This summer QGEM created a unique ratiometric application program.
Our program outlines the steps required to build specific bifunctional E.coli biofilms, based on designated conditions - as deemed by the user. As such, the user inputs the designated ratio of the two proteins to be found in the biofilm, as well as the protein coding sequences, and organism/plasmid. The program then outputs the required promoter sequences and RBS sequences necessary to achieve such a ratio under the given conditions.
Various components of the program were modeled, predominately by ordinary differential equations, as outlined on QGEM's "Mathematic Theory" wiki-page. These models were then directly integrated into our program's code, to ensure reliable results.
QGEM also had the opportunity to integrate the Salis Lab's RBS Calculator code directly into our program, thanks to the gracious help and support from Dr. Howard Salis. Dr. Salis provided QGEM with the Python helper script necessary to access the web-based API. Given the nature of the system, QGEM was given an authentication token for the file. Thus, it is not accessible to be run externally without contacting Dr. Salis.
The program is run in Python 2.7, and can be found on our GitHub page.