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The role of composition and aggregation in modeling macromolecular regulatory networks

Published: 03 December 2006 Publication History

Abstract

Today's macromolecular regulatory network models are small compared to the amount of information known about a particular cellular pathway, in part because current modeling languages and tools are unable to handle significantly larger models. Thus, most pathway modeling work today focuses on building small models of individual pathways since they are easy to construct and manage. The hope is someday to put these pieces together to create a more complete picture of the underlying molecular machinery. While efforts to make large models benefit from reusing existing components, unfortunately, there currently exists little tool or representational support for combining or composing models. We have identified four distinct modeling processes related to model composition: fusion, composition, aggregation, and flattening. We present concrete proposals for implementing all four processes in the context of the Systems Biology Markup Language (SBML).

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  • (2018)Building simulation models of complex ecological systems by successive composition and reusing simulation experimentsProceedings of the 2018 Winter Simulation Conference10.5555/3320516.3320799(2363-2374)Online publication date: 9-Dec-2018
  • (2018)JigCell Model ConnectorSimulation10.1177/003754971775412194:11(993-1008)Online publication date: 1-Nov-2018
  • (2014)Towards semantic model composition via experimentsProceedings of the 2nd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation10.1145/2601381.2601394(151-162)Online publication date: 18-May-2014
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  1. The role of composition and aggregation in modeling macromolecular regulatory networks

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    Published In

    cover image ACM Conferences
    WSC '06: Proceedings of the 38th conference on Winter simulation
    December 2006
    2429 pages
    ISBN:1424405017

    Sponsors

    • IIE: Institute of Industrial Engineers
    • ASA: American Statistical Association
    • IEICE ESS: Institute of Electronics, Information and Communication Engineers, Engineering Sciences Society
    • IEEE-CS\DATC: The IEEE Computer Society
    • SIGSIM: ACM Special Interest Group on Simulation and Modeling
    • NIST: National Institute of Standards and Technology
    • (SCS): The Society for Modeling and Simulation International
    • INFORMS-CS: Institute for Operations Research and the Management Sciences-College on Simulation

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    Winter Simulation Conference

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    Published: 03 December 2006

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    • IIE
    • ASA
    • IEICE ESS
    • IEEE-CS\DATC
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    • NIST
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    • INFORMS-CS
    WSC06: Winter Simulation Conference 2006
    December 3 - 6, 2006
    California, Monterey

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    WSC '06 Paper Acceptance Rate 177 of 252 submissions, 70%;
    Overall Acceptance Rate 3,413 of 5,075 submissions, 67%

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    Cited By

    View all
    • (2018)Building simulation models of complex ecological systems by successive composition and reusing simulation experimentsProceedings of the 2018 Winter Simulation Conference10.5555/3320516.3320799(2363-2374)Online publication date: 9-Dec-2018
    • (2018)JigCell Model ConnectorSimulation10.1177/003754971775412194:11(993-1008)Online publication date: 1-Nov-2018
    • (2014)Towards semantic model composition via experimentsProceedings of the 2nd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation10.1145/2601381.2601394(151-162)Online publication date: 18-May-2014
    • (2010)Model Composition for Macromolecular Regulatory NetworksIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2008.647:2(278-287)Online publication date: 1-Apr-2010
    • (2007)Fusing and composing macromolecular regulatory network modelsProceedings of the 2007 spring simulation multiconference - Volume 210.5555/1404680.1404732(337-344)Online publication date: 25-Mar-2007
    • (2006)Challenges for modeling and simulation methods in systems biologyProceedings of the 38th conference on Winter simulation10.5555/1218112.1218425(1720-1730)Online publication date: 3-Dec-2006

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