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RuleBuilder is a tool for drawing graphs that can be represented by theBioNetGen language (BNGL), which is used to formulate mathematical, rule-basedmodels of biochemical systems. BNGL provides an intuitive plain-text, orstring, representation of such systems, which is based on a graphicalformalism. Reactions are defined in terms of graph-rewriting rules that specifythe necessary intrinsic properties of the reactants, a transformation, and arate law. Rules may also contain contextual constraints that restrictapplication of the rule. In some cases, the specification of contextualconstraints can be verbose, making a rule difficult to read. RuleBuilder isdesigned to ease the task of reading and writing individual reaction rules, aswell as individual BNGL patterns similar to those found in rules. The softwareassists in the reading of existing models by converting BNGL strings ofinterest into a graph-based representation composed of nodes and edges.RuleBuilder also enables the user to construct de novo a visual representationof BNGL strings using drawing tools available in its interface. As objects areadded to the drawing canvas, the corresponding BNGL string is generated on thefly, and objects are similarly drawn on the fly as BNGL strings are enteredinto the application. RuleBuilder thus facilitates construction andinterpretation of rule-based models.

Using RuleBuilder to graphically define and visualize BioNetGen-language patterns and reaction rules