Welcome to the Dry Lab
Bridging the gap between theory and experimentation.
The Dry Lab team of ARGUS-2440 was responsible for the computational and modeling aspects of our project. Our efforts range from modelling the kinetics of our pathway, to using machine learning to make predictions about soil data. We have also created a GenBank alternative to improve user experience, and have also used AlphaFold to predict protein structures to aid our Wet Lab team.
Our Computational Workflow
Modeling
An ODE to ammonifiers, using system of ordinary differential equations to predict the efficiency of our bacterium.
GenBank Improvised
Our team of future iGEM'ers collaborated to create an alternative to GenBank, GenBank Improvised. The problems in GenBank, which include a lack of user-friendly interface, poor accuracy in search results and limitations in visualisation were addressed in GenBank Improvised. This was also a great learning experience for our juniors, who were introduced to multiple real-world applications of coding.
Machine Learning
We built model based on machine learning to predict the concentration of ammonium in soil, by inputting various initial soil conditions. The model was trained on a dataset consisting of various soil parameters, like temperature, pH, C/N ratio, particle size, location, etc. and the corresponding ammonium concentration. The model was able to predict the ammonium concentration to a fairly accurate degree, considering the complexity of the soil conditions and interactions of various components.
Alphafold
We used AlphaFold2, a deep learning model developed by Google DeepMind, to make predictions about the 3D structure of proteins based on the amino acid sequences. This was done to aid our Wet Lab team in making decisions about performing experiments on the integration of genes responsible for nitrite reductase activity. The information provided by the software helped in predicting how similar the modified protein is to the native protein, and thus helped in evaluating the risk of extraneous DNA sequences interfering with the functioning of the protein.