DSD
Summary
The DNA Strand Displacement language (DSD) is a programming language for designing and simulating computational circuits made of DNA, in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, branch migration and strand displacement, and assumes that strands do not possess any secondary structure. The language allows a given model to be simulated and analysed at varying levels of abstraction, without changing the model code. DSD is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.
Download
- Web Simulator (requires Silverlight 4.0 for Windows or Mac).
- Command-line simulator for Windows, OS X and OCaml Bytecode.
Case studies
- Lulu Qian, Erik Winfree & Jehoshua Bruck. Neural network computation with DNA strand displacement cascades. Nature 475: 368–372. July 2011.
- Lulu Qian and Erik Winfree. Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades. Science 332: 1196-1201. June 2011.
Related publications
- Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, and John Reif, Localized Hybridization Circuits, in International Conference on DNA Computing and Molecular Programming, vol. 6937, pp. 64-83, Springer Verlag, September 2011
- Matthew Lakin and Andrew Phillips, Modelling, simulating and verifying Turing-powerful strand displacement systems, in International Conference on DNA Computing and Molecular Programming , vol. 6937, pp. 130-144, Springer Verlag, September 2011
- Matthew Lakin, Simon Youssef, Luca Cardelli, and Andrew Phillips, Abstractions for DNA circuit design, in Journal of the Royal Society Interface, vol. Published Online, The Royal Society, July 2011
- Andrew Phillips and Luca Cardelli, A programming language for composable DNA circuits, in Journal of the Royal Society Interface, 17 June 2009
People
- Matthew Lakin, Filippo Polo, Luca Cardelli, Andrew Phillips. Microsoft Research.
- Simon Youssef. Microsoft Research & University of Munich.
Acknowledgements
- DSD was developed by Matthew Lakin, Filippo Polo, Simon Youssef and Andrew Phillips at Microsoft Research.
- Luca Cardelli assisted with extensive testing of DSD together with the design of the DSD language.
- Neil Dalchau assisted with the development of an ODE solver for DSD.
- Erik Winfree and his group have provided valuable feedback on DSD, together with Georg Seelig and his group.
- The core DSD language was developed in F#.
- DSD uses Dynamic Data Display for visualising simulation plots.
- DSD uses Microsoft Automatic Graph Layout for visualising networks.
