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首页> 外文期刊>Current drug targets-The International journal for timely in-depth reviews on drug targets >Engineering Simulations for Cancer Systems Biology
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Engineering Simulations for Cancer Systems Biology

机译：癌症系统生物学的工程模拟

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Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions.
机译：计算机仿真可用于为体内和体外实验提供信息，从而实现快速，低成本的假设生成，并指导实验设计以测试这些假设。这样，计算机模拟模型就成为研究的科学工具，因此应发展为高标准，进行仔细校准并以可再现的形式呈现其发现。在这里，我们概述了一个框架，该框架支持将模拟作为科学仪器进行开发，并且我们选择癌症系统生物学作为示例域，并特别关注细胞信号模型。我们考虑在快速变化的知识库中缺少数据，知识不完整和建模的挑战。我们的框架包括一个清晰地分离模型和仿真开发中的科学和工程问题的过程，以及一个用于记录模型的论证方法，以严格方式记录假设和知识缺口。我们提出了交互式的动态可视化工具，以使生物界能够直接与细胞信号模型进行交互以进行实验设计。这些细胞模型和受肿瘤影响的组织结构之间在规模上不匹配，并且弥合这一差距需要大量的计算资源。我们将并发编程作为一种链接规模的技术，而不会因为模型简化而丢失重要细节。我们讨论了将该技术，交互式可视化，论证和模型分离相结合以支持多尺度模型开发的价值，这些模型代表了以生物学上合理的结构排列的生物学上可行的细胞，该模型在细胞行为，相互作用和对治疗干预的反应中建模。

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