License: Creative Commons Attribution 3.0 Unported license (CC-BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.DNA.2020.9
URN: urn:nbn:de:0030-drops-129624
URL: https://drops.dagstuhl.de/opus/volltexte/2020/12962/
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Doty, David ; Lee, Benjamin L ; Stérin, Tristan

scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures

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LIPIcs-DNA-2020-9.pdf (2 MB)


Abstract

We introduce scadnano (short for "scriptable cadnano"), a computational tool for designing synthetic DNA structures. Its design is based heavily on cadnano [Douglas et al., 2009], the most widely-used software for designing DNA origami [Paul W. K. Rothemund, 2006], with three main differences: 1) scadnano runs entirely in the browser, with no software installation required. 2) scadnano designs, while they can be edited manually, can also be created and edited by a well-documented Python scripting library, to help automate tedious tasks. 3) The scadnano file format is easily human-readable. This goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. The format is also somewhat more expressive than that of cadnano, able to describe a broader range of DNA structures than just DNA origami.

BibTeX - Entry

@InProceedings{doty_et_al:LIPIcs:2020:12962,
  author =	{David Doty and Benjamin L Lee and Tristan St{\'e}rin},
  title =	{{scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures}},
  booktitle =	{26th International Conference on DNA Computing and Molecular Programming (DNA 26)},
  pages =	{9:1--9:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-163-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{174},
  editor =	{Cody Geary and Matthew J. Patitz},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2020/12962},
  URN =		{urn:nbn:de:0030-drops-129624},
  doi =		{10.4230/LIPIcs.DNA.2020.9},
  annote =	{Keywords: computer-aided design, structural DNA nanotechnology, DNA origami}
}

Keywords: computer-aided design, structural DNA nanotechnology, DNA origami
Collection: 26th International Conference on DNA Computing and Molecular Programming (DNA 26)
Issue Date: 2020
Date of publication: 04.09.2020
Supplementary Material: [stable/dev apps]: https://scadnano.org, https://scadnano.org/dev; [repositories]: https://github.com/UC-Davis-molecular-computing/scadnano https://github.com/UC-Davis-molecular-computing/scadnano-python-package; [Python library API]: https://scadnano-python-package.readthedocs.io [tutorials]: https://github.com/UC-Davis-molecular-computing/scadnano-python-package/blob/master/tutorial/tutorial.md, https://github.com/UC-Davis-molecular-computing/scadnano/blob/master/tutorial/tutorial.md


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