Structure, function, and behaviour of computational models in systems biology.
Structure, function, and behaviour of computational models in systems biology.
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DOI：
10.1186/1752-0509-7-43
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发表时间：
2013-05-31
影响因子：
--
通讯作者：
Le Novère N
中科院分区：
文献类型：
--
作者：
Knüpfer C;Beckstein C;Dittrich P;Le Novère N
系统生物学开发计算模型，以了解生物现象。这种“生物模型”的数量和复杂性不断增加，需要计算机支持整个建模任务。计算机辅助建模必须基于生物模型的正式语义描述。但是，即使计算生物模型本身精确地用数学表达式表示，它们的全部含义还没有正式指定，只能用自然语言描述。我们提出了一个概念框架-意义方面-它可以用来严格指定的语义生物模型。生物模型具有双重解释：一方面，它是一种可用于计算模拟的数学表达式（内在含义）。另一方面，模型与生物现实（外在意义）有关。我们表明，在这两种情况下，这种解释应该从三个角度进行：模型的组件（结构）的意义，模型的预期用途（功能）的意义，和模型的动态（行为）的意义。为了证明意义方面的框架的优势，我们将其应用到两个语义相关的细胞周期模型。因此，我们尽可能地利用现有的方法来计算机表示生物模型，并勾勒出缺失的部分。意义方面的框架提供了一个系统的深入的方法来语义的生物模型。它可以服务于两个重要目的：首先，它指定和结构化生物学家在建立，使用和交换模型时必须考虑的信息。其次，因为它可以形式化，框架是生物建模中任何类型的计算机支持的坚实基础。拟议的概念框架建立了系统生物学建模的新方法，并构成了计算机辅助合作研究的基础。
Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such “bio-models” necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natural language. We present a conceptual framework – the meaning facets – which can be used to rigorously specify the semantics of bio-models. A bio-model has a dual interpretation: On the one hand it is a mathematical expression which can be used in computational simulations (intrinsic meaning). On the other hand the model is related to the biological reality (extrinsic meaning). We show that in both cases this interpretation should be performed from three perspectives: the meaning of the model’s components (structure), the meaning of the model’s intended use (function), and the meaning of the model’s dynamics (behaviour). In order to demonstrate the strengths of the meaning facets framework we apply it to two semantically related models of the cell cycle. Thereby, we make use of existing approaches for computer representation of bio-models as much as possible and sketch the missing pieces. The meaning facets framework provides a systematic in-depth approach to the semantics of bio-models. It can serve two important purposes: First, it specifies and structures the information which biologists have to take into account if they build, use and exchange models. Secondly, because it can be formalised, the framework is a solid foundation for any sort of computer support in bio-modelling. The proposed conceptual framework establishes a new methodology for modelling in Systems Biology and constitutes a basis for computer-aided collaborative research.
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影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
7
作者：
Ashburner, M;Ball, CA;Yoon, J
通讯作者：
Yoon, J
DOI：
10.1177/0037549703040939
发表时间：
2003-12-01
影响因子：
1.6
作者：
Cuellar, AA;Lloyd, CM;Hunter, PJ
通讯作者：
Hunter, PJ
影响因子：
14.9
作者：
The UniProt Consortium
通讯作者：
The UniProt Consortium
影响因子：
12.3
作者：
Bard J;Rhee SY;Ashburner M
通讯作者：
Ashburner M