🧬 GenomeAI

Open-source AI platform for genomics, bioinformatics, biomedical research,
and evidence-based AI powered by public scientific databases and multi-provider LLMs.

🚀 Live Demo

Try GenomeAI right now — no install required. Click the link and use the working application:

🌐 Open the Live Demo → https://genomeai.vercel.app
_{Backend API: https://genomeai-api.onrender.com · free-tier hosts, deployed automatically on every release. See docs/deployment/releases.md for how it works.}

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What is GenomeAI?

GenomeAI is a unified platform that brings together public biological databases, workflow automation, data visualization, and AI-powered analysis — all in one open-source stack.

It connects directly to 18 free public APIs (NCBI, Ensembl, UniProt, ClinVar, gnomAD, PDB, AlphaFold, ChEMBL, PubChem, Reactome, KEGG, STRING, OpenTargets, Monarch, Disease Ontology, DGIdb, Europe PMC, Semantic Scholar) to give researchers instant access to genomic, proteomic, chemical, and clinical data — without expensive licenses or proprietary infrastructure.

Goal: Make biomedical research accessible, reproducible, and AI-augmented for every researcher, clinician, and developer — anywhere in the world.

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Why GenomeAI?

Problem	GenomeAI Solution
Biomedical data is scattered across 100+ databases	Unified connector layer — one API for all sources
Existing tools require expensive licenses	100% open-source, runs on free-tier APIs
No integrated AI for genomic analysis	Multi-provider LLM support (Gemini cloud, Ollama local)
Workflows are manual and error-prone	DAG-based workflow engine with retry, scheduling, and parallel execution
Results are hard to visualize	Built-in genome browser, protein viewer, network graphs, scientific charts
Reproducibility is difficult	Versioned workflows, provenance tracking, audit logs

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Features

Built and Working

Feature	Status
Biological domain models (Genome, Sample, Gene, Variant, Transcript, Protein, …)	✅
REST API with CRUD + enhanced analysis endpoints (24 route modules)	✅
Workflow DAG engine (definitions, steps, dependencies, validation)	✅
Deterministic, parallel DAG execution	✅
Cron-based workflow scheduler	✅
Queue & worker (Redis-backed background execution)	✅
Retry & failure handling (classification, backoff, policies)	✅
18 real external-data connectors (NCBI, UniProt, ClinVar, gnomAD, …)	✅
AI-powered analysis (gene, variant, protein, drug, pathway, disease, literature, multi-domain report) with Gemini + Ollama	✅
Genome browser, protein viewer, network graphs, scientific charts, molecular structure	✅
Live demo — genomeai.vercel.app	✅

Coming Next

Feature	Phase
Knowledge graph (gene-disease-drug-protein associations)	5
More AI providers (OpenAI, Anthropic, Groq, Mistral)	6
PubMed/Europe PMC deep-dive literature QA	6
Plugin SDK and marketplace	7
Full-text ingestion workers (scheduled sync of source databases)	7
Authentication & multi-user organizations	8

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Public Data Sources (Free APIs)

GenomeAI ships with 18 real connectors to free public databases (implemented, live, and tested):

Domain	Sources
Genomic	NCBI E-utilities, Ensembl (VEP)
Protein	UniProt, RCSB PDB, AlphaFold DB
Drug/Compound	ChEMBL, PubChem, DGIdb, Open Targets
Literature	Europe PMC, Semantic Scholar
Pathway	Reactome, KEGG
Network	STRING
Variant	ClinVar, gnomAD
Disease	Disease Ontology, Monarch, Open Targets

See docs/data-integration/ for the live connectors and docs/external-data/MASTER_PLAN.md for the historical full integration plan (including future sources).

