A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD

GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing genetic sequences. GenoCAD provides a graphical interface that allows users to design sequences consistent with formalized design 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 and latest build are available from SourceForge to allow advanced users to install and customize GenoCAD for their unique needs. This chapter focuses primarily on how the GenoCAD tools can be used to organize genetic parts into customized personal libraries, then how these libraries can be used to design sequences. In addition, GenoCAD's parts management system and search capabilities are described in detail. Instructions are provided for installing a local instance of GenoCAD on a server. Some of the future enhancements of this rapidly evolving suite of applications are briefly described.