Ganor Dor, Pinter Ron Y, Zehavi Meirav
IEEE/ACM Trans Comput Biol Bioinform. 2020 Jan-Feb;17(1):316-320. doi: 10.1109/TCBB.2018.2878749.
Discrete simulations of genetic regulatory networks have been used to study subsystems of yeast successfully. Existing models underling these simulations are based on specific transition functions, which determine the node states in the network. However, implementations of existing models are not freely available and support only a textual user interface (TUI). Additionally, even if an implementation that supports a graphic user interface (GUI) were available, the computations necessary to analyze the simulations would still have to be done manually. Furthermore, the usage of different transition functions by existing models suggests that an enriched model is needed. We developed a software tool, called GRegNetSim, that allows the end-user (a biologist) to describe genetic regulatory networks graphically. The input is displayed visually via Cytoscape (an open-source platform for the representation and analysis of biological networks). The user can specify various transition functions at different nodes of the network, supporting, for example, threshold and gradient effects, thereby analyzing the network under a variety of modes dictated by these functions. GRegNetSim displays the relationship between the inputs and the mode of behavior of the network in a graphic form that is easy to interpret. Furthermore, it automatically extracts statistical data such as the percentage of simulations that reached a steady state or the percentage of simulations that terminated with a certain state. The discrete simulations performed by GRegNetSim can be used to elucidate and predict the behavior, structure, and properties of genetic regulatory networks in a unified manner. GRegNetSim is implemented as a Cytoscape App. Installation files, examples, and source code, along with a detailed user guide, are freely available at https://sites.google.com/site/gregnetsim/.
遗传调控网络的离散模拟已成功用于研究酵母的子系统。这些模拟所基于的现有模型是基于特定的转换函数，这些函数决定了网络中的节点状态。然而，现有模型的实现并非免费可得，且仅支持文本用户界面（TUI）。此外，即使有支持图形用户界面（GUI）的实现，分析模拟所需的计算仍需手动完成。此外，现有模型使用不同的转换函数表明需要一个更丰富的模型。我们开发了一个名为GRegNetSim的软件工具，它允许终端用户（生物学家）以图形方式描述遗传调控网络。输入通过Cytoscape（一个用于生物网络表示和分析的开源平台）进行可视化显示。用户可以在网络的不同节点指定各种转换函数，例如支持阈值和梯度效应，从而在这些函数规定的各种模式下分析网络。GRegNetSim以易于解释的图形形式显示输入与网络行为模式之间的关系。此外，它会自动提取统计数据，例如达到稳态的模拟百分比或终止于特定状态的模拟百分比。GRegNetSim执行的离散模拟可用于以统一的方式阐明和预测遗传调控网络的行为、结构和特性。GRegNetSim作为一个Cytoscape应用程序实现。安装文件、示例和源代码以及详细的用户指南可在https://sites.google.com/site/gregnetsim/上免费获取。
