Abstract

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 publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages90-101
Number of pages12
Volume5347 LNCS
DOIs
StatePublished - 2009
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)03029743
ISSN (Electronic)16113349

Other

Other14th International Meeting on DNA Computing, DNA14
CountryCzech Republic
CityPrague
Period6/2/086/9/08

Fingerprint

DNA
Three-dimensional
Visualization
Automatic Sequences
Molecular Modeling
Molecular modeling
Random Sequence
Graphical User Interface
Graphical user interfaces
Nanostructures
Simplification
Data structures
Labels
Data Structures
Molecules
Generator
Demonstrate
Design
Model

Keywords

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

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Williams, S., Lund, K., Lin, C., Wonka, P., Lindsay, S., & Yan, H. (2009). Tiamat: A three-dimensional editing tool for complex DNA structures. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 5347 LNCS, pp. 90-101). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5347 LNCS). https://doi.org/10.1007/978-3-642-03076-5_8

Tiamat : A three-dimensional editing tool for complex DNA structures. / Williams, Sean; Lund, Kyle; Lin, Chenxiang; Wonka, Peter; Lindsay, Stuart; Yan, Hao.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5347 LNCS 2009. p. 90-101 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5347 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Williams, S, Lund, K, Lin, C, Wonka, P, Lindsay, S & Yan, H 2009, Tiamat: A three-dimensional editing tool for complex DNA structures. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 5347 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5347 LNCS, pp. 90-101, 14th International Meeting on DNA Computing, DNA14, Prague, Czech Republic, 6/2/08. https://doi.org/10.1007/978-3-642-03076-5_8
Williams S, Lund K, Lin C, Wonka P, Lindsay S, Yan H. Tiamat: A three-dimensional editing tool for complex DNA structures. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5347 LNCS. 2009. p. 90-101. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-03076-5_8
Williams, Sean ; Lund, Kyle ; Lin, Chenxiang ; Wonka, Peter ; Lindsay, Stuart ; Yan, Hao. / Tiamat : A three-dimensional editing tool for complex DNA structures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5347 LNCS 2009. pp. 90-101 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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