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Architecture

┌──────────────────────────────────────────────────────────────────┐
│                         User Interfaces                          │
│         CLI   |   REST API   |   Web UI   |   Python SDK         │
└──────────────────────────────┬───────────────────────────────────┘
                               │
┌──────────────────────────────┴───────────────────────────────────┐
│                     API Gateway (FastAPI)                        │
│           Auth  |  Rate Limiting  |  Validation  |  Audit        │
└──────────────────────────────┬───────────────────────────────────┘
                               │
┌──────────────────────────────┴───────────────────────────────────┐
│                      Orchestration Layer                         │
│  Workflow DAG Engine  |  Cron Scheduler  |  Redis Queue Worker   │
│  (parallel exec)      |  (scheduling)    |  (retry, backoff)    │
└──────────────────────────────┬───────────────────────────────────┘
                               │
┌──────────────┬───────────────┼───────────────┬───────────────────┐
│              │               │               │                   │
│  Biological  │   Data        │   AI/LLM      │   Visualization   │
│  Domains     │   Integration │   Gateway     │   Platform        │
│              │               │               │                   │
│  Genome      │   NCBI        │   Gemini     │   Genome Browser  │
│  Sample      │   Ensembl VEP │   Ollama     │   Protein Viewer  │
│  Gene        │   UniProt     │   (local)    │   Network Graphs  │
│  Variant     │   ClinVar     │              │   Scientific      │
│  Transcript  │   gnomAD      │              │   Charts          │
│  Protein     │   PDB/AlphaFold │            │   3D Molecular    │
│              │   ChEMBL/PubChem │           │                   │
│              │   Reactome/KEGG  │           │                   │
│              │   STRING/OpenTargets│         │                   │
│              │   EuropePMC/S2     │          │                   │
└──────────────┴───────────────┴───────────────┴───────────────────┘
                               │
┌──────────────────────────────┴───────────────────────────────────┐
│                          Storage Layer                            │
│           PostgreSQL  |  Redis  |  Object Storage                 │
└──────────────────────────────────────────────────────────────────┘

See ARCHITECTURE.md for the full technical breakdown.

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Quick Start

# Clone the repository
git clone https://github.com/dsk-dev-ai/GenomeAI.git
cd GenomeAI

# Install all dependencies and start infrastructure
make setup

# Run tests (over 2,150 passing)
make test

# Start the API server
uvicorn genomeai_api.main:app --reload

Requirements: Python 3.12+, Node.js 20+, PostgreSQL 16+, Redis 7+

See docs/development/ for detailed setup guides.

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Tech Stack

Layer	Technology
API	Python 3.12, FastAPI, SQLAlchemy, Pydantic
Database	PostgreSQL 16+, Redis 7+
Workflow Engine	Python asyncio, DAG execution, Redis queue
Frontend	Next.js, React, TypeScript, Tailwind CSS
Visualization	D3.js, Three.js, Cytoscape.js, Mol*
AI/LLM	Gemini (cloud, default gemini-3.6-flash), Ollama (local)
DevOps	Docker, GitHub Actions, Turbo (monorepo)
Testing	pytest (2,150+ tests), biome, ruff, pyright

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Documentation

Topic	Location
Architecture	ARCHITECTURE.md
Roadmap	ROADMAP.md
API Reference	docs/api/
Database Schema	docs/database/
Workflow Engine	docs/workflows/
External Data & APIs	docs/external-data/
AI/ML Guide	docs/ai/
Visualization	docs/visualization/
Decisions	docs/decisions/
Contributing	CONTRIBUTING.md

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Contributing

We welcome contributions from bioinformaticians, software engineers, data scientists, and researchers.

See CONTRIBUTING.md for guidelines.

# Quick contribution workflow
git checkout -b feat/my-feature
make lint make typecheck make test
git commit -m "feat(domain): add my feature"
git push origin feat/my-feature
# Open a Pull Request

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Community

• Live demo: genomeai.vercel.app
• Discussions: GitHub Discussions — Q&A, ideas, show & tell
• Issues: Report a bug · Request a feature
• Code of conduct: CODE_OF_CONDUCT.md
• Security: SECURITY.md

Star History

⭐ Live chart — updates automatically as the repo gains stars. Click the graphic for the interactive view (GitHub restricts public star data, so the embed uses an encrypted star-history.com sealed token).

Sponsor

GenomeAI is built and maintained by Darshan Kachare through NextGenAI Labs.

Sponsorship supports development infrastructure, documentation, and long-term maintenance of this open-source platform.

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License

GenomeAI is open source under the Apache 2.0 License.

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Built with care for the global research community.
GitHub · Discussions · Sponsor