Tiamat: A three-dimensional editing tool for complex DNA structures

Sean Williams*, Kyle Lund, Chenxiang Lin, Peter Wonka, Stuart Lindsay, Hao Yan

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

95 Scopus citations


We present the development of a new graphical user interface driven molecular modeling, editing and visualization tool called Tiamat. Tiamat addresses the challenge of how to efficiently model large and complex DNA nanostructures. We describe the three major components of our system. First, we discuss design guidelines and data structures that form the basis of flexible and large-scale editing. Second, we explain a semi-automatic sequence generator that combines user input with random sequence generation to efficiently label the molecules in the DNA structure. Third, we outline the visualization techniques including a simplification algorithm that are used to render large designs. The results demonstrate how Tiamat was used to generate large and complex designs.

Original languageEnglish (US)
Title of host publicationDNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers
Number of pages12
StatePublished - 2009
Externally publishedYes
Event14th International Meeting on DNA Computing, DNA14 - Prague, Czech Republic
Duration: Jun 2 2008Jun 9 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5347 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Other14th International Meeting on DNA Computing, DNA14
Country/TerritoryCzech Republic


  • 3D DNA structure display
  • DNA sequence design
  • DNA tile
  • Structural DNA nanotechnology

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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