The application takes in a protein sequence of a length up to 128 amino acids and predicts the secundary structure of the protein. The application uses a Neural Network (machine learning) to make predictions. There are two parts to the application: frontend and backend. The backend was written in Python, and consists of a trained model and a simple web framework (Flask). The frontend was written using React (TypeScript), and is used to as a "communicator" between the user and the prediction model by providing a simple user-friendly user interface.
The dataset we use to train the model was downloaded from kaggle. The dataset contains more than 300 000 rows of cleaned data, but we will only use the rows where the length of the sequence is less than or equal to 128 and has standard amino acids. The columns we are using for training the model are the sequences and their respective secondary sequence (seq and sst3).
It is highly recommended to do this in Windows Subsystem for Linux (WSL) or a VM. Also to use a conda environment. We used a conda environment with python 3.9. To create such an environment simply add the python=3.9 at the end when creating the environment.
Backend uses Flask, which is a simple web framework written in Python. Make sure you are in your correct environment and inside the 'backend' folder, then run these commands.
Install flask
pip install flask
pip install flask_restful
pip install flask_cors
Other necessary installs
pip install tensorflow==2.11.*
pip install pandas
pip install -U scikit-learn
pip install matplotlib
This should be all the prerequisites for the backend.
Make sure npm is installed
sudo apt install npm
Then enter the frontend folder of the project
cd frontend
And run
npm install
This should be all the prerequisites for the frontend.
If the setup is done properly then this is the only thing you have to do every time you wish to start the application.
Make sure you are in the backend folder and in the correct environment then run this command
FLASK_APP=app.py flask run
If the above doesn't work for some reason, you can also try running this:
python3 -m flask run
or this:
python -m flask run
If everything works correctly you should see a message in the terminal saying "Running on http://127.0.0.1:5000" or something simillar.
In a new terminal Make sure you are in the frontend folder then run this command
npm start
The application should now be available for you through localhost. Note that both frontend and backend should be running at the same time on two terminals for it to work properly. Enter any browser with the url "localhost" at port 3000 (localhost:3000), and you should see the application.