OmniBioAI Studio

Desktop orchestration platform for AI-powered bioinformatics computation

OmniBioAI Studio is an Electron desktop app that launches and manages the full OmniBioAI stack — locally, on HPC clusters, or in the cloud — with a single click.

✨ What's New in v0.2.0-beta

License key system — 30-day trial keys (OMNI-XXXX-XXXX-XXXX-XXXX format)
Sentry error tracking — automatic error reporting across all services
Bug report button — 🐛 in-app bug reporting via Studio UI
Cython IP protection — core business logic compiled to .so binaries
MySQL-backed license server — license validation with MySQL persistence
DEV_MODE flag — replaces BETA_MODE for cleaner build configuration
500+ bioinformatics tools — 350 HTTP API tools + 144 Slurm execution tools
Windows installer — NSIS .exe installer added alongside DMG and AppImage
Zero-trust security control plane — JWT authentication + RBAC/ABAC policy enforcement on every request
API Gateway — single enforced entry point for all service traffic
HPC Policy Engine — per-user GPU/CPU quota governance
Security Audit Service — async audit logging via Redis Streams (user, action, decision, latency, trace ID)
Redis token caching — validated tokens cached (TTL=300s) with pub/sub invalidation on logout
Internal service header propagation (X-Internal-Service, X-Trace-Id, X-User-Id) across all TES calls
Fail-closed on auth/policy/HPC failure; fail-open on audit (never blocks requests)
RAG V6 FAISS index — persistent vector store with recursive document indexing for large literature corpora

v0.1.0-beta.1

Full local stack launch with containerized services
Live service health monitoring (Control Center)
Docker image dashboard (platform + plugin images)
Dev Hub with knowledge graph + RAG UI
SDK Launcher for OmniBioAI Python SDK
Mode-aware startup: Local / HPC / Cloud / Hybrid
LLM configuration: Ollama (local) + Claude API + OpenAI
Cloud execution: AWS Batch / Azure Batch / GCP Batch / Kubernetes
HPC execution: Slurm / PBS / LSF via TES

📦 Downloads

Platform	File	Requirements
macOS (M1/M2/M3/M4)	OmniBioAI-Studio-arm64.dmg	macOS 12+
macOS (Intel)	OmniBioAI-Studio-x64.dmg	macOS 12+
Linux	OmniBioAI-Studio.AppImage	Ubuntu 20.04+
Windows	OmniBioAI-Studio-Setup.exe	Windows 10/11

Download from: https://github.com/man4ish/omnibioai-studio/releases/latest

🔐 Security Control Plane

All requests are enforced through a zero-trust pipeline:

Internet / Client
       ↓
api-gateway :8080     ← single entry point, JWT enforcement
       ↓
auth-service :8001    ← JWT validation + Redis cache (TTL=300s)
       ↓
policy-engine :8002   ← RBAC/ABAC authorization decision
       ↓
hpc-policy-engine :8003  ← GPU/CPU quota check (compute requests only)
       ↓
target service (workbench / tes / toolserver / rag)
       ↓
security-audit :8004  ← async audit log → Redis Streams (never blocks)

Failure policy:

Layer	On failure
Auth	FAIL CLOSED → HTTP 401
Policy	FAIL CLOSED → HTTP 403
HPC quota	FAIL CLOSED → HTTP 403
Audit	FAIL OPEN → ignored

🖥 Services

Service	Port	Description
API Gateway	:8080	Zero-trust entry point — auth + policy + HPC enforcement
Auth Service	:8001	JWT issuance, validation, refresh, logout
Policy Engine	:8002	RBAC/ABAC authorization decisions
HPC Policy Engine	:8003	GPU/CPU quota governance per user/team
Security Audit	:8004	Async audit logging via Redis Streams
Workbench	:8000	Main bioinformatics platform (Django)
TES	:8081	Task Execution Service (Slurm / AWS / Azure / GCP / K8s)
ToolServer	:9090	FastAPI bioinformatics tool server
Model Registry	:8095	ML model versioning and serving
LIMS	:7000	Lab Information Management System
Control Center	:7070	Service health + Docker image dashboard
RAG	:8090 (ext) / :8096 (int)	PubMed literature AI + DeepSeek RAG (V6 FAISS, persistent vector store)
Dev Hub	:5173 / :8082	Knowledge graph + embeddings UI
Workflow Bundles	:8098	WDL/Nextflow/Snakemake/CWL workflow bundle server
Tool Images	:8097	Bioinformatics tool image registry
Videos	:8086	Tutorial and demo video server
SDK Launcher	:5190	OmniBioAI Python SDK UI
Ollama	:11434	Local LLM inference
OPA	:8181	Open Policy Agent (policy rules backend)

