Boolink: a graphical interface for open access Boolean network simulations and use in guard cell CO2 signaling
Boolink: a graphical interface for open access Boolean network simulations and use in guard cell CO2 signaling
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DOI：
10.1093/plphys/kiab344
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发表时间：
2021-07-24
期刊：
影响因子：
7.4
通讯作者：
Rappel, Wouter-Jan
中科院分区：
文献类型：
--
作者：
Karanam, Aravind;He, David;Rappel, Wouter-Jan
信号网络是几乎所有生物过程的核心。这些网络大多包含大量的组分，通常这些组分之间的连接是未知的，或者控制可溶性信号组分动力学的速率方程没有被量化。这种网络拓扑和参数的不确定性使得制定详细的数学模型具有挑战性。布尔网络，其中所有的组件要么开要么关，已经成为包含速率常数和其他参数的详细数学模型的可行替代方案。因此，社区使用布尔模型的开源平台是可取的。在这里，我们提出了Boolink，一个免费的图形用户界面，允许用户轻松地构建和分析现有的布尔网络。布尔链接可以应用于任何布尔网络。我们使用先前发表的拟南芥（Arabidopsis thaliana）中脱落酸（ABA）驱动的气孔关闭网络来证明其应用。我们还展示了如何使用Boolink通过扩展网络来生成可测试的预测，以包括气孔运动的二氧化碳调节。对模型的预测进行了实验验证，并根据ABA在接近零CO2浓度（1.5 ppm CO2）下有效关闭拟南芥气孔的实验结果对模型进行了迭代修正。因此，Boolink支持公共生成和使用现有的布尔模型，包括先前开发的带有添加的CO2信号组件的ABA信号模型。
Signaling networks are at the heart of almost all biological processes. Most of these networks contain large number of components, and often either the connections between these components are not known or the rate equations that govern the dynamics of soluble signaling components are not quantified. This uncertainty in network topology and parameters can make it challenging to formulate detailed mathematical models. Boolean networks, in which all components are either on or off, have emerged as viable alternatives to detailed mathematical models that contain rate constants and other parameters. Therefore, open-source platforms of Boolean models for community use are desirable. Here, we present Boolink, a freely available graphical user interface that allows users to easily construct and analyze existing Boolean networks. Boolink can be applied to any Boolean network. We demonstrate its application using a previously published network for abscisic acid (ABA)-driven stomatal closure in Arabidopsis spp. (Arabidopsis thaliana). We also show how Boolink can be used to generate testable predictions by extending the network to include CO2 regulation of stomatal movements. Predictions of the model were experimentally tested, and the model was iteratively modified based on experiments showing that ABA effectively closes Arabidopsis stomata at near-zero CO2 concentrations (1.5-ppm CO2). Thus, Boolink enables public generation and the use of existing Boolean models, including the prior developed ABA signaling model with added CO2 signaling components.