Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules.
Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules.
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使用 RuleBuilder 以图形方式定义和可视化 BioNetGen 语言模式和反应规则。
DOI：
10.1007/978-1-4939-9102-0_2
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发表时间：
2019
期刊：
影响因子：
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通讯作者：
Hlavacek,WilliamS
中科院分区：
文献类型：
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作者：
Suderman,Ryan;Fricke,GMatthew;Hlavacek,WilliamS
RuleBuilder是一种绘制图形的工具，可以用BioNetGen语言（BNGL）表示，用于制定生物化学系统的数学，基于规则的模型。BNGL提供了一个直观的纯文本，或字符串，表示这样的系统，这是基于图形形式主义。反应是根据重写图形的规则来定义的，这些规则指定了反应物的必要内在性质、变换和速率定律。规则还包含限制规则应用的上下文约束。在某些情况下，上下文约束的规范可能很冗长，使得规则难以阅读。RuleBuilder旨在简化阅读和编写单个反应规则或模型制定所需的其他BNGL模式的任务。该软件通过将感兴趣的BNGL字符串转换为由节点和边组成的基于图形的表示来帮助阅读现有模型。RuleBuilder还使用户能够使用其界面中提供的绘图工具重新构建BNGL字符串的视觉表示。当对象被添加到绘图画布时，相应的BNGL字符串被动态生成，并且当BNGL字符串被输入到应用程序中时，对象被类似地动态绘制。因此，RuleBuilder有助于构建和解释基于规则的模型。
RuleBuilder is a tool for drawing graphs that can be represented by the BioNetGen language (BNGL), which is used to formulate mathematical, rule-based models of biochemical systems. BNGL provides an intuitive plain text, orstring, representation of such systems, which is based on a graphical formalism. Reactions are defined in terms of graph-rewriting rules that specify the necessary intrinsic properties of the reactants, a transformation, and a rate law. Rules also contain contextual constraints that restrict application of the rule. In some cases, the specification of contextual constraints can be verbose, making a rule difficult to read. RuleBuilder is designed to ease the task of reading and writing individual reaction rules or other BNGL patterns required for model formulation. The software assists in the reading of existing models by converting BNGL strings of interest into a graph-based representation composed of nodes and edges. RuleBuilder also enables the user to construct de novo a visual representation of BNGL strings using drawing tools available in its interface. As objects are added to the drawing canvas, the corresponding BNGL string is generated on the fly, and objects are similarly drawn on the fly as BNGL strings are entered into the application. RuleBuilder thus facilitates construction and interpretation of rule-based models.