A system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical system comprising a plurality of chemical reactions. The system also includes a simulation engine accepting as input the constructed model of the chemical or biochemical system and generating as output an expected result. Each time a chemical reaction executes during a simulation of the chemical or biochemical system, the simulation engine stores the reaction time and an identifier for the reaction that executes at that reaction time to produce a time-ordered history list. The history list can be replayed by simulating the reactions as the reactions occur in the history list to produce the same state sequence as the original simulation.