The goal is to create a series of programs to model and simulate the complex interactions of molecules in an arbitrary biological system. Molecules in biological systems are often times linked to the presence or absence of other molecules; in this way, the biological system can be modeled similarly to a digital circuit. The process includes as an input a table (as a csv file) of molecule dependencies, and should output the logical expression for the molecules. The model should also have the capabilities of determining the strength of molecular signals as well as take into account delays of other molecules. The model will be created in C and may have system verilog capabilities in the future. Results should include the ability to predict the resultant state of a biological system given a set of rules for molecular dependencies, and an initial state for the biological system.