Synthetic logic gates in python format & preliminary database integration

Abstract

The human body is host to many biological processes that are important to us. As a result researchers have constantly been characterizing the biological processes that happen within the cell. However there is a problem where characterization unfortunately has steps that take a significant amount of time to perform. Using synthetic biology however, it is possible to create and store synthetic parts which are made from already characterized parts. With a large enough database, it would be possible to mix and match whatever parts that are needed to run a new characterization entirely on a computer, thus greatly decreasing the amount of time needed. This project was conducted to create a system in python code format for ease of use and affordability. The initial systems chosen were logic gates as they were relatively simple systems to design. Four synthetic logic gates in python code format were created and stored in a database for easy retrieval. The four logic gates: NOT, OR, NOR and AND gates were designed using information from journal papers and tested in simulink and python. Results indicated that they were successfully verified to be functional and subsequently successfully integrated with another student’s database code. Future directions involve searching for more parameters and better designs from more papers online and also include the idea of using mutagenesis to change specific values to values that were naturally not possible so that a wider range of variable testing might be possible.