Software Contribution
Our team made a valuable contribution to future iGEM teams and the synthetic biology community by creating
Toehold Switch Creator
, a software tool built upon the existing software Toehold Designer, created by EPFL 2017 iGEM Team [1].
During the research process for our project, we realized that designing and analyzing RNA toehold switches sequences required the use of separate bioinformatic tools and that the overall process was time consuming and needed previous coding knowledge. Therefore, we decided to create an all-in-one software tool where users can design, analyze, and visualize toehold switches in a manner of minutes with little to no coding experience required.
For that, we combined three bioinformatic tools in one to ease the process: PrimedRPA for primer design, Toehold Designer for the assembly of toehold switches, and ViennaRNA for the thermodynamic analysis of the sequences. Especifically, we implemented some of the functions involved with the assembly of the Toehold Switches from the open source python code of Toehold Designer available at GitHub, and by combining them with our own code we were able to generate a more robust and practical bioinformatic tool for the community to use.
Additionally, we are currently working on a web app that will allow users to skip the whole installation process of the software and generate both primers and toehold switches from their web browser in a couple of minutes with just three inputs (see more on Software>Web app ). We believe that this will reinforce our contribution given that this web application will allow anyone from all over the world with or without coding experience to generate toehold switches for any DNA sequence they wish to detect.
References
- EPFL. (2017). Toehold Designer. Available at: https://2017.igem.org/Team:EPFL/Software