GeneEx is an interactive web-app that uses an ODE-based mathematical modeling approach to simulate, visualize and analyze gene regulatory circuits (GRCs) for an explicit kinetic parameter set or for a large ensemble of random parameter sets. GeneEx offers users the freedom to modify many aspects of the simulation such as the parameter ranges, the levels of gene expression noise and the GRC network topology itself. This degree of flexibility allows users to explore a variety of hypotheses by providing insight into the number and stability of attractors for a given GRC. Moreover, users have the option to upload, and subsequently compare, experimental gene expression data to simulated data generated from the analysis of a built or uploaded custom circuit. Finally, GeneEx offers a curated database that contains circuit motifs and known biological GRCs to facilitate further inquiry into these. Overall, GeneEx enables users to investigate the effects of parameter variation, stochasticity and/or topological changes on gene expression for GRCs using a systems-biology approach.

中文翻译：

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基因电路浏览器 (GeneEx)：用于可视化、模拟和分析基因调控电路的交互式网络应用程序

GeneEx 是一个交互式网络应用程序，它使用基于 ODE 的数学建模方法来模拟、可视化和分析显式动力学参数集或大量随机参数集的基因调控电路 (GRC)。GeneEx 为用户提供了修改模拟的许多方面的自由，例如参数范围、基因表达噪声水平和 GRC 网络拓扑本身。这种灵活性允许用户通过深入了解给定 GRC 的吸引子的数量和稳定性来探索各种假设。此外，用户可以选择上传并随后将实验基因表达数据与分析构建或上传的自定义电路生成的模拟数据进行比较。最后，GeneEx 提供了一个精选的数据库，其中包含电路图案和已知的生物 GRC，以促进对这些的进一步调查。总体而言，GeneEx 使用户能够使用系统生物学方法研究参数变化、随机性和/或拓扑变化对 GRC 基因表达的影响。