| # Quickstart Guide | |
| Get DeepBoner running in 5 minutes. | |
| ## Prerequisites | |
| - Python 3.11+ installed | |
| - Repository cloned and dependencies installed (see [Installation](installation.md)) | |
| ## 1. Start the Application | |
| ```bash | |
| # From the repository root | |
| uv run python src/app.py | |
| ``` | |
| You should see: | |
| ``` | |
| Running on local URL: http://127.0.0.1:7860 | |
| ``` | |
| ## 2. Open the UI | |
| Navigate to http://localhost:7860 in your browser. | |
| You'll see a chat interface with: | |
| - Input field for research questions | |
| - Optional API key input (for premium features) | |
| - Research results display | |
| ## 3. Ask Your First Question | |
| Try one of these example queries: | |
| ``` | |
| What drugs improve female libido post-menopause? | |
| ``` | |
| ``` | |
| Clinical trials for ED alternatives to PDE5 inhibitors? | |
| ``` | |
| ``` | |
| Evidence for testosterone therapy in women with HSDD? | |
| ``` | |
| ## 4. Understanding the Output | |
| DeepBoner will: | |
| 1. **Search** multiple biomedical databases: | |
| - PubMed (peer-reviewed literature) | |
| - ClinicalTrials.gov (active/completed trials) | |
| - Europe PMC (preprints and papers) | |
| - OpenAlex (scholarly metadata) | |
| 2. **Judge** evidence quality using LLM | |
| 3. **Loop** if more evidence is needed | |
| 4. **Synthesize** a research report with citations | |
| You'll see status updates as each phase completes. | |
| ## 5. Free vs Premium Mode | |
| ### Free Mode (No API Key) | |
| - Uses HuggingFace Inference API | |
| - Model: Qwen 2.5 7B Instruct | |
| - Slower but fully functional | |
| ### Premium Mode (With OpenAI Key) | |
| - Enter your OpenAI API key in the UI | |
| - Uses GPT-5 for better synthesis | |
| - Faster and more detailed reports | |
| To use premium mode: | |
| 1. Get an API key from [OpenAI](https://platform.openai.com) | |
| 2. Enter it in the "OpenAI API Key" field | |
| 3. Your queries will automatically use GPT-5 | |
| ## 6. Using MCP Tools | |
| DeepBoner exposes MCP (Model Context Protocol) tools for integration with Claude Desktop and other clients. | |
| ### MCP Server URL | |
| ``` | |
| http://localhost:7860/gradio_api/mcp/ | |
| ``` | |
| ### Available Tools | |
| - `search_pubmed` - Search peer-reviewed literature | |
| - `search_clinical_trials` - Search clinical trials | |
| - `search_europepmc` - Search Europe PMC | |
| - `search_all_sources` - Search all sources with deduplication | |
| ### Claude Desktop Configuration | |
| Add to your `claude_desktop_config.json`: | |
| ```json | |
| { | |
| "mcpServers": { | |
| "deepboner": { | |
| "url": "http://localhost:7860/gradio_api/mcp/" | |
| } | |
| } | |
| } | |
| ``` | |
| ## Example Scripts | |
| For programmatic usage, see the example scripts: | |
| ```bash | |
| # Search demo | |
| uv run python examples/search_demo/run_search.py | |
| # Full orchestrator demo | |
| uv run python examples/orchestrator_demo/run_agent.py | |
| # Multi-agent demo (requires OpenAI key) | |
| uv run python examples/orchestrator_demo/run_magentic.py | |
| ``` | |
| ## Next Steps | |
| - [Configuration Guide](configuration.md) - Customize settings | |
| - [MCP Integration](../deployment/mcp-integration.md) - Set up Claude Desktop | |
| - [Architecture Overview](../architecture/overview.md) - Understand how it works | |
| ## Troubleshooting | |
| **Slow first response?** | |
| - First query loads ML models (sentence-transformers) | |
| - Subsequent queries are faster | |
| **No results?** | |
| - Check your internet connection | |
| - External APIs may have rate limits | |
| **Rate limit errors?** | |
| - Add NCBI_API_KEY for higher PubMed limits | |
| - Wait and retry | |
| See [Troubleshooting](troubleshooting.md) for more help. | |