Video Tip of the Week: GenoCAD for Synthetic Biology

The field of synthetic biology has been simmering for quite a while. It occasionally takes a big leap, such as when Venter’s team published about their work on M. genitalium, and it took a big leap recently with the paper about modeling a lot of the cellular processes in a simple cell that I talked about, and in the virtual journal club we had soon after on Google+ .

But there have been folks who have been building and working on supporting software for this field for quite a while, and I wanted to explore one of those tools today. For this week’s tip we’ll explore GenoCAD. Computer-aided Design (CAD) for genomics will be necessary at some point–you’ll be able to mock up some system, enter some parameters, and test out the equations you’ve established. But as the recent paper showed–the foundation of this has to be extensive amounts of benchwork and existing information from publications and databases. But that information has to be assembled, corralled, and coded in new ways to make analysis and predictions possible.

GenoCAD will let you begin to construct and test cellular activities of this type. Here’s how they describe themselves:

GenoCAD is an open-source computer-assisted-design (CAD) application for synthetic biology. The foundation of GenoCAD is to consider DNA as a language to program synthetic biological systems. GenoCAD includes a large database of annotated genetic parts which are the words of the language. GenoCAD also includes design rules describing how parts should be combined in genetic constructs. These rules are used to build a wizard that guides users through the process of designing complex genetic constructs and artificial gene networks.

You’ll find it has a nice organization with 3 major steps: you can create and select the parts you want to use in step 1. In step 2 you assemble them into a construct. And if you want to take it further and model the activity of this item you can do that as a third step.

With the GenoCAD options you can select from parts lists that exist or upload more (including BioBricks and items from their Parts Registry) and use existing grammar rules for organizing your parts, but you aren’t limited to those. You an add your own parts and create your own grammar rules to accompany your components. You can quickly see how flexible and easy it is to construct these features. You can save them with an account there, and build on them on the future.

In this tip we’ll only have time to examine the basic features of the interface, but you can go back and explore it yourself with further details from their help and documentation. There are also a number of helpful publications that I’ve linked below in the references sections.

There are related tools that were recently explored in an article in The Scientist: Move Over, Mother Nature. GenoCAD is one of the featured tools, but you can read about others as well. Soon it will no longer be sufficient to use the software to find existing information (although that will still be crucial), but you’ll be modeling your ideas with some software to help refine and extend your research too. One of the really fascinating aspects of that Whole Cell Simulation paper recently was how there were cases where the models weren’t reflecting the biology, and the  refinement of the models and a better understanding of the biology came out of that.

Start modeling your favorite biological systems in silico.  Or at least start thinking about it.

Quick links:

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

Handy new collection of PLoS papers on synthetic biology: http://blogs.plos.org/everyone/2012/08/15/plos-one-launches-synthetic-biology-collection/

Biology’s Master Programmers: http://www.technologyreview.com/featured-story/428187/biologys-master-programmers/

Move Over, Mother Nature: http://the-scientist.com/2012/07/01/move-over-mother-nature/

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. , 498, 173-188 DOI: 10.1016/B978-0-12-385120-8.00008-5

Czar, M.J., Cai, Y. & Peccoud, J. (2009). Writing DNA with GenoCADTM, Nucleic Acids Research, 37 (Web Server) W47. DOI: 10.1093/nar/gkp361

Cai, Y., Wilson, M.L. & Peccoud, J. (2010). GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs, Nucleic Acids Research, 38 (8) 2644. DOI: 10.1093/nar/gkq086

Tyson, J.J. & Novák, B. (2010). Functional Motifs in Biochemical Reaction Networks, Annual Review of Physical Chemistry, 61 (1) 240. DOI: 10.1146/annurev.physchem.012809.103457

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