Hayat

Synthetic Arab genomics, variant atlas, and precision-medicine research workbench.

RESEARCH SANDBOX — NOT CLINICAL OR DIAGNOSTIC

Hayat is a runnable, safety-bounded reference MVP for synthetic genomics research. It uses fictional or synthetic demo data only and keeps regulated integrations behind documented adapter boundaries.

Architecture

flowchart LR
  Portal[research-portal] --> API[Node HTTP API]
  API --> Core[packages/core deterministic domain engine]
  Core --> Seed[data/samples synthetic fixtures]
  API --> Contracts[OpenAPI 3.1 + JSON Schemas]
  Core -. future adapter .-> Postgres[(PostgreSQL)]
  Core -. future adapter .-> MinIO[(MinIO)]

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MVP features

• Synthetic sample registry and family trio viewer
• Pedigree graph data with fictional consanguinity examples
• Toy Arab variant atlas and frequency lookup
• Consent event simulator with revocation state
• Research report export with clinical limitations

Prerequisites

Tool	Version	Required for
Node.js	20+	API, tests, static portal
npm	bundled with Node	script runner
Docker Compose	v2+	optional service topology validation
GitHub CLI	latest	optional publication and roadmap issues

One-command local setup

npm run verify && npm start

Open http://localhost:4172. The local API also serves /openapi.json.

Environment

Copy .env.example if you want to override defaults.

Variable	Default	Purpose
PORT	4172	Local API and portal port
APP_ENV	development	Runtime mode label
DATA_MODE	synthetic	Documents the demo-data boundary

Demo data

Seed data lives in data/samples/seed.json. It is fictional or synthetic and intentionally small enough for tests and code review.

API examples

curl http://localhost:4172/health
curl http://localhost:4172/v1/families/:id/pedigree

Route	Purpose
POST /v1/samples/import-synthetic	Import a synthetic VCF-like fixture
GET /v1/families/:id/pedigree	Get synthetic family pedigree
GET /v1/variants	List toy variants
POST /v1/prioritization/run	Run toy variant prioritization
GET /v1/prioritization/runs/:id	Get prioritization run
POST /v1/consent/events	Append synthetic consent event
POST /v1/data-access-requests	Create a sandbox data access request
GET /v1/reports/:id	Get a research sandbox report
GET /v1/audit/events	List audit events

Verification

npm run lint
npm run build
npm test
npm run verify

Privacy, safety, and compliance limits

• No real genomic data, health records, diagnosis, treatment recommendation, or clinical decision support.
• Toy variant interpretation requires certified labs, licensed medical geneticists, genetic counseling, ethics approval, and validated pipelines before real use.
• The consent ledger is an educational simulator, not a legal consent-management system.

Read NOT_FOR_PRODUCTION.md, docs/safety-boundaries.md, and docs/security-privacy.md before extending this MVP.

Arabic quick start

Arabic setup notes are in docs/ar/QUICKSTART.md.

Roadmap

• Add GA4GH Beacon-compatible synthetic endpoint
• Implement Phenopackets import/export for toy data
• Create Arabic genetic counseling glossary
• Build synthetic genome fixture generator
• Draft secure enclave architecture note

Contributing

See CONTRIBUTING.md, CODE_OF_CONDUCT.md, and SECURITY.md.

License

Apache-2.0. See LICENSE.