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A Multiscale Modeling Framework Based on P Systems

机译：基于P系统的多尺度建模框架

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摘要

Cellular systems present a highly complex organization at different scales including the molecular, cellular and colony levels. The complexity at each one of these levels is tightly interrelated. Integrative systems biology aims to obtain a deeper understanding of cellular systems by focusing on the systemic and systematic integration of the different levels of organization in cellular systems.rnThe different approaches in cellular modeling within systems biology have been classified into mathematical and computational frameworks. Specifically, the methodology to develop computational models has been recently called executable biology since it produces executable algorithms whose computations resemble the evolution of cellular systems.rnIn this work we present P systems as a multiscale modeling framework within executable biology. P system models explicitly specify the molecular, cellular and colony levels in cellular systems in a relevant and understandable manner. Molecular species and their structure are represented by objects or strings, compartmentalization is described using membrane structures and finally cellular colonies and tissues are modeled as a collection of interacting individual P systems.rnThe interactions between the components of cellular systems are described using rewriting rules. These rules can in turn be grouped together into modules to characterize specific cellular processes. One of our current research lines focuses on the design of cell systems biology models exhibiting a prefixed behavior through the automatic assembly of these cellular modules. Our approach is equally applicable to synthetic as well as systems biology.
机译：细胞系统在包括分子，细胞和集落水平在内的不同尺度上呈现出高度复杂的组织。这些级别中每个级别的复杂性都紧密相关。集成系统生物学旨在通过专注于细胞系统中不同层次组织的系统性和系统性集成来获得对细胞系统的更深入的理解。系统生物学内细胞建模的不同方法已被分类为数学和计算框架。特别地，开发计算模型的方法最近被称为可执行生物学，因为它产生可执行算法，其计算类似于细胞系统的演化。在这项工作中，我们将P系统呈现为可执行生物学内的多尺度建模框架。 P系统模型以相关且可理解的方式明确指定了细胞系统中的分子，细胞和集落水平。分子种类及其结构用物体或细绳表示，使用膜结构描述区室化，最后将细胞菌落和组织建模为相互作用的各个P系统的集合。使用重写规则描述细胞系统各组成部分之间的相互作用。这些规则可以依次组合到模块中以表征特定的细胞过程。我们目前的研究重点之一是通过自动组装这些细胞模块来表现出前缀行为的细胞系统生物学模型的设计。我们的方法同样适用于合成生物学和系统生物学。

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  • 来源
    《Membrane computing》|2008年|63-77|共15页
  • 会议地点 Edinburgh(GB);Edinburgh(GB)
  • 作者

    Francisco Jose Romero-Campero; Jamie Twycross; Hongqing Cao; Jonathan Blakes; Natalio Krasnogor;

  • 作者单位

    Automated Scheduling, Optimisation and Planning Research Group School of Computer Science, Jubilee Campus, University of Nottingham Nottingham NG8 1BB, United Kingdom;

    Automated Scheduling, Optimisation and Planning Research Group School of Computer Science, Jubilee Campus, University of Nottingham Nottingham NG8 1BB, United Kingdom Centre for Plant Integrative Biology Sutton Bonington Campus, University of Nottingham Nottingham LE12 5RD, United Kingdom;

    Automated Scheduling, Optimisation and Planning Research Group School of Computer Science, Jubilee Campus, University of Nottingham Nottingham NG8 1BB, United Kingdom;

    Automated Scheduling, Optimisation and Planning Research Group School of Computer Science, Jubilee Campus, University of Nottingham Nottingham NG8 1BB, United Kingdom;

    Automated;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 混合集成电路;
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