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首页> 外文期刊>Current Protocols in Bioinformatics >Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzer
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Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzer

机译：用生物汇聚仪构建和分析细胞信号的计算模型

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摘要

BioModelAnalyzer (BMA) is an open‐source graphical tool for the development of executable models of protein and gene networks within cells. Based upon the Qualitative Networks formalism, the user can rapidly construct large networks, either manuallyor by connecting motifs selected from a built‐in library. After the appropriate functions for each variable are defined, the user has access to three analysis engines to test the model. In addition to standard simulation tools, BMA includes an interfaceto the stability‐testing algorithm and to a graphical Linear Temporal Logic (LTL) editor and analysis tool. Alongside this, we have developed a novel ChatBot to aid users constructing LTL queries and to explain the interface and run through tutorials.Here we present worked examples of model construction and testing via the interface. As an initial example, we discuss fate decisions in Dictyostelium discoidum and cAMP signaling. We go on to describe the workflow leading to the construction of a published model of the germline of C. elegans. Finally, we demonstrate how to construct simple models from the built‐in network motif library.
机译：Biomodelanalyzer（BMA）是一种开源图形工具，用于开发细胞内蛋白质和基因网络的可执行模型。基于定性网络的形式主义，用户可以通过从内置库中选择的图案来快速构建大型网络，无论是通过从内置库中选择的主机。在定义每个变量的适当函数之后，用户可以访问三个分析引擎以测试模型。除了标准仿真工具之外，BMA还包括稳定性测试算法的Interfaceto和图形线性时间逻辑（LTL）编辑器和分析工具。除此之外，我们开发了一个新的Chatbot，以帮助构建LTL查询的用户，并通过教程解释界面并通过教程运行。我们通过接口呈现模型构造和测试的工作示例。作为最初的例子，我们讨论了Dictyostelium Discopum和CAMP信号中的命运决定。我们继续描述工艺，导致建造了C.秀丽隐杆线虫的种系的发表模型。最后，我们演示了如何从内置网络图书馆构建简单模型。

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