Model

Rational design of biobrick parts and protocols is an iGEM tenet that Team Edinburgh UG have embraced this year through mathematical modelling. The mechanistic modelling of our DNA degrading killswitch was used to check for viability and to decide which promoters and ribosome binding sites to use in the final parts. Modelling the probability of failure of our Semantic Containment system to prevent horizontal gene transfer allowed us to calculate the failure rate of our parts combining engineering safety techniques with Synthetic Biology. Using ordinal logistic regression we were able to use growth curve data to identify which of our Semantic Containment parts was present within an organism providing a quick way to diagnose instances of Semantic Containment failure. In our collaboration with Team Vilnius-Lithuania we produced a mechanistic model of protein synthesis within the PURE cell free system to assess how addition of mRNA would effect protein expression.

All our code can be found on our Github using the link below. All of our code was written in Python3 making use of the Numpy, SciPy, Sklearn, Matplotlib and SALib libraries.