Gener: a minimal programming module for chemical controllers based on DNA strand displacement

Bioinformatics. 2015 Sep 1;31(17):2906-8. doi: 10.1093/bioinformatics/btv286. Epub 2015 May 7.

Abstract

: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research's DSD tool as well as to LaTeX.

Availability and implementation: Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono.

Contact: ozan@cosbi.eu.

MeSH terms

  • Computational Biology*
  • Computers, Molecular*
  • DNA / chemistry*
  • DNA Replication
  • Humans
  • Models, Molecular
  • Programming Languages*
  • Sequence Analysis, DNA / methods
  • Software*

Substances

  • DNA