The National Science Foundation (NSF) has awarded a three-year $1,421,725 grant to Jean Peccoud, associate professor at the Virginia Bioinformatics Institute at Virginia Tech, to develop GenoCAD — a web-based computer-assisted design environment for synthetic biology.

Synthetic biology, a rapidly emerging area of biological research, applies methods developed in engineering to design artificial biological systems that meet user-defined specifications. It has also been used to re-design natural systems to better understand the fundamental properties of living organisms. "We are considering DNA as a language to program living organisms instead of computers," said Peccoud. "This analogy has led us to apply methods and results from computer science to biology. In particular, rules describing how different functional elements should be combined can be described in the language grammar."

The GenoCAD point-and-click user interface guides the user through the process of designing new sequences. By successively clicking on icons representing structural features or functional blocks, complex DNA sequences composed of dozens of functional blocks can be designed in a matter of minutes. Upon completion of the design process, the sequence can be downloaded for synthesis or further analysis. Users who elect to create a personal account on the system can customize their workspace by creating their own parts libraries, adding new parts to the libraries, or reusing designs to quickly generate sets of related constructs.

"The development of GenoCAD will be a community-driven project," said Peccoud. "We intend to involve the synthetic biology research community in helping to advance this project in such a way that it meets the needs of a wide user base." The use of the public version of GenoCAD is free to anyone, while the open source distribution of the software makes it possible for research groups to install GenoCAD on their own servers and, if required, customize it to meet specific needs.

The GenoCAD project will benefit from the guidance of an external advisory board comprised of the following scientists:

  • Chris Anderson, University of California Berkeley;
  • Brian Bramlett, Intel;
  • Malcolm Campbell, Davidson College;
  • Jacques Cohen, Brandeis University;
  • Otto Folkerts, Virginia Bioinformatics Institute;
  • Claes Gustafsson, DNA2.0; and
  • Ron Weiss, Massachusetts Institute of Technology.

The GenoCAD project will also have a strong educational component. In particular, it will actively support teams of undergraduate students enrolled in iGEM, the international Genetically Engineered Machine competition.

Early applications for GenoCAD include the development of vaccines, sensing devices for biodefense, and metabolic pathways for biofuel production.

The activities described in this release are being funded through the American Recovery and Reinvestment Act.

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