Modern biological experiments generate large amounts of data describing intracellular dynamics. Rule-based languages for describing intracellular biochemistry allow for the construction and simulation of detailed models with unprecedented scope and precision. Rule-Based Models (RBM) can be used to suggest new hypotheses and new ideas for future experimentation.

Rule-based models can be difficult to understand and time consuming to debug. RuleBender is a free tool for constructing, debugging, simulating and analyzing rule-based biological models in the BioNetGen language. The MOSBIE extension further provides a tool for the comparison and analysis of biochemical model families.