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

  • Authors:

  • Derrel Blain;Max Garzon;Soo-Yong Shin;Byoung-Tak Zhang;Satoshi Kashiwamura;Masahito Yamamoto;Atsushi Kameda;Azuma Ohuchi

  • Affiliations:

  • Computer Science Division, The University of Memphis, Memphis, U.S.A 38152-3240;Computer Science Division, The University of Memphis, Memphis, U.S.A 38152-3240;Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, Korea 151-742;Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, Korea 151-742;Graduate School of Engineering, Hokkaido University, Sapporo, Japan 060-8628;Aff4 Aff5;Japan Science and Technology Corporation (JST), CREST, Japan;Aff4 Aff5

  • Venue:
  • Natural Computing: an international journal
  • Year:
  • 2004

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Abstract

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.