Plugin images (pulled on-demand by TES)

Image	Description
`omnibioai-plugin-scanpy`	Single-cell RNA-Seq analysis
`omnibioai-plugin-fastq-qc`	FASTQ quality control (FastQC + MultiQC)
`omnibioai-plugin-fastq-trimmer`	Read trimming (Trimmomatic)
`omnibioai-plugin-rnaseq-analysis`	Bulk RNA-Seq (DESeq2/edgeR)
`omnibioai-plugin-workflow-runner`	WDL/Nextflow/Snakemake/CWL execution
`omnibioai-plugin-variant-annotation`	Variant annotation (SnpEff/ANNOVAR)
`omnibioai-plugin-marker-identification`	Marker gene identification
`omnibioai-plugin-phenotype-association`	GWAS + phenotype association

🧰 Bioinformatics Tools (500+)

HTTP API Tools (350)

Direct REST API integrations — no compute needed:

Genomics: Ensembl, NCBI, ClinVar, gnomAD, dbSNP
Proteins: UniProt, AlphaFold, PDB, InterPro
Pathways: KEGG, Reactome, WikiPathways, GO
Literature: PubMed, Europe PMC, Semantic Scholar
Drugs: ChEMBL, DrugBank, PharmGKB, OpenFDA
Single Cell: CellxGene, HCA, Broad SCP
Metabolomics: HMDB, LipidMaps, MetaboAnalyst
And 280+ more across all omics domains

Slurm/HPC Tools (144)

Compute-heavy tools executed on HPC/cloud:

Alignment: BWA, STAR, HISAT2, Minimap2
Variant Calling: GATK, DeepVariant, Clair3, Mutect2
RNA-seq: DESeq2, edgeR, Salmon, Kallisto
Single Cell: Seurat, Scanpy, Cell Ranger
ML/AI: PyTorch, TensorFlow, ESM2, AlphaFold2
Proteomics: MSFragger, MaxQuant, DIA-NN
And 90+ more

🧬 Bioinformatics Modules

Core Platform

Home · OnboardAI · Omni Assistant · Job Monitor · Plugin Manager · Admin

Workflows

Workflow Runner · Workflow Builder · Agent Studio · Pipeline Dashboard · Multi-Agent Bio Orchestrator · Workflow Compiler

Omics Analysis

RNA-Seq · Single Cell (scRNA-Seq) · Exome Analysis · FASTQ QC · Proteomics · Metabolomics

AI & Intelligence

Drug Target AI · Literature AI · Pathway Enrichment · Bio Hypothesis AI · Bio Narrator AI

Learn

Getting Started · Tutorials · Demo Workflows · Example Pipelines · Developer Hub · Videos

📋 Requirements

Requirement	Minimum	Recommended
RAM	16GB	32GB
Disk	50GB free	100GB free
Docker	Engine 24+	Docker Desktop
OS	Ubuntu 20.04+	Ubuntu 22.04+
GPU	—	NVIDIA + nvidia-container-toolkit

Also required:

jq — sudo apt install jq or brew install jq
Docker Compose v2 — included with Docker Engine 24+

🚀 Quick Start

Stack only (headless / no Electron)

git clone https://github.com/man4ish/omnibioai-studio
cd omnibioai-studio
cp .env.example .env
# Edit .env — fill in your paths and secrets
docker compose up -d

Then register your first user and get a token:

# Register
curl -X POST http://localhost:8001/auth/register \
  -H "Content-Type: application/json" \
  -d '{"email":"admin@example.com","password":"yourpassword","full_name":"Admin"}'

# Login — returns JWT token
curl -X POST http://localhost:8001/auth/login \
  -H "Content-Type: application/json" \
  -d '{"email":"admin@example.com","password":"yourpassword"}'

# Use token through gateway
curl -H "Authorization: Bearer <token>" http://localhost:8080/api/tools

Linux (AppImage)

chmod +x "OmniBioAI-Studio.AppImage"
./"OmniBioAI-Studio.AppImage"

Enter your license key when prompted
Select execution mode (Local recommended for first run)
Set Data Directory and Work Directory in Settings
Click Boot System on the Launch page
Open Workbench at http://localhost:8000

From source

npm install
npm run dev              # development mode
npm run build            # build AppImage (Linux)
npm run build:mac        # build DMG (macOS)
npm run build:win        # build EXE (Windows)

🔑 License & Access

OmniBioAI Studio requires a license key for first launch.

