Video Tip of the Week: Advanced Topics in GenoCAD

Recently we announced our newest training materials on GenoCAD. The introductory tutorial provides a great foundation for understanding the features that are available and how it could help you in the lab. But for those folks who want to take their design skills further–now you can use the GenoCAD Advanced Topics materials to do so.

As before, these materials are freely available for you to use because they were provided by the Peccoud Lab. There is a video that covers the same ground that you can find in the slides, but the slides are available too in case you’d rather cover the material with some workshop attendees or in a classroom. The exercises are there as well. Click on this image to go to the full video. It’s longer than our tips, of course, but worth it.

Click to access the tutorial suite with video, slides, exercises.

Click to access the tutorial suite with video, slides, exercises.

This relies on having completed the intro part, so don’t forget to accomplish the import that is needed from the first round. And if you want to see a bit more about the export of GenBank format files you might also want to see our quick tip on VectorEditor.

In this tutorial we examine the idea of creating custom grammars for a project that you might need to use–say, for example, chloroplast expression systems that are specific for your model system. We point you to the features you need to establish or modify to create a custom expression grammar for a system like that–and now conveniently we have a paper that describes that need and those aspects in more detail (linked below).

So check out the computer-assisted design features of GenoCAD and see if they can benefit your lab, or consider incorporating ideas from this material into classroom sessions. It’s a good way to get students thinking about important engineering concepts for synthetic biology.

Quick links:

GenoCAD Advanced Topics suite: http://openhelix.com/genocad2

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

Figshare required import file: http://figshare.com/articles/GenoCAD_Training_Set_I/153827

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

Wilson M.L., Okumoto S., Adam L. & Peccoud J. (2013). Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors, Bioinformatics, DOI: