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DyNAMiC Workbench
Welcome, Molecular Programming Project! Please sign up for the alpha test. below. Email us if you have issues!

DyNAMiC Workbench

DyNAMiC Workbench is an integrated development environment for developing dynamic DNA nanosystems in-silico. Workbench lets you begin with a behavioral description of a computational or assembly process, and then helps you automatically implement that process with DNA. It includes behavioral designers, sequence designers, and powerful sequence editing tools, as well as integration with industry-standard analysis tools. Sign up to be an alpha tester today.

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Features

Behavioral designers, sequence designers, powerful sequence editors, analysis tools, and more.

Features »

Alpha testers

Get early access to the software, contribute suggestions and feature requests, and help us work out bugs.

Alpha »

Contact

We'd love to hear from you!

Contact »

Features

Here's a sampling of available features:

Behavioral system design

  • Implements fully-featured molecular compiler for the nodal abstraction &em; Design using a high-level language, compile to segments and sequences
  • Compose programs from built-in hairpin motifs, or design new motifs based on collections of DNA strands with abritrary secondary structure
  • Generate input for several sequence designers

Segment (domain)-level system design

  • Full-featured, graphical system editor &em; no coding required to quickly design a DNA system
  • Enumerate reactions between species to analyze system behavior

Sequence design and editing

  • Includes the fast, domain-based sequence designer, DD which can run right in your web browser; also design sequences using the NUPACK multi-objective sequence designer
  • Quickly transfer sequence designs to NUPACK, Mfold, or RNAfold for thermodynamic analysis
  • Powerful sequence editor for DNA/RNA sequence manipulation and preparation

Interface

  • Fully integrated design workflow and file management
  • Server manages computationally intensive tasks, so you don't have to
  • Customizable and scriptable interface lets you automate repetitive tasks

Screenshots

Tutorial Videos

Alpha

We're conducting a limited public "alpha" release to members of the research community who are interested in trying out the software. Keep in mind that this is not the final release, and some features may be missing, incomplete, or non-functional. The purpose of the alpha release is to solicit feedback from the community&em;to find bugs, get feature suggestions, and test stability and usability.

Warning: You are welcome to use Workbench's available features once accepted into the alpha, but don't depend on them as they may break or change. Make sure to backup critical files stored in Workbench, as they may disappear during the alpha.

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Contact and Contributions

DyNAMiC Workbench is a project of Casey Grun, Justin Werfel, and Peng Yin at Harvard. Significant contributions have also been made by David Zhang, John Sadowski, and Erik Winfree.

Please email Casey with suggestions, comments, or questions. Contact us

References

  1. Yin, P., Choi, H. M. T., Calvert, C. R. & Pierce, N. A. Programming biomolecular self-assembly pathways. Nature 451, 318–322 (2008).
  2. Zhang, D. Towards domain-based sequence design for DNA strand displacement reactions. DNA Computing and Molecular Programming 162–175 (2011).
  3. Zadeh, J. N. et al. NUPACK: Analysis and design of nucleic acid systems. J Comput Chem 32, 170–173 (2011).