Monday, April 16, 2012

Tech Report on Biological Part Characterization

Last year in synthetic biology, my TASBE project spent a lot of time sprinting hard in the lab and producing new results.  This year, we should finally finish writing up a lot of this material and hope to end up with some nice articles reporting it all and laying down the foundations for a new and more integrated approach to predictive design of DNA circuits for controlling cell behavior.

Perhaps the biggest effort over the past year has been improving the characterization of DNA parts: in order to design cellular controls effectively, we need to be able to quantify fairly precisely how gene expression (the output of our computing devices) is regulated by the concentration of transcription factors or other such input signals.  We started out without this as a goal, as there have been excellent claims with nice looking curves for years, but we quickly found out that the prior methods just weren't up to our requirements.  (You see, suitability for computer automated design is actually a much stricter test than ability to pass even the most stringent peer review, since the computer doesn't know a damned thing about the field and can't fill in any gaps from experience).  And thus began a long and magical journey that I'll probably say more about in a future post...

Bottom line: we've got a new and better methodology, which combines a little more experimental work with a lot better analytic methods, and it's giving us the data we need.  And now, in this Characterization Tech Report, we're sharing that method with the rest of the world, since we want other people to produce usable data as well...

Soon, we should have a web service up that lets people use our whole suite of software tools as well... stay tuned...

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