Web-Based CAD System for Synthetic Biology Designs DNA Sequences in Minutes

A web-based computer-assisted design (CAD) environment for synthetic biology is under development, and after 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 U.S. National Science Foundation (NSF; Arlington, VA, USA) has awarded a three-year US$1.4 million grant to Dr. Jean Peccoud, associate professor at the Virginia Bioinformatics Institute (VBI) at Virginia Polytechnic Institute and State University (Virginia Tech; Blacksburg, VA, USA), to develop the GenoCAD application.

Synthetic biology, a rapidly emerging area of biologic research, applies methods developed in engineering to design artificial biologic systems that meet user-defined specifications. It has also been used to redesign natural systems to better understand the fundamental characteristics of living organisms. "We are considering DNA as a language to program living organisms instead of computers," said Dr. 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. "The development of GenoCAD will be a community-driven project," said Dr. 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.

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

The Virginia Bioinformatics Institute at Virginia Tech has a research platform based on understanding the "disease triangle" of host-pathogen-environment interactions in plants, humans, and other animals.

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Virginia Bioinformatics Institute at Virginia Tech