MCP Clinical Research Server

This project exposes an MCP server that can:

search ClinicalTrials.gov for studies by condition or keyword
fetch the latest stock price for a company ticker from Yahoo Finance

Local setup

Create a virtual environment if you want one.
Install dependencies:
python -m pip install -e .
Set your PAT and the server endpoint:
export MCP_PAT="your_personal_access_token" export MCP_ACCESS_URL="http://localhost:8000/mcp" export MCP_HOST="0.0.0.0" export MCP_PORT="8000"
Start the server:
python -m mcp_clinical.server
or:
mcp-clinical

Access pattern

Your MCP client should connect to:

URL: http://localhost:8000/mcp
Auth header: Authorization: Bearer

The server expects the same token in the MCP_PAT environment variable when it starts.

Available tools

server_access_info()
clinical_trials_search(condition, max_results=5)
get_company_price(ticker, range_name="1d")

Example calls

ClinicalTrials.gov

condition: "breast cancer"
max_results: 5

Market ticker

ticker: "AAPL"
range_name: "1d"

Public EC2 deployment

The safest public setup is:

EC2 instance with a public IP or Elastic IP
security group allowing 22, 80, and 443 inbound
NGINX listening on 80/443 and proxying to the MCP app on 127.0.0.1:8000
systemd service running the Python app with MCP_PAT set via a .env file
GitHub Actions on pushes to main that SSHs into the instance and redeploys the app

EC2 setup

Launch an Ubuntu or Amazon Linux 2023 EC2 instance.
Open inbound ports:
- 22 for SSH
- 80 for HTTP
- 443 for HTTPS
Install nginx and Python dependencies on the EC2 VM:

sudo apt-get update
sudo apt-get install -y python3 python3-venv python3-pip git nginx

Clone the repo:

cd /home/ubuntu
git clone git@github.com:Harshahi/ClinicalMCP.git
cd ClinicalMCP
python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -e .
cp .env.example .env

Update .env with a real PAT and your public URL:

MCP_PAT=your-real-pat
MCP_ACCESS_URL=https://your-domain.example.com/mcp
MCP_PUBLIC_URL=https://your-domain.example.com
MCP_HOST=0.0.0.0
MCP_PORT=8000

Configure NGINX to proxy traffic:

sudo tee /etc/nginx/conf.d/clinicalmcp.conf <<'EOF'
server {
    listen 80;
    server_name your-domain.example.com;

    location / {
        proxy_pass http://127.0.0.1:8000;
        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;
    }
}
EOF

sudo nginx -t
sudo systemctl enable --now nginx

Create a systemd service:

sudo tee /etc/systemd/system/clinicalmcp.service <<'EOF'
[Unit]
Description=ClinicalMCP Server
After=network.target

[Service]
WorkingDirectory=/home/ubuntu/ClinicalMCP
EnvironmentFile=/home/ubuntu/ClinicalMCP/.env
ExecStart=/home/ubuntu/ClinicalMCP/.venv/bin/python -m mcp_clinical.server
Restart=always
RestartSec=5
User=ubuntu
Group=ubuntu

[Install]
WantedBy=multi-user.target
EOF

sudo systemctl daemon-reload
sudo systemctl enable --now clinicalmcp.service
sudo systemctl status clinicalmcp.service --no-pager

GitHub Actions deployment to EC2

Add the following repository secrets in GitHub:

EC2_HOST
EC2_USER
EC2_SSH_KEY
MCP_PAT
MCP_PUBLIC_URL

Example workflow:

name: deploy-to-ec2

on:
  push:
    branches: [main]

jobs:
  deploy:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.13'

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .

      - name: Deploy to EC2
        uses: appleboy/ssh-action@v1.1.0
        with:
          host: ${{ secrets.EC2_HOST }}
          username: ${{ secrets.EC2_USER }}
          key: ${{ secrets.EC2_SSH_KEY }}
          script: |
            set -e
            cd /home/ubuntu/ClinicalMCP || git clone git@github.com:Harshahi/ClinicalMCP.git /home/ubuntu/ClinicalMCP
            cd /home/ubuntu/ClinicalMCP
            git pull origin main
            python3 -m venv .venv
            . .venv/bin/activate
            python -m pip install --upgrade pip
            python -m pip install -e .
            cat > .env <<EOF
            MCP_PAT=${{ secrets.MCP_PAT }}
            MCP_ACCESS_URL=${{ secrets.MCP_PUBLIC_URL }}/mcp
            MCP_PUBLIC_URL=${{ secrets.MCP_PUBLIC_URL }}
            MCP_HOST=0.0.0.0
            MCP_PORT=8000
            EOF
            sudo cp infra/clinicalmcp.service /etc/systemd/system/clinicalmcp.service
            sudo systemctl daemon-reload
            sudo systemctl restart clinicalmcp.service
            sudo systemctl reload nginx || true

Notes

Use a public DNS name with HTTPS in front of the EC2 instance if you want a stable public URL.
If you want to terminate TLS at the EC2 load balancer or NGINX layer, install Certbot and configure 443 with Let’s Encrypt.
Keep the PAT in GitHub secrets and never commit it to source control.

MCP Clinical Research Server

MCP Clinical Research Server

Local setup

Access pattern

Available tools

Example calls

ClinicalTrials.gov

Market ticker

Public EC2 deployment

EC2 setup

GitHub Actions deployment to EC2

Notes

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