Am J Physiol 274 1998 C1158 C1173
    • (1998) Am J Physiol , vol.274
    • Magnus, G.1    Keizer, J.2
  • 19
  • 20
    • 0041742200 scopus 로고    scopus 로고
    • Role of individual ionic current systems in ventricular cells hypothesized by a model study
    • S. Matsuoka, N. Sarai, S. Kuratomi, K. Ono, and A. Noma Role of individual ionic current systems in ventricular cells hypothesized by a model study Jpn. J. Physiol. 53 2003 105 123
    • (2003) Jpn. J. Physiol. , vol.53 , pp. 105-123
    • Matsuoka, S.1    Sarai, N.2    Kuratomi, S.3    Ono, K.4    Noma, A.5
  • 21
    • 15744398852 scopus 로고    scopus 로고
    • An in silico study of energy metabolism in cardiac excitation-contraction coupling
    • S. Matsuoka, H. Jo, N. Sarai, and A. Noma An in silico study of energy metabolism in cardiac excitation-contraction coupling Jpn. J. Physiol. 54 2004 517 522
    • (2004) Jpn. J. Physiol. , vol.54 , pp. 517-522
    • Matsuoka, S.1    Jo, H.2    Sarai, N.3    Noma, A.4
  • 22
    • 2442501446 scopus 로고    scopus 로고
    • Simulation of ATP metabolism in cardiac excitation-contraction coupling
    • S. Matsuoka, N. Sarai, H. Jo, and A. Noma Simulation of ATP metabolism in cardiac excitation-contraction coupling Prog. Biophys. Mol. Biol. 85 2004 279 299
    • (2004) Prog. Biophys. Mol. Biol. , vol.85 , pp. 279-299
    • Matsuoka, S.1    Sarai, N.2    Jo, H.3    Noma, A.4
  • 23
    • 2942694772 scopus 로고    scopus 로고
    • Artificial gene networks for objective comparison of analysis algorithms
    • P. Mendes, W. Sha, and K. Ye Artificial gene networks for objective comparison of analysis algorithms Bioinformatics 19 Suppl. 2 2003 122 129
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2 , pp. 122-129
    • Mendes, P.1    Sha, W.2    Ye, K.3
  • 24
    • 4444343665 scopus 로고    scopus 로고
    • Assessing the impact of predictive biosimulation on drug discovery and development
    • S. Michelson Assessing the impact of predictive biosimulation on drug discovery and development J Bioinform Comput Biol 1 2003 169 177
    • (2003) J Bioinform Comput Biol , vol.1 , pp. 169-177
    • Michelson, S.1
  • 25
    • 0030066512 scopus 로고    scopus 로고
    • A cardiac muscle model relating sarcomere dynamics to calcium kinetics
    • J.A. Negroni, and E.C. Lascano A cardiac muscle model relating sarcomere dynamics to calcium kinetics J. Mol. Cell. Cardiol. 28 1996 915 929
    • (1996) J. Mol. Cell. Cardiol. , vol.28 , pp. 915-929
    • Negroni, J.A.1    Lascano, E.C.2
  • 26
    • 28344452830 scopus 로고    scopus 로고
    • The noble cardiac ventricular electrophysiology models in CellML
    • D.P. Nickerson, and P.J. Hunter The noble cardiac ventricular electrophysiology models in CellML Prog. Biophys. Mol. Biol. 89 2005
    • (2005) Prog. Biophys. Mol. Biol. , vol.89
    • Nickerson, D.P.1    Hunter, P.J.2
  • 27
    • 0036499997 scopus 로고    scopus 로고
    • Modeling the heart-from genes to cells to the whole organ
    • D. Noble Modeling the heart-from genes to cells to the whole organ Science 295 2002 1678 1682
    • (2002) Science , vol.295 , pp. 1678-1682
    • Noble, D.1
  • 28
    • 0031917543 scopus 로고    scopus 로고
    • Improved guinea-pig ventricular cell model incorporating a diadic space, IKr and IKs, and length- and tension-dependent processes
