seeks to achieve an ensemble defect below N/100. Empirically, the design algorithm exhibits asymptotic optimality as N increases: for sufficiently large N, the cost of sequence design is typically only 4/3 the cost of a single evaluation of the ensemble defect. Utilities The Utilities page allows users to evaluate, display, and annotate the equilibrium properties of a complex of interacting nucleic acid strands. The page accepts as input either sequence information, structure information, or both, performing diverse functions based on the information provided, including automatic layout and rendering of secondary structures with or without ideal helical geometry. In either case, the structure layout can be edited dynamically within the web application. Implementation The NUPACK web application is programmed within the Ruby on Rails framework, employing Ajax and the Dojo Toolkit to implement dynamic features and interactive graphics. Plots and graphics are generated using NumPy and matplotlib. The site is supported on current versions of the web browsers Safari, Chrome, and Firefox. The NUPACK library of analysis and design algorithms is written in the programming language C. Dynamic programs are parallelized using Message Passing Interface (MPI). Terms of use The NUPACK web server and NUPACK source code are provided for non-commercial research purposes and is with this restriction not Free and open source software. Funding NUPACK development is funded by the National Science Foundation via the Molecular Programming Project and by the Beckman Institute at the California Institute of Technology (Caltech). See also RNA RNA structure List of RNA structure prediction software Comparison of nucleic acid simulation software External links Source download page Molecular Programming Project Homepage The Beckman Institute at Caltech References Molecular modelling software DNA nanotechnology