Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications
Fig 8
RuleRailRoad package workflow.
The bngl_parser.js module preprocesses strings from BNGL code files. expanded.js returns fully expanded BNGL strings and compare_reactions.js finds differences between reactants and products in a BNGL reaction rule. Molecules_BNGL_to_Python.js is designed to take these parsed BNGL strings and translate them into formatted diagram code to be drawn by railroad diagram classes. railroad.js is a railroad-diagram renderer that reads the diagram code and generates the SVG railroad visualization. These diagrams show molecular interactions by highlighting sites, states, bonds, and changes through reactions.