Team:Calgary/Software
Overview
In a fast-paced world like today, we need systems that can keep up with the ever changing world. Software programs can help address this issue. Within the field of synthetic biology, software programs are developed to solve problems regarding proteins and biological organisms through methods like machine learning, specifically neural networks.
Software Goals
Birnam Wood
When proceeding with modelling for the packed absorber column, we realized that the kinetic rate constants of the forward and reverse reactions of lanmodulin’s binding to lanthanides is needed. Although, the current lack of characterization of lanmodulin's properties makes literature review an infeasible method of extracting these parameters. Additionally, results from the lab were unobtainable due to barriers to resources and lab access. Thus we set out to implement a system that can predict these rate constants using protein structure alone with a high degree of accuracy. We’re introducing Birnam Wood, a program which offers accurate rate constant predictions without inhibitive requirements of supplies or expertise.
Learn more here.
Access the code on the iGEM Github here.
EF Hand Evaluator (EFHE)
When better characterizing lanmodulin, we found that one of the binding pockets shows potential for weak binding capabilities in addition to the three known pockets. .Additionally, when trying to optimize lanmodulin’s fourth binding pocket we needed a way to evaluate if it contained the EF hand binding motif seen in the other pockets. Therefore, we needed a program to identify the presence of the EF hand binding motif, and potentially improve on them. This led us to create EFHE, a program that utilizes deep machine learning through a network consisting of a long short term memory layer with a bi-convolutional layer. The program is able to find the locations of the ef hands based on a protein sequence alone, and evaluate them.
Learn more here.
Access the code on the iGEM Github here.
Lumos
Optical biosensors such as luminometers are often expensive and complicated to use. In order to provide a cost-effective solution to our lanthanide measurement problem, we developed Lumos. This luminometer features a modular design, which facilitates future hardware revisions and component replacements. Lumos is also equipped with Bluetooth Low Energy capability to wirelessly provide information to an Android phone. Usability and efficiency was paramount to developing a user interface for Lumos.
Learn more here.
Access the code on the iGEM Github here.
Misadventures of LanE
In an effort to help spread the word about the growing e-waste problem, we created an educational video game using the Ren'Py game engine. Learn more here.
