ASPred, Antibody Specificity Predictor

ASPred (Antibody Specificity Predictor) is an innovative computational strategy developed to predict antigen-specific B-cell receptors (BCRs)

Features

• User registration with email verification
• reCAPTCHA protection for registration
• One sequence submission per day limit
• Sequence validation (amino acids only, max 130 length)
• Results tracking and viewing

Development Setup

1. Create a conda environment:

conda create -n aspred python=3.11
conda activate aspred

2. Install dependencies:

pip install -r requirements.txt

3. Apply migrations:

python manage.py migrate

4. Run development server:

python manage.py runserver

Production Deployment

1. Clone the repository to your production server

2. Install dependencies:

pip install -r requirements.txt

3. Create a .env file based on env.prod.example:

cp env.prod.example .env

4. Edit the .env file with your production settings:

• Generate a new Django secret key
• Configure your MySQL database credentials
• Set up your email backend credentials
• Add your reCAPTCHA keys (get them from Google reCAPTCHA)

5. Create required directories:

mkdir logs
mkdir staticfiles

6. Collect static files:

python manage.py collectstatic --settings=labsite.settings_prod

7. Apply migrations:

python manage.py migrate --settings=labsite.settings_prod

8. Set up Gunicorn: Create a systemd service file (e.g., /etc/systemd/system/labsite.service):

[Unit]
Description=Laboratory Sequence Analyzer
After=network.target

[Service]
User=www-data
Group=www-data
WorkingDirectory=/path/to/your/project
Environment="PATH=/path/to/your/virtualenv/bin"
EnvironmentFile=/path/to/your/project/.env
ExecStart=/path/to/your/virtualenv/bin/gunicorn --workers 3 --bind unix:/run/labsite.sock labsite.wsgi:application

[Install]
WantedBy=multi-user.target

9. Set up Nginx: Create a Nginx configuration file (e.g., /etc/nginx/sites-available/labsite):

server {
    listen 80;
    server_name yourwebsite.com www.yourwebsite.com;
    return 301 https://$server_name$request_uri;
}

server {
    listen 443 ssl;
    server_name yourwebsite.com www.yourwebsite.com;

    ssl_certificate /path/to/your/certificate.pem;
    ssl_certificate_key /path/to/your/private.key;

    location = /favicon.ico { access_log off; log_not_found off; }
    
    location /static/ {
        root /path/to/your/project;
    }

    location / {
        include proxy_params;
        proxy_pass http://unix:/run/labsite.sock;
    }
}

10. Start services:

sudo systemctl start labsite
sudo systemctl enable labsite
sudo systemctl restart nginx

Security Notes

• Always use HTTPS in production
• Keep your .env file secure and never commit it to version control
• Regularly update dependencies
• Monitor logs for any security issues
• Back up your database regularly