jsomics

JSOMICS — Multi-Omics Research Intelligence Platform

Live: https://jsomics.com

AI-powered biomedical research platform combining GEO mRNA-seq DEG analysis, PubMed literature mining, and GPT-4o-mini interpretation into one unified workflow.

What makes JSOMICS different

Most research tools are siloed. You run DESeq2 separately, search PubMed separately, and manually reconcile the results. JSOMICS runs both in parallel and cross-references them automatically — genes confirmed by both expression data AND published literature are surfaced as HIGH CONFIDENCE targets.

Architecture## Core user workflow

  1. Enter a GEO accession (e.g. GSE12345) or search by disease keyword
  2. Platform auto-detects case vs control sample groups
  3. DEG analysis (t-test + BH correction) runs in parallel with PubMed search
  4. Cross-reference engine finds genes confirmed in both tracks
  5. GPT-4o-mini interprets findings and suggests follow-up analyses

API endpoints

Method Path Description
POST /v1/auth/signup Create account
POST /v1/auth/signin Sign in, get JWT
GET /v1/auth/me Current user
GET /v1/users/me Profile + usage stats
GET /v1/users/me/history Query history
POST /v1/research Multi-agent literature research
POST /v1/geo/search Search GEO datasets by keyword
GET /v1/geo/fetch Fetch GEO dataset + sample list
POST /v1/geo/analyse Full DEG + literature + AI analysis
POST /v1/ingest/pubmed Fetch PubMed articles (paid plans)
GET /v1/ingest/status Evidence store record count
GET /health Liveness probe
GET /ready Readiness + DB check

Plans

Plan Queries/day
free 100
researcher 10,000
lab unlimited

Environment variables (set in Vercel dashboard)

Variable Description
SUPABASE_URL https://ajfxbmnzfrrlvzjozygt.supabase.co
SUPABASE_ANON_KEY Supabase public anon key
SUPABASE_SERVICE_ROLE_KEY Supabase service role key (secret)
SUPABASE_JWT_SECRET JWT signing secret
SUPABASE_DATABASE_URL Postgres connection URI (session pooler)
NCBI_EMAIL Email for NCBI rate limit compliance
OPENAI_API_KEY GPT-4o-mini for AI interpretation
ENV production
KV_REST_API_URL Upstash Redis URL (optional, for persistent cache)
KV_REST_API_TOKEN Upstash Redis token (optional)

Local development

pip install -e ".[storage,dev]"
cp .env.example .env
# fill in .env values
uvicorn jsomics_api.main:app --reload --port 8000

Tech stack

FastAPI · Supabase · Vercel · GitHub OAuth · NCBI E-utilities · KEGG REST API · PubChem REST API · GEO FTP · GPT-4o-mini · scipy · statsmodels · pandas · numpy · httpx