What is GenoCAD? GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing plasmids, gene expression systems, or artificial gene networks. GenoCAD provides a graphical interface allowing users to design sequences consistent with formalized strategies specific to a domain, organization, or project. Design strategies include limited sets of user-defined parts and rules indicating how these parts are to be combined in genetic constructs. In addition to reducing design time to minutes, GenoCAD improves the quality and reliability of the finished sequence by ensuring that the designs follow established rules of sequence construction. GenoCAD.org is a publicly available instance of GenoCAD that can be found at www.genocad.org. The source code is available from SourceForge to allow advanced users to install and customize GenoCAD for their unique needs.
Tutorial: This is a hands-on tutorial that will be broken down into two sessions. During the first session, the students will use GenoCAD’s parts management system to build a library of parts that they will use to design several genetic constructs. The first session also includes an overview of GenoCAD’s SBML-based simulation tool.
The second session focuses on more advanced features of the application. We will introduce the search engine to retrieve specific parts from large parts libraries. We will show how the design management tool allows users to quickly make several variants of a plasmid. Finally, we will show how to use the grammar editor to customize the design rules associated with a specific project.
Target Audience: Biologists who design plasmids for their research projects. Computational biologists and bioinformatics specialists interested in identifying opportunities to collaboration opportunities with experimentalists
Location: Matas Library Mezzanine Lab (207). Attendees must enter on the 2nd floor entrance to go downstairs to the Mezzanine Lab. Click here for more information.
When & Where
Jean Peccoud, Virginia Tech
Jean Peccoud is an expert in computational synthetic biology. His current scientific interests include the development of linguistic models of DNA sequences, the optimization of DNA fabrication processes, and the development of new instruments to measure the dynamics of gene networks in live cells. Dr Peccoud’s group is leading the development of GenoCAD, an open source web-based application to design synthetic DNA molecules from libraries of standard genetic parts. In the 1990s, Dr Peccoud pioneered the development of stochastic models of genetic networks.
Dr Peccoud joined the Virginia Bioinformatics Institute at Virginia Tech in 2006 as Associate Professor. Prior to joining VBI, he was involved in a research program at Du Pont focused on gene and regulatory network discovery, the design of DNA transformation vectors, and the development of methods to analyze the genetic properties of gene networks. Dr Peccoud has been a visiting professor in the department of electrical engineering at the University of Washington, a visiting scholar with Wolfram Research, and the recipient of a NATO Fellowship. Since 2009, he has been an Academic Editor of PLoS ONE. He co-edits the PLoS ONE Synthetic Biology Collection. He is also a member of the editorial board of Trends in Biotechnology.