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Semi-quantitative Abstraction and Analysis of Chemical Reaction Networks (Extended Abstract)

机译:化学反应网络的半定​​量抽象和分析(扩展抽象)

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Introduction. Chemical Reaction Networks (CRNs) are a versatile language widely used for modelling and analysis of biochemical systems as well as for high-level programming of molecular devices. Motivated by numerous potential applications ranging from system biology to synthetic biology, various techniques allowing simulation and formal analysis of CRNs have been proposed, and embodied in the design process of biochemical systems. The time-evolution of CRNs is governed by the Chemical Master Equation (CME), which describes the probability of the molecular counts of each chemical species. Many important biochemical systems lead to complex dynamics that includes state space explosion, stochasticity, stiffness, and multimodality of the population distributions, and that fundamentally limits the class of systems the existing techniques can effectively handle. More importantly, biologist and engineers often seek for plausible explanations why the system under study has or has not the required behaviour. In many cases, a set of system simulations/trajectories or population distributions are not sufficient and the ability to provide an accurate explanation for the temporal or steady-state behaviour is another major challenge for the existing techniques.
机译:介绍。化学反应网络(CRN)是一种通用语言,广泛用于生化系统的建模和分析以及分子设备的高级编程。受系统生物学到合成生物学等众多潜在应用的推动,已经提出了各种允许对CRNs进行模拟和形式分析的技术,并将其体现在生化系统的设计过程中。 CRN的时间演化由化学主方程(CME)控制,该方程描述了每种化学物种的分子计数的概率。许多重要的生化系统导致复杂的动力学,包括状态空间爆炸,随机性,刚度和种群分布的多模态,并且从根本上限制了现有技术可以有效处理的系统类别。更重要的是,生物学家和工程师经常寻求合理的解释,说明所研究的系统为何具有或不具有所需的行为。在许多情况下,一组系统模拟/轨迹或总体分布是不够的,而为时间或稳态行为提供准确解释的能力是现有技术的另一个主要挑战。

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