• Login
    View Item 
    •   DSpace Home
    • INVESTIGACIÓN
    • Artículos WOS
    • View Item
    •   DSpace Home
    • INVESTIGACIÓN
    • Artículos WOS
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    El Repositorio Institucional de la Universidad Mayor, tiene como objetivo publicar, en formato digital, todos los objetos derivados de su producción científica, académica, cultural y artística. En palabras simples es una vitrina que pone en valor su patrimonio documental.


    InformaciónInicioAcerca deFormulariosManuales

    Browse

    All of DSpaceCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

    xmlui.EPerson.Navigation.loginxmlui.EPerson.Navigation.register

    Pleione: A tool for statistical and multi-objective calibration of Rule-based models

    Thumbnail
    Date
    2019
    Author

    Martin, Alberto J. M. [Univ Mayor, Fac Ciencias, Network Biol Lab, Ctr Genom & Bioinformat]

    Santibáñez, Rodrigo [Univ Mayor, Fac Ciencias, Network Biol Lab, Ctr Genom & Bioinformat]

    Garrido, Daniel

    Geographic location

    Note
    Tools
    Cite
    Vea como citar este artículo

    Show full item record
    Abstract
    Mathematical models based on Ordinary Differential Equations (ODEs) are frequently used to describe and simulate biological systems. Nevertheless, such models are often difficult to understand. Unlike ODE models, Rule-Based Models (RBMs) utilise formal language to describe reactions as a cumulative number of statements that are easier to understand and correct. They are also gaining popularity because of their conciseness and simulation flexibility. However, RBMs generally lack tools to perform further analysis that requires simulation. This situation arises because exact and approximate simulations are computationally intensive. Translating RBMs into ODEs is commonly used to reduce simulation time, but this technique may be prohibitive due to combinatorial explosion. Here, we present the software called Pleione to calibrate RBMs. Parameter calibration is essential given the incomplete experimental determination of reaction rates and the goal of using models to reproduce experimental data. The software distributes stochastic simulations and calculations and incorporates equivalence tests to determine the fitness of RBMs compared with data. The primary features of Pleione were thoroughly tested on a model of gene regulation in Escherichia coli. Pleione yielded satisfactory results regarding calculation time and error reduction for multiple simulators, models, parameter search strategies, and computing infrastructures.
    URI
    https://doi.org/10.1038/s41598-019-51546-6
    https://www.nature.com/articles/s41598-019-51546-6
    http://repositorio.umayor.cl/xmlui/handle/sibum/6558
    Collections
    • Artículos WOS
    • Centro de Investigación en Genómica y Bioinformática (CGB)

    Si usted es autor(a) de este documento y NO desea que su publicación tenga acceso público en este repositorio, por favor complete el formulario aquí.


    Contact Us | Send Feedback
    Modificado por: Sistema de Bibliotecas Universidad Mayor - SIBUM
    DSpace software copyright © 2002-2018  DuraSpace
     

     



    Contact Us | Send Feedback
    Modificado por: Sistema de Bibliotecas Universidad Mayor - SIBUM
    DSpace software copyright © 2002-2018  DuraSpace