Alexander J. Hartemink, Tarjei S. Mikkelsen, and David K. Gifford
5th Annual DIMACS Workshop on DNA-Based Computers, Boston, Massachusetts, June 1999

We develop a general framework for simulating a sequence of biological reactions using small simulation modules. We demonstrate the usefulness of such a framework by implementing a simulator called the cybercycler. The cybercycler contains DNA hybridization, polymerization, ligation, and melting modules linked together to simulate a thermocycling process. This simulator enables us to interpret the behavior of our own programmed mutagenic unary counter in the laboratory. We describe the modules we implemented and then present a comparison of output from the cybercycler with the results of laboratory experiments to evaluate the effectiveness of the cybercycler simulator. We define a concrete specification for transformation modules and for populations of molecules passed between modules. This specification enables the construction of tools for simulating an arbitrarily complex sequence of biological reactions. We provide Java interfaces and classes for building such tools.

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