GenHotel, Univ Evry, University of Paris-Saclay, Genopole, 91025 Evry, France and Lifeware Group, Inria Saclay-île de France, Palaiseau 91120, France.
Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
Brief Bioinform. 2021 Jul 20;22(4). doi: 10.1093/bib/bbaa236.
Mechanistic computational models enable the study of regulatory mechanisms implicated in various biological processes. These models provide a means to analyze the dynamics of the systems they describe, and to study and interrogate their properties, and provide insights about the emerging behavior of the system in the presence of single or combined perturbations. Aimed at those who are new to computational modeling, we present here a practical hands-on protocol breaking down the process of mechanistic modeling of biological systems in a succession of precise steps. The protocol provides a framework that includes defining the model scope, choosing validation criteria, selecting the appropriate modeling approach, constructing a model and simulating the model. To ensure broad accessibility of the protocol, we use a logical modeling framework, which presents a lower mathematical barrier of entry, and two easy-to-use and popular modeling software tools: Cell Collective and GINsim. The complete modeling workflow is applied to a well-studied and familiar biological process-the lac operon regulatory system. The protocol can be completed by users with little to no prior computational modeling experience approximately within 3 h.
机制计算模型能够研究各种生物过程中涉及的调节机制。这些模型提供了一种分析它们所描述系统动态的方法，并研究和探究其性质，以及在存在单一或组合扰动时提供关于系统涌现行为的见解。针对那些对计算建模不熟悉的人，我们在此提供了一个实用的实践方案，将生物系统的机制建模过程分解为一系列精确的步骤。该方案提供了一个框架，包括定义模型范围、选择验证标准、选择合适的建模方法、构建模型和模拟模型。为了确保协议的广泛适用性，我们使用了逻辑建模框架，该框架降低了数学准入门槛，并且使用了两个易于使用和流行的建模软件工具：Cell Collective 和 GINsim。完整的建模工作流程应用于一个研究充分且熟悉的生物过程——乳糖操纵子调控系统。用户大约在 3 小时内即可完成该协议，即使他们之前几乎没有计算建模经验。
