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    Results: 1 to 20 of 131

    1.

    A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems.

    Cook DL, Farley JF, Tapscott SJ.

    Genome Biol. 2001;2(4):RESEARCH0012. Epub 2001 Mar 22.

    PMID:
    11305940
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases.

    Srdanovic M, Schenk U, Schwieger M, Campagne F.

    BMC Bioinformatics. 2005 Jan 10;6:5.

    PMID:
    15642112
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    MILANO--custom annotation of microarray results using automatic literature searches.

    Rubinstein R, Simon I.

    BMC Bioinformatics. 2005 Jan 20;6:12.

    PMID:
    15661078
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

    Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum.

    Bioinformatics. 2003 Mar 1;19(4):524-31.

    PMID:
    12611808
    [PubMed - indexed for MEDLINE]
    Free Article
    5.

    MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

    Cai JJ, Smith DK, Xia X, Yuen KY.

    BMC Bioinformatics. 2005 Mar 22;6:64.

    PMID:
    15780146
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    Modeling biochemical transformation processes and information processing with Narrator.

    Mandel JJ, Fuss H, Palfreyman NM, Dubitzky W.

    BMC Bioinformatics. 2007 Mar 27;8:103.

    PMID:
    17389034
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    BioDataServer: a SQL-based service for the online integration of life science data.

    Freier A, Hofestädt R, Lange M, Scholz U, Stephanik A.

    In Silico Biol. 2002;2(2):37-57.

    PMID:
    12066840
    [PubMed - indexed for MEDLINE]
    Free Article
    8.

    Specifications of insilicoML 1.0: a multilevel biophysical model description language.

    Asai Y, Suzuki Y, Kido Y, Oka H, Heien E, Nakanishi M, Urai T, Hagihara K, Kurachi Y, Nomura T.

    J Physiol Sci. 2008 Dec;58(7):447-58. Epub 2008 Nov 6.

    PMID:
    18983726
    [PubMed - indexed for MEDLINE]
    9.

    Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems.

    Roux-Rouquié M, Caritey N, Gaubert L, Rosenthal-Sabroux C.

    Biosystems. 2004 Jul;75(1-3):3-14.

    PMID:
    15245800
    [PubMed - indexed for MEDLINE]
    10.

    A data integration approach for cell cycle analysis oriented to model simulation in systems biology.

    Alfieri R, Merelli I, Mosca E, Milanesi L.

    BMC Syst Biol. 2007 Aug 1;1:35.

    PMID:
    17678529
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    UML as a cell and biochemistry modeling language.

    Webb K, White T.

    Biosystems. 2005 Jun;80(3):283-302. Epub 2005 Feb 17.

    PMID:
    15888343
    [PubMed - indexed for MEDLINE]
    12.

    Integration of the Gene Ontology into an object-oriented architecture.

    Shegogue D, Zheng WJ.

    BMC Bioinformatics. 2005 May 10;6:113.

    PMID:
    15885145
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    XML-based data model and architecture for a knowledge-based grid-enabled problem-solving environment for high-throughput biological imaging.

    Ahmed WM, Lenz D, Liu J, Paul Robinson J, Ghafoor A.

    IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):226-40.

    PMID:
    18348952
    [PubMed - indexed for MEDLINE]
    14.

    From ODES to language-based, executable models of biological systems.

    Palmisano A, Mura I, Priami C.

    Pac Symp Biocomput. 2009:239-50.

    PMID:
    19209705
    [PubMed - indexed for MEDLINE]
    Free Article
    15.

    Design of a description language for generating wrapper to collect biological data.

    Lim M, Chung M, Bae M, Park S.

    Bioinformatics. 2005 Sep 1;21 Suppl 2:ii31-2.

    PMID:
    16204120
    [PubMed - indexed for MEDLINE]
    Free Article
    16.

    Computer support for physiological cell modelling using an ontology on cell physiology.

    Takao S, Kazuhiro K, Akira A, Takeshi I, Masanori K, Tetsuya M.

    Conf Proc IEEE Eng Med Biol Soc. 2006;1:4171-4.

    PMID:
    17946607
    [PubMed - indexed for MEDLINE]
    17.

    Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

    Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H.

    Syst Biol (Stevenage). 2004 Jun;1(1):41-53. Review.

    PMID:
    17052114
    [PubMed - indexed for MEDLINE]
    18.

    Atlas - a data warehouse for integrative bioinformatics.

    Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

    BMC Bioinformatics. 2005 Feb 21;6:34.

    PMID:
    15723693
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    19.

    BIOZON: a system for unification, management and analysis of heterogeneous biological data.

    Birkland A, Yona G.

    BMC Bioinformatics. 2006 Feb 15;7:70.

    PMID:
    16480510
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    Simulating complex intracellular processes using object-oriented computational modelling.

    Johnson CG, Goldman JP, Gullick WJ.

    Prog Biophys Mol Biol. 2004 Nov;86(3):379-406. Review.

    PMID:
    15302205
    [PubMed - indexed for MEDLINE]

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