    • D. Noble, A. Varghese, P. Kohl, and P. Noble Improved guinea-pig ventricular cell model incorporating a diadic space, IKr and IKs, and length- and tension-dependent processes Can. J. Cardiol. 14 1998 123 134
    • (1998) Can. J. Cardiol. , vol.14 , pp. 123-134
    • Noble, D.1    Varghese, A.2    Kohl, P.3    Noble, P.4
  • 29
    • 0035658721 scopus 로고    scopus 로고
    • LabHEART: An interactive computer model of rabbit ventricular myocyte ion channels and Ca transport
    • J.L. Puglisi, and D.M. Bers LabHEART: an interactive computer model of rabbit ventricular myocyte ion channels and Ca transport Am. J. Physiol. Cell Physiol. 281 2001 C2049 C2060
    • (2001) Am. J. Physiol. Cell Physiol. , vol.281
    • Puglisi, J.L.1    Bers, D.M.2
  • 30
    • 1542300950 scopus 로고    scopus 로고
    • Development of the Cardiac Cell Model by Applying Object-Oriented Methods
    • N. Sarai, A. Amano, S. Matsuoka, T. Matsuda, and A. Noma Development of the Cardiac Cell Model by Applying Object-Oriented Methods IEEE EMBC 2003 2702 2705
    • (2003) IEEE EMBC , pp. 2702-2705
    • Sarai, N.1    Amano, A.2    Matsuoka, S.3    Matsuda, T.4    Noma, A.5
  • 31
    • 0042196441 scopus 로고    scopus 로고
    • Role of individual ionic current systems in the SA node hypothesized by a model study
    • N. Sarai, S. Matsuoka, S. Kuratomi, K. Ono, and A. Noma Role of individual ionic current systems in the SA node hypothesized by a model study Jpn. J. Physiol. 53 2003 125 134
    • (2003) Jpn. J. Physiol. , vol.53 , pp. 125-134
    • Sarai, N.1    Matsuoka, S.2    Kuratomi, S.3    Ono, K.4    Noma, A.5
  • 32
    • 0347511691 scopus 로고    scopus 로고
    • Next generation simulation tools: The systems biology workbench and BioSPICE integration
    • H.M. Sauro, M. Hucka, A. Finney, C. Wellock, H. Bolouri, J. Doyle, and H. Kitano Next generation simulation tools: the systems biology workbench and BioSPICE integration OMICS 7 2003 355 372
    • (2003) OMICS , vol.7 , 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
  • 34
    • 0037461036 scopus 로고    scopus 로고
    • Cellerator: Extending a computer algebra system to include biochemical arrows for signal transduction simulations
    • B.E. Shapiro, A. Levchenko, E.M. Meyerowitz, B.J. Wold, and E.D. Mjolsness Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations Bioinformatics 19 2003 677 678
    • (2003) Bioinformatics , vol.19 , pp. 677-678
    • Shapiro, B.E.1    Levchenko, A.2    Meyerowitz, E.M.3    Wold, B.J.4    Mjolsness, E.D.5
  • 35
    • 0025071276 scopus 로고
    • Volume-activated chloride permeability can mediate cell volume regulation in a mathematical model of a tight epithelium
    • J. Strieter, J.L. Stephenson, L.G. Palmer, and A.M. Weinstein Volume-activated chloride permeability can mediate cell volume regulation in a mathematical model of a tight epithelium J. Gen. Physiol. 96 1990 319 344
    • (1990) J. Gen. Physiol. , vol.96 , pp. 319-344
    • Strieter, J.1    Stephenson, J.L.2    Palmer, L.G.3    Weinstein, A.M.4
  • 38
    • 28344454210 scopus 로고    scopus 로고
    • Role of stretch-activated channels on the stretch-induced changes of rat atrial myocytes
    • J.B. Youm, J. Han, and N. Kim Role of stretch-activated channels on the stretch-induced changes of rat atrial myocytes Prog. Biophys. Mol. Biol. 89 2005
    • (2005) Prog. Biophys. Mol. Biol. , vol.89
    • Youm, J.B.1    Han, J.2    Kim, N.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.