| --- |
| title: BioAgent - AI Bioinformatics Demo |
| emoji: 🧬 |
| colorFrom: blue |
| colorTo: green |
| sdk: docker |
| app_file: app.py |
| pinned: false |
| license: mit |
| --- |
| |
| # 🧬 BioAgent: AI-Powered Bioinformatics |
|
|
| **BioAgent** demonstrates AI-augmented bioinformatics workflows combining Claude's reasoning capabilities with real scientific database APIs. |
|
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| ## Features |
|
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| ### 💊 Drug Discovery Pipeline |
| - Search compounds via PubChem API (real data) |
| - Lipinski's Rule of Five assessment |
| - AI-powered drug-likeness analysis |
| - 2D structure visualization |
|
|
| ### 🧬 Sequence Analysis |
| - UniProt protein search (real data) |
| - Amino acid composition analysis |
| - AI-powered sequence interpretation |
| - Hydrophobicity and structure predictions |
|
|
| ### 🎯 Patient Stratification (NEW) |
| - Multi-omics integration (GEX, Mutations, CNV) |
| - Interactive UMAP patient clustering |
| - Modality attention visualization |
| - Kaplan-Meier survival analysis |
| - Biomarker discovery pipeline |
| - AI-generated clinical insights |
|
|
| ### 📚 Literature Intelligence |
| - PubMed search integration (real data) |
| - AI-synthesized research summaries |
| - Theme and gap identification |
| - Citation management |
|
|
| ### 🔬 Single-Cell Analysis Demo |
| - Interactive UMAP visualization |
| - Cluster statistics |
| - AI-powered biological interpretation |
|
|
| ## Technology Stack |
|
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| - **AI Backend**: Claude 3.5 Sonnet via Anthropic API |
| - **Scientific Skills**: [K-Dense Claude Scientific Skills](https://github.com/K-Dense-AI/claude-scientific-skills) |
| - **Data Sources**: PubChem, PubMed, UniProt (live APIs) |
| - **Frontend**: Streamlit with custom scientific theme |
|
|
| ## Usage |
|
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| 1. Enter your Anthropic API key in the sidebar |
| 2. Select an analysis module |
| 3. Input your query (compound name, protein, sequence, etc.) |
| 4. Get AI-augmented insights combined with real data |
|
|
| ## Skills Integration |
|
|
| This demo implements Claude Scientific Skills as **context injection** - loading relevant SKILL.md documentation into the system prompt so Claude follows domain-specific best practices for: |
|
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| - BioPython (sequence analysis) |
| - RDKit (molecular properties) |
| - Scanpy (single-cell analysis) |
| - PubMed/UniProt/ChEMBL APIs |
|
|
| ## Built By |
|
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| **Excelra Data Sciences** - Powering drug discovery with AI-augmented bioinformatics. |
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| Part of the **Risentia** platform for Bioinformaticians as a Service. |
|
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| ## License |
|
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| MIT License - Free for commercial and non-commercial use. |
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|
