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Petri Nets Are a Biologist's Best Friend

机译：Petri Nets是生物学家的最好朋友

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摘要

Understanding how genes regulate each other and how gene expression is controlled in living cells is crucial to cure genetic diseases such as cancer and represents a fundamental step towards personalised medicine. The complexity and the high concurrency of gene regulatory networks require the use of formal techniques to analyse the dynamical properties that control cell proliferation and differentiation. However, for these techniques to be used and be useful, they must be accessible to biologists, who are currently not trained to operate with abstract formal models of concurrency. Petri nets, owing to their appealing graphical representation, have proved to be able to bridge this interdisciplinary gap and provide an accessible framework for the construction and execution of biological networks. In this paper, we propose a novel Petri net representation, tightly designed around the classic basic definition of the formalism by introducing only a small number of extensions while making the framework intuitively accessible to a biology-trained audience with no expertise in concurrency theory. Finally, we show how this Petri net framework has been successfully applied in practice to capture haematopoietic stem cell differentiation, and the value of this approach in understanding the heterogeneity of a stem cell population.
机译：了解基因之间如何相互调节以及如何在活细胞中控制基因表达对于治愈遗传性疾病（例如癌症）至关重要，是朝着个性化医学迈出的重要一步。基因调控网络的复杂性和高并发性要求使用形式化技术来分析控制细胞增殖和分化的动力学特性。但是，要使这些技术得以使用和有用，生物学家必须可以使用它们，而这些生物学家目前尚未受过使用抽象的并行并发正式模型进行操作的培训。 Petri网由于其吸引人的图形表示，已被证明能够弥合这一跨学科的差距，并为构建和执行生物网络提供了可访问的框架。在本文中，我们提出了一种新颖的Petri网表示形式，它通过仅引入少量扩展名而围绕形式主义的经典基本定义进行了紧密设计，同时使该框架对于没有并发理论专业知识的经过生物学培训的读者可以直观地访问。最后，我们展示了此Petri网框架如何在实践中成功应用于捕获造血干细胞分化，以及该方法在理解干细胞群体异质性中的价值。

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  • 来源
    《Formal methods in macro-biology》|2014年|102-116|共15页
  • 会议地点 Noumea(NC)
  • 作者

    Nicola Bonzanni; K. Anton Feenstra; Wan Fokkink; Jaap Heringa;

  • 作者单位

    VU University Amsterdam, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands,The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands;

    VU University Amsterdam, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands;

    VU University Amsterdam, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands;

    VU University Amsterdam, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands;

  • 会议组织
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    Petri nets; biology; gene regulatory networks;

    机译：培养皿;生物学;基因调控网络;

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