Getting a License

Contact: mandecent.gupta@gmail.com for beta access

License Key Format

OMNI-XXXX-XXXX-XXXX-XXXX (30-day trial)

First Launch Flow

Download installer (DMG / AppImage / EXE)
Launch OmniBioAI Studio
Enter license key when prompted
App validates key against license server
Platform pulls images from ghcr.io automatically
Studio launches — ready to use!

Offline Grace Period

License is cached locally for 7 days offline use.

🔑 Environment Variables

Copy .env.example to .env and fill in:

# Database
MYSQL_ROOT_PASSWORD=your-db-password
MYSQL_DEFAULT_DB=omnibioai

# Auth (change in production)
AUTH_SECRET_KEY=your-secret-key-here

# Network
HOST_IP=0.0.0.0

# Paths (absolute paths on host)
DB_INIT_DIR=/path/to/omnibioai-studio/db-init
WORKSPACE_HOST=/path/to/workspace
WORK_DIR=/path/to/work
DATA_DIR=/path/to/data
VIDEO_DIR=/path/to/videos

# AI API Keys (optional)
ANTHROPIC_API_KEY=
OPENAI_API_KEY=

# Build
DEV_MODE=false

# Error reporting (set empty to disable)
SENTRY_DSN=

🔗 GHCR Authentication

Private service images require authentication. Beta users receive a GitHub token automatically with their license key.

Manual setup:

export GITHUB_TOKEN=your_github_personal_access_token
export GITHUB_USER=your_github_username
echo $GITHUB_TOKEN | docker login ghcr.io -u $GITHUB_USER --password-stdin

Token needs read:packages scope.

Public images (no auth needed):

omnibioai-base (3.4GB — heavy dependencies, pull once)
omnibioai-dev-env
omnibioai-tool-runtime
All omnibioai-plugin-* images (122 plugins)

Private images (token required):

omnibioai-app (~170MB — app code only, fast updates)
All core service images

🐛 Error Reporting

OmniBioAI Studio includes built-in error reporting via Sentry.

Click the 🐛 Report Bug button in the Studio UI
Fill in title, description and severity
Report sent automatically to our dashboard
We'll respond within 24 hours during beta

To disable: set SENTRY_DSN= (empty) in .env

☁️ Execution Backends

Local

CPU/GPU execution via Docker
NVIDIA GPU support with nvidia-container-toolkit

HPC

Slurm — cluster job submission via TES
PBS / LSF — alternative schedulers
Apptainer/Singularity — container runtime for HPC
SSH-based remote execution

Cloud

AWS Batch — S3 input/output, IAM profiles
Azure Batch — Blob storage, managed identity
GCP Batch — Cloud Storage, service accounts
Kubernetes — any K8s cluster via kubeconfig

LLM

Ollama — local inference (Llama, DeepSeek, Mistral, etc.)
Claude API — Anthropic cloud API
OpenAI — GPT-4 and compatible APIs

🏗 Architecture

┌─────────────────────────────────────────┐
│        OmniBioAI Studio                 │
│     Electron + React (Wizard UI)        │
└──────────────┬──────────────────────────┘
               │ IPC
               ▼
┌─────────────────────────────────────────┐
│        Electron Main Process            │
│  - Config manager (JSON)                │
│  - Docker Compose lifecycle             │
│  - Health check polling                 │
│  - Log streaming                        │
└──────────────┬──────────────────────────┘
               │ docker compose
               ▼
┌─────────────────────────────────────────┐
│     Security Control Plane              │
│  API Gateway · Auth · Policy Engine     │
│  HPC Policy · Security Audit · Redis    │
└──────────────┬──────────────────────────┘
               │ verified requests only
               ▼
┌─────────────────────────────────────────┐
│        Docker Compose Runtime           │
│  Workbench · TES · ToolServer           │
│  Model Registry · LIMS · RAG            │
│  Control Center · Dev Hub · SDK         │
└──────────────┬──────────────────────────┘
               │
               ▼
┌─────────────────────────────────────────┐
│        Execution Backends               │
│  Local GPU/CPU · Slurm/PBS/LSF          │
│  AWS Batch · Azure Batch · GCP          │
│  Kubernetes · Ollama · Claude API       │
└─────────────────────────────────────────┘

⚙ Configuration

Studio stores config at:

Linux: ~/.config/omnibioai/omnibioai.config.json
macOS: ~/Library/Application Support/omnibioai-studio/omnibioai.config.json

Key settings:

