Video Tip of the Week: GenoCAD, computer-assisted design for synthetic biology

For this week’s video tip of the week, we’ve got a real treat. This time it’s a whole tutorial. Freely available to everyone because it is sponsored by the Peccoud Lab team, you have access to the full introductory video, the slides that you could use yourself in classrooms or workshops, and the handouts and exercises that we use in our workshops.

Click to go to the page where you can access the movie, slides, and exercises.

Click to go to the page where you can access the movie, slides, and exercises.

This software allows you to store parts that you use for making various types of genetic constructs. You can establish grammars that specify the appropriate parts for your different design needs. And you can then easily swap in and out various different parts to make new variations. But have a look at the full tutorial to imagine ways you can incorporate this into your lab work.

The other cool thing about this project is that for the first time we used FigShare to store the downloadable set of data that you need for the training.  I have to say that’s been working out great in the workshops we’ve run with this training.

There are a lot of folks who would benefit from using this tool. Students learning about creating expression constructs could do them quickly in silico here. DIY biologists could create collections of parts they use and share. But anyone creating constructs could find the organization and outputs really useful.

The software is freely available on the web for anyone to use. But you can also download it and use it for local projects as well.

Quick links:

GenoCAD introductory tutorial: http://www.openhelix.com/genocad

GenoCAD site: http://www.genocad.org/

FigShare data for the tutorial: http://figshare.com/articles/GenoCAD_Training_Set_I/153827

Press release: Virginia Bioinformatics Institute announces an OpenHelix tutorial suite on GenoCAD.

References:
Wilson ML., Hertzberg R., Adam L., & Peccoud J. (2011). A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD Methods Enzymol. DOI: 10.1016/B978-0-12-385120-8.00008-5

Lux M.W., Bramlett B.W., Ball D.A. & Peccoud J. (2012). Genetic design automation: engineering fantasy or scientific renewal?, Trends in Biotechnology, 30 (2) 120-126. DOI: