Bio

Try the hosted version here 🙌

Then fork and get building...

Enterprise-grade biomedical research behind a chat interface - Access PubMed, clinical trials, FDA drug labels, and run complex Python analyses through natural language. Powered by specialized biomedical data APIs.

Why Bio?

Traditional biomedical research is fragmented across dozens of databases and platforms. Bio changes everything by providing:

• Comprehensive Medical Data - PubMed articles, ClinicalTrials.gov data, FDA drug labels, and more
• One Unified Search - Powered by Valyu's specialized biomedical data API
• Advanced Analytics - Execute Python code in secure Daytona sandboxes for statistical analysis, pharmacokinetic modeling, and custom calculations
• Interactive Visualizations - Beautiful charts and dashboards for clinical data
• Real-Time Intelligence - Web search integration for breaking medical news
• Local AI Models - Run with Ollama or LM Studio for unlimited, private queries using your own hardware
• Natural Language - Just ask questions like you would to a colleague

Key Features

Powerful Biomedical Tools

• PubMed & ArXiv Search - Access to millions of scientific papers and biomedical research
• Clinical Trials Database - Search ClinicalTrials.gov for active and completed trials
• FDA Drug Labels - Access comprehensive drug information from DailyMed
• Drug Information - Detailed medication data, warnings, and contraindications
• Interactive Charts - Visualize clinical data, drug efficacy, patient outcomes
• Python Code Execution - Run pharmacokinetic calculations, statistical analyses, and ML models

Advanced Tool Calling

• Python Code Execution - Run complex biomedical calculations, statistical tests, and data analysis
• Interactive Charts - Create publication-ready visualizations of clinical data
• Multi-Source Research - Automatically aggregates data from multiple biomedical sources
• Export & Share - Download results, share analyses, and collaborate

Quick Start (Self-Hosted)

Self-hosted mode is the recommended way to run Bio. It provides a complete local environment with:

• No authentication required - Auto-login as dev user
• Local SQLite database - No external database setup needed
• Unlimited queries - No rate limits
• Ollama/LM Studio support - Use local LLMs for privacy and unlimited usage

Prerequisites

• Node.js 18+
• npm or yarn
• Valyu API key (get one at platform.valyu.ai)
• Daytona API key (for code execution)
• Ollama or LM Studio installed (optional but recommended)

Installation

1. Clone the repository

   git clone https://github.com/yorkeccak/bio.git
   cd bio

2. Install dependencies

   npm install

3. Set up environment variables

   Create a .env.local file in the root directory:

   # Enable Self-Hosted Mode
   NEXT_PUBLIC_APP_MODE=self-hosted
   
   # Valyu API Configuration (Required)
   VALYU_API_KEY=your-valyu-api-key
   
   # Daytona Configuration (Required for Python execution)
   DAYTONA_API_KEY=your-daytona-api-key
   DAYTONA_API_URL=https://api.daytona.io
   DAYTONA_TARGET=latest
   
   # Local LLM Configuration (Optional - for unlimited, private queries)
   OLLAMA_BASE_URL=http://localhost:11434   # Default Ollama URL
   LMSTUDIO_BASE_URL=http://localhost:1234  # Default LM Studio URL
   
   # OpenAI Configuration (Optional - fallback if local models unavailable)
   OPENAI_API_KEY=your-openai-api-key

4. Run the development server

   npm run dev

5. Open your browser

   Navigate to http://localhost:3000

   You'll be automatically logged in as dev@localhost with full access to all features.

Self-Hosted Mode Guide

What is Self-Hosted Mode?

Self-hosted mode provides a complete local environment without any external dependencies beyond the core APIs (Valyu, Daytona). It's perfect for:

• Local Development - No Supabase setup required
• Offline Work - All data stored locally in SQLite
• Testing Features - Unlimited queries without billing
• Privacy - Use local Ollama models, no cloud LLM needed
• Quick Prototyping - No authentication or rate limits

How It Works

When NEXT_PUBLIC_APP_MODE=self-hosted:

1. Local SQLite Database (/.local-data/dev.db)

   • Automatically created on first run
   • Stores chat sessions, messages, charts, and CSVs
   • Full schema matching production tables
   • Easy to inspect with sqlite3 .local-data/dev.db

2. Mock Authentication

   • Auto-login as dev user (dev@localhost)
   • No sign-up/sign-in required
   • Unlimited tier access with all features

3. No Rate Limits

   • Unlimited chat queries
   • No usage tracking
   • No billing integration

4. LLM Selection

   • Ollama models (if installed) - Used first, unlimited and free
   • LM Studio models (if installed) - Alternative local option with GUI
   • OpenAI (if API key provided) - Fallback if no local models available
   • See local models indicator in top-right corner with provider switching

Setting Up Ollama (Recommended)

Ollama provides unlimited, private LLM inference on your local machine - completely free and runs offline!

