metadata
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.
Features
💊 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
- AI Backend: Claude 3.5 Sonnet via Anthropic API
- Scientific Skills: K-Dense Claude Scientific Skills
- Data Sources: PubChem, PubMed, UniProt (live APIs)
- Frontend: Streamlit with custom scientific theme
Usage
- Enter your Anthropic API key in the sidebar
- Select an analysis module
- Input your query (compound name, protein, sequence, etc.)
- 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:
- BioPython (sequence analysis)
- RDKit (molecular properties)
- Scanpy (single-cell analysis)
- PubMed/UniProt/ChEMBL APIs
Built By
Excelra Data Sciences - Powering drug discovery with AI-augmented bioinformatics.
Part of the Risentia platform for Bioinformaticians as a Service.
License
MIT License - Free for commercial and non-commercial use.