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