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. 2011 Nov 15;27(22):3211-3.
doi: 10.1093/bioinformatics/btr543. Epub 2011 Oct 7.

Visual DSD: a design and analysis tool for DNA strand displacement systems

Matthew R Lakin  1 , Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips
Affiliations

Visual DSD: a design and analysis tool for DNA strand displacement systems

Matthew R Lakin et al. Bioinformatics. .

Abstract

The Visual DSD (DNA Strand Displacement) tool allows rapid prototyping and analysis of computational devices implemented using DNA strand displacement, in a convenient web-based graphical interface. It is an implementation of the DSD programming language and compiler described by Lakin et al. (2011) with additional features such as support for polymers of unbounded length. It also supports stochastic and deterministic simulation, construction of continuous-time Markov chains and various export formats which allow models to be analysed using third-party tools.

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Figures

Fig. 1.
Fig. 1.
Screenshot of the Visual DSD tool, with the code entry box on the left and the output tabs on the right. Along the top of the screen there are options to select example programs, adjust the semantics and control the simulator. The example shown implements a simple transducer gate. The Compilation tab on the right-hand side displays output from the compiler, in this case a visualization of all the individual reactions. The Simulation tab shows time-course plots and data tables from stochastic and deterministic simulations, and the Analysis tab shows various representations of the continuous-time Markov chain.
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References

    1. Cardelli L. Two-domain DNA strand displacement. In: Cooper S.B., et al., editors. Proceedings of DCM 2010. Vol. 26. Open Publishing Association; 2010. pp. 47–61. EPTCS.
    1. Fehlberg E. Low-order classical Runge-Kutta formulas with stepsize control and their application to some heat transfer problems. NASA, USA: Technical Report NASA-TR-R-315; 1969.
    1. Gillespie D. Exact stochastic simulation of coupled chemical reactions. J. Phy. Chem. 1977;81:2340–2361.
    1. Hinton A., et al. PRISM: a tool for automatic verification of probabilistic systems. In: Hermanns H., Palsberg J., editors. Proceedings of TACAS 2006. Vol. 3920. Berlin/Heidelberg, Germany: Springer; 2006. pp. 441–444. LNCS.
    1. Hucka M., et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;9:524–531. - PubMed