Calgary/evoGEM results


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A simple method to evaluate the effectivness of EvoGEM would be to run EvoGEM against several proposed behaviors and see whether or not the simulator can find a circuit or circuits that produce the correct behaviors. However at this point our system is still very naive produces ineffecient circuts (ie designing a circut consisting of 12 parts that should only require 6 parts).

The solution is to take a more comparative approach and specify the behavior required from the circut and then compare the ciructs produced via evolution to previous working systems.

The approach accomplishes two goals. By comparing the evolved circut to a previously completed circut there is no need to test the evolved system in the lab. EvoGEM's results will either match the real world results or not. The other and more interesting accomplishment is that this approach tests the system against human design. Given the final goal of designing a system that generates reliable and effecient ciructs it is very important to see how the evolved circut compares to a human designed one.

Currently our only means of assessing these accomplishments is by qualitatively comparing the results of our 3D graphical simulation to the wetlab results. While this is not ideal it represents an excellent starting point.

Videos 1 and 2 show the results of a simulation run of the light sensor part described in our schematic. Specifically the movies show the series of steps involved in having the light sensor part work.

( 1 )

An angled view of a simulation showing expression of by the light sensor. The large fairly transparent purple spheres represent RNA Polymerases. These polymerases are preprogrammed in with characteristics that define their ability to bind to the promoter, which is the darker green bar at the end of the main circut. The lighter green portion corresponds to a ribosome binding site, the purpleish pink component represents the protein coding region and lastly the red part at the end of the circut is a terminator. The definitions of the other spheres floating around represent various proteins and other factors whose function will be dependent on the type of simulation being run.

( 2 )

The same video as above except from a different angle.