Quick Setup:

1. Download Ollama App

   • Visit ollama.com and download the app for your OS
   • Install and open the Ollama app
   • It runs in your menu bar (macOS) or system tray (Windows/Linux)

2. Download a Model

   • Open Ollama app and browse available models
   • Download qwen2.5:7b (recommended - best for biomedical research with tool support)
   • Or choose from: llama3.1, mistral, deepseek-r1
   • That's it! Bio will automatically detect and use it

3. Use in Bio

   • Start the app in self-hosted mode
   • Ollama status indicator appears in top-right corner
   • Shows your available models
   • Click to select which model to use

Terminal Setup (Advanced):

# Install Ollama
brew install ollama              # macOS
# OR
curl -fsSL https://ollama.com/install.sh | sh  # Linux

# Start Ollama service
ollama serve

# Download recommended models
ollama pull qwen2.5:7b          # Recommended - excellent tool support
ollama pull llama3.1:8b         # Alternative - good performance

Setting Up LM Studio (Alternative)

LM Studio provides a beautiful GUI for running local LLMs - perfect if you prefer visual interfaces over terminal commands!

1. Download LM Studio from lmstudio.ai
2. Download Models - Search for qwen/qwen3-14b or google/gemma-3-12b
3. Start the Server - Click LM Studio menu bar icon -> "Start Server on Port 1234..."
4. Configure Context Window - Set to at least 8192 tokens (16384+ recommended)

Managing Local Database

View Database:

sqlite3 .local-data/dev.db
# Then run SQL queries
SELECT * FROM chat_sessions;
SELECT * FROM charts;

Reset Database:

rm -rf .local-data/
# Database recreated on next app start

Valyu Mode (OAuth Coming Soon)

Note: Valyu OAuth apps will be in general availability soon. Currently client id/secret are not publicly available. Contact contact@valyu.ai if you need access.

Valyu mode provides:

• Full authentication via Valyu Platform OAuth
• Supabase for persistent data storage
• Usage tracking and billing via Valyu Platform
• Rate limiting based on subscription tier

For Valyu mode setup, set NEXT_PUBLIC_APP_MODE=valyu and configure the OAuth credentials. See .env.example for the full list of required variables.

Example Queries

Try these powerful queries to see what Bio can do:

• "What are the latest clinical trials for CAR-T therapy in melanoma?"
• "Find recent PubMed papers on CRISPR gene editing safety"
• "Calculate the half-life of warfarin based on these concentrations"
• "Search for drug interactions between metformin and lisinopril"
• "Analyze Phase 3 clinical trial data for immunotherapy drugs"
• "Create a chart comparing efficacy rates of different COVID-19 vaccines"

With Local Models (Ollama/LM Studio):

• Run unlimited queries without API costs
• Keep all your medical research completely private
• Perfect for sensitive patient data analysis
• Choose your preferred interface: terminal (Ollama) or GUI (LM Studio)

Architecture

• Frontend: Next.js 15 with App Router, Tailwind CSS, shadcn/ui
• AI: OpenAI GPT-5 with function calling + Ollama/LM Studio for local models
• Data: Valyu API for comprehensive biomedical data
• Code Execution: Daytona sandboxes for secure Python execution
• Visualizations: Recharts for interactive charts
• Real-time: Streaming responses with Vercel AI SDK
• Local Models: Ollama and LM Studio integration for private, unlimited queries

Security

• Secure API key management
• Sandboxed code execution via Daytona
• No storage of sensitive medical data
• HTTPS encryption for all API calls
• HIPAA-compliant architecture (when self-hosted)

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Acknowledgments

• Built with Valyu - The unified biomedical data API
• Powered by Daytona - Secure code execution
• UI components from shadcn/ui

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Made with love for biomedical researchers

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