In support of our project’s need to transfer a number of genes between organisms, during iGEM 2015 our modelling team has focused on the development of mathematical approaches to explore and optimise this process.
TransOpt (Translation-Optimiser) represents a new method for codon usage optimisation, building upon recent advances in the understanding of the role codons play in translation. Rather than optimising individual codon choices, it aims to match longer-term trends in translation rate and mRNA folding between the heterologous expression and native hosts. In doing this TransOpt aims to address many issues inherent in the overly-simplified codon optimisation approaches that are currently ubiquitous in the synthetic biology community.
Visualisation tools have been developed in conjunction with TransOpt, allowing users to appreciate how changes to codon usage and ribosome binding affect the behaviour of the translation process.
ElectroStop is a device we have designed and built as a secondary project related (somewhat) to modelling. This device serves a useful purpose, automatically terminating Gel Electrophoresis experiments once marker dyes reach a certain location, whilst demonstrating the potential of rapid prototyping and open-source technologies to be used throughout the iGEM community.
Supplementary Material for all tools is available, and includes the codes and data files used in their operation.