Collaboration with Waterloo

This summer, QGEM's Dry Lab created a ratiometric software application. This program works to read user input of designated protein ratio in the biofilm. Based on other user input constraints, such as organism and plasmid backbone, the program then outputs the required promoter and RBS sequences needed to produce such a biofilm.

Given the striking similarity in QGEM's bifunctional biofilm optimization project, to that of Waterloo's prion based, a logical collaboration existed between the two team. This summer QGEM faced a deficit in web development knowledge, which Waterloo was eager to aid with - graciously offering to building a web accessible version of the software for public use. Both teams planned to build upon the existing software program, broadening its bases of organism knowledge. QGEM primarily worked with E.coli this summer, and thus, the program solely contained an E.coli database. In contrast, Waterloo worked with Yeast this summer, and therefore planned to add Yeast data to our organism database. Waterloo hoped to then utilize the program, allowing faster progression of their project - as optimal parts of their organism would be quickly brought to their knowledge, saving valuable time.

Unfortunately, this collaboration between teams did not happen until late into the summer, and not enough time existed to complete the collaboration to its full extent. Nevertheless, the opportunity to discuss projects to parallel in idea and execution provided imperative problem solving aid to both teams. Waterloo brought to the attention of QGEM, various parameters that should and could be incorporated into the ratiometric program. For example, looking into the effects of degradation rates of protein production. Incorporating these aspects produced in much stronger, more accurate results from the ratiometric program. Similar feedback, along with tips and tricks, were given back to Waterloo who similarly directly benefited from the ongoing collaboration.