Development, evaluation and benchmarking of simulation software for biomolecule-based computing


Simulators for biomolecular computing, (both in vitro and in silico), have come to play an important role in experimentation, analysis, and evaluation of the efficiency and scalability of DNA and biomolecule based computing. Simulation in silico of DNA computing is useful to support DNA-Computing algorithm design and to reduce the cost and effort of lab experiments. Although many simulations have now been developed, there exists no standard for simulation software in this area. Reliability, performance benchmarks, user interfaces, and accessibility are arguably the most important criteria for development and wide spread use of simulation software for BMC. The requirements and evaluation of such software packages for DNA computing software are discussed, particularly questions about software development, appropriate user environments, standardization of benchmark data sets, and centrally available common repositories for software and/or data. © 2004 Kluwer Academic Publishers.

Publication Title

Natural Computing