A collection of toxicology workflows for research and analysis. This portal provides tools and workflows for toxicology research, including hazard prediction, data management, and more.

• Project Overview
• Services
• Development Setup
• Production Setup
• Troubleshooting
• Roadmap
• Tech Stack
• Contributing
• License

Toxindex Portal is designed to streamline toxicology research by providing a unified interface for running workflows, managing data, and visualizing results. It integrates modern web technologies with robust backend services for a seamless research experience.

add your user to the docker group sudo usermod -aG docker $USER and reboot to take it effect. type "groups" in terminal and see if "docker" is in the list

# Clean up previous environments (if needed)
rm -rf .venv ~/.cache/uv
unset LD_LIBRARY_PATH

# Enter development environment
nix develop

# Install frontend dependencies
cd frontend && npm install

Development Commands:

• Start Flask app:

  python -m webserver.app

• Start redis listener:

  python redis_listener_standalone.py

• Start Celery worker:

  celery -A workflows.celery_worker worker --loglevel=info -Q celery,probra,openai,raptool,pathway
  
  celery -A workflows.celery_worker_probra worker --loglevel=info -Q probra
  celery -A workflows.celery_worker_raptool worker --loglevel=info -Q raptool
  celery -A workflows.celery_worker_ranking worker --loglevel=info -Q ranking
  celery -A workflows.celery_worker_plain worker --loglevel=info -Q openai
  celery -A workflows.celery_worker_sparql worker --loglevel=info -Q sparql

• Start frontend:

  cd frontend && npm run dev

• Run Redis Listener

python redis_listener_standalone.py

=======

ssh kyu-ubuntu30

sudo dd if=/dev/zero of=/swapfile bs=1M count=1024
sudo chmod 600 /swapfile
sudo mkswap /swapfile
sudo swapon /swapfile
echo '/swapfile swap swap defaults 0 0' | sudo tee -a /etc/fstab

# Clear RAM cache
sudo sync; sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'

# Check RAM usage
free -h

cd toxindex && nix develop

cd frontend && npm install
npm run build

sudo apt update
sudo apt install nginx

• Create Nginx config file:

  sudo nano /etc/nginx/conf.d/toxindex.conf

  Example config:

  server {
      listen 80;
      server_name 18.118.10.140; # Use 'localhost' for dev
  
      root /home/ubuntu/toxindex/frontend/dist;
      index index.html;
  
      location / {
          try_files $uri /index.html;
      }
  
      location /api/ {
          proxy_pass http://127.0.0.1:6513;
          proxy_set_header Host $host;
          proxy_set_header X-Real-IP $remote_addr;
          proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
          proxy_set_header X-Forwarded-Proto $scheme;
      }
  
      location /socket.io/ {
          proxy_pass http://127.0.0.1:6513;
          proxy_http_version 1.1;
          proxy_set_header Upgrade $http_upgrade;
          proxy_set_header Connection "upgrade";
          proxy_set_header Host $host;
          proxy_set_header X-Real-IP $remote_addr;
          proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
          proxy_set_header X-Forwarded-Proto $scheme;
      }
  }

• Test config:

  sudo nginx -t

• Set permissions to expose frontend static files to Nginx:

  sudo chown -R ubuntu:www-data /home/kyu/toxindex/frontend/dist
  sudo chmod -R 755 /home/kyu/toxindex/frontend/dist
  sudo chmod -R o+rx /home/kyu/toxindex/frontend/dist
  sudo chmod o+x /home/kyu

• Reload Nginx:

  sudo systemctl reload nginx

• Create a systemd Service File for backend sudo nano /etc/systemd/system/toxindex-backend.service

[Unit] Description=Toxindex Backend Service After=network.target

[Service]

User=kyu WorkingDirectory=/home/kyu/toxindex

ExecStart=/usr/bin/bash -c 'source /home/kyu/toxindex/.venv/bin/activate && python -m webserver.app'

Restart=on-failure RestartSec=5

[Install] WantedBy=multi-user.target

• Create a systemd Service File for celery worker sudo nano /etc/systemd/system/toxindex-celery.service

[Unit] Description=Toxindex Celery Worker After=network.target

[Service] User=kyu WorkingDirectory=/home/kyu/toxindex Environment="PATH=/home/kyu/.nix-profile/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" ExecStart=/usr/bin/bash -c 'cd /home/kyu/toxindex && nix develop --command celery -A workflows.celery_worker worker --loglevel=info' Restart=on-failure RestartSec=5

[Install] WantedBy=multi-user.target

Reload systemd sudo systemctl daemon-reload

Start the Service sudo systemctl start toxindex-backend sudo systemctl start toxindex-celery

Enable the Service at Boot sudo systemctl enable toxindex-backend sudo systemctl enable toxindex-celery

Check Status and Logs

Check status: sudo systemctl status toxindex-backend sudo systemctl status toxindex-celery

• If a port is in use:

  lsof -i :8000
  kill <PID>

The basic workflow:

1. Users create environments.
2. Users execute workflows in their environments.

• Users can predict hazard with toxtransformer.
• Example: User enters prompt: "Is PFOA hepatotoxic?"
• System creates a task, adds it to a table, sends it to the workflow, and creates a webhook for activities/results.

• Frontend: React, Tailwind CSS, Vite, TypeScript
• Backend: Flask, Eventlet, Celery, Postgres, Flyway
• Data: Langchain, Agno, Scikit-learn

Contributions are welcome! Please open issues or submit pull requests for improvements.

Distributed under the MIT License. See LICENSE for more information.