Systems and synthetic biology are cross-fertilizing each other in unexpected but very productive ways. For several years ICSB has included synthetic biology sessions. Many keynote speakers are known for their work in synthetic biology or at the interface between synthetic and systems biology.
This tutorial will give ICSB participant an opportunity to practice synthetic biology in a classroom environment using GenoCAD, 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.
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.
The tutorial material is published on figshare.org. Prospective students are encouraged to review the material prior to signing up for the tutorial.
Participants should bring their laptop as the tutorial will be based on a series of practical exercises.
For more information about the ICSB Workshops and Tutorials go to http://www.icsb2013.dk/scientific-programme