archives –––––––– @btnaughton

I first learned about Arcturus BioCloud a few months ago from their irreverent youtube videos.

Arcturus are one of the new crop of robotic labs that allow you to run wet-lab experiments from a web or command-line interface. They appear to be smaller and less well funded than Transcriptic and Emerald Cloud Lab, both of which have opened enormous new lab spaces recently. Arcturus is much more focused on the biohacker / synthetic biology space, where Transcriptic and ECL are focused on taking on common wet-lab procedures like Western blots. (For completeness, the other robot lab I know about is Riffyn, though I don't know how that one fits in yet).

The most impressive aspect of Arcturus to me was that I could create and execute a synthetic biology project within literally a few minutes. Granted, the experiment simply grows a bacterium up with one of three available genes and takes a photograph, but I am still extremely impressed by how easy it was, and by the $80 price.

arcturus

I'm looking forward to seeing how Arcturus develops their interface to allow for custom proteins and analyses.

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Synthetic Biology Software

Ideally I would like some software to help me create proteins and expression vectors.

I have tried Genome Compiler, Benchling and Teselagen before but I haven't really gotten the hang of any of them. I don't think they are designed for me, and I don't really trust that they are doing what I intend them to do. For example, if I create a promoter–gene–terminator unit, it's often not clear to me if a Kozak sequence is included. My ideal software would flag that and other potential issues.

Generally, the world of synthetic biology is concerned with creating pathways and circuits to perform tasks like processing chemical A into chemical B. This makes sense, since metabolic engineering is a huge opportunity. Large companies like Amyris and Synthetic Genomics spend their time on this stuff.

I don't really want to do that. For one thing, it is extremely difficult; there are a lot of ways it can go wrong. So what do you do if you just want to express a synthetic recombinant protein? It's not as futuristic or as complex as creating a genetic circuit but it's still surprisingly difficult using the current crop of software. (Or perhaps I am just using the wrong software and I really need protein engineering software...)

GenoCAD

GenoCAD is open-source synthetic biology software from Virginia Tech. I stumbled onto GenoCAD after noticing that their intro tutorial is one of the most popular shares on figshare.

GenoCAD is similar to other synthetic biology software in most ways. However, it also uses the interesting concept of a "grammar" (which I would have probably called a template) that allows you to fill-in-the-blanks for a synthetic biology task (e.g., building an oscillator or repressor).

I went through the GenoCAD tutorials and found it to be impressive, though clearly academic software. GenoCAD has some nice features:

  • it's open-source, though it only exists as a zip file hosted on sourceforge — let's put the code on github or bitbucket guys..
  • it has comprehensive tutorials (thanks to OpenHelix)
  • it has a small number of defined grammars for some common synthetic biology tasks.

There aren't many examples of community-defined grammars, but I could see this eventually growing into a useful library of templates.

genocad
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