{
  "mode": "local",
  "settings": {
    "data_dir": "/path/to/omnibioai/data",
    "work_dir": "/path/to/omnibioai/work"
  },
  "llm": {
    "enable_ollama": true,
    "enable_claude": false,
    "claude_api_key": "",
    "enable_openai": false
  },
  "cloud": {
    "enable_aws_batch": false,
    "enable_gcp_batch": false,
    "gcp_project": "",
    "gcp_region": ""
  },
  "hpc": {
    "enabled": false,
    "scheduler": "slurm",
    "hostname": "hpc.university.edu",
    "username": "",
    "private_key": "~/.ssh/id_rsa"
  }
}

🔗 OmniBioAI Ecosystem

OmniBioAI Studio is the desktop control layer for:

Repository	Role
`omnibioai`	Main Django workbench + 80+ plugins
`omnibioai-api-gateway`	Zero-trust API gateway
`omnibioai-auth`	JWT authentication service
`omnibioai-policy-engine`	RBAC/ABAC authorization
`omnibioai-hpc-policy-engine`	GPU/CPU quota governance
`omnibioai-security-audit`	Async audit logging
`omnibioai-iam-client`	Python SDK for auth integration
`omnibioai-tes`	Task Execution Service
`omnibioai-toolserver`	FastAPI tool API
`omnibioai-lims`	Lab data management
`omnibioai-model-registry`	ML model versioning
`omnibioai-control-center`	Health + image dashboard
`omnibioai-rag`	PubMed RAG pipeline
`omnibioai-dev-hub`	Knowledge graph + embeddings
`omnibioai-workflow-bundles`	WDL/Nextflow/Snakemake bundles
`omnibioai-tool-images`	80+ bioinformatics tool containers
`omnibioai_sdk`	Python SDK + React launcher
`omnibioai-dev-docker`	DGX/GPU development environment
`omnibioai-security-sdk`	Security SDK for service auth integration
`omnibioai-design-tokens`	Shared design tokens and theme system
`omnibioai-ui`	Shared UI component library
`omnibioai-landing`	Public-facing landing page

🗺 Roadmap

v0.2.0-beta — Current Release ✅

License key system (OMNI-XXXX-XXXX-XXXX-XXXX, 30-day trial)
Sentry error tracking + in-app bug report button
Cython IP protection (.so compiled binaries)
MySQL-backed license server
DEV_MODE flag (replaces BETA_MODE)
500+ bioinformatics tools (350 HTTP API + 144 Slurm)
Windows NSIS .exe installer
Zero-trust JWT authentication on every request
RBAC/ABAC policy engine
HPC quota governance
Async audit logging via Redis Streams
Redis token caching with pub/sub invalidation
Internal service header propagation

v0.3 — Beta Launch (July 4th 2026 target)

DMG + AppImage + EXE installers via GitHub Actions
Auto-updater for all platforms
Cloudflare-integrated beta signup with automatic license delivery
Public beta announcement

v0.4 — Cloud & HPC

AWS/Azure/GCP job submission UI
Cost estimation per workflow
Multi-tenant workspace isolation

v0.5 — Enterprise

SSO / SAML integration
Role management UI
HIPAA compliance reporting from audit logs
Cost attribution per user/team

🖥 Platform Notes

ARM machines (Apple Silicon, AWS Graviton): Some service images were built for linux/amd64. They run via emulation on ARM with a warning:

The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8)

This is expected and harmless for development. For production ARM deployments, rebuild affected images with --platform linux/arm64.

🐛 Known Issues (Beta)

System MySQL/Redis must be stopped before starting: sudo systemctl stop mysql redis-server
GITHUB_TOKEN must be set manually for private image pull
macOS DMG not yet code-signed (GateKeeper warning expected)
Windows installer not yet code-signed
Kubernetes health check requires ~/.kube/config
policy-engine and hpc-policy-engine do not expose a /health endpoint (returns 404, services are running)
License server requires MySQL (included in docker-compose)
First launch requires internet connection for license validation
7-day offline grace period after initial validation
Bug reports sent to Sentry (can be disabled via SENTRY_DSN= in .env)

📄 License

Apache 2.0 — see LICENSE

👤 Author

Manish Kumar — GitHub

OmniBioAI Studio is not a bioinformatics tool — it is a desktop orchestration system for distributed, secure, AI-native scientific computation.

Name		Name	Last commit message	Last commit date
Latest commit History 133 Commits
.github/workflows		.github/workflows
backend		backend
build		build
db-init		db-init
docker		docker
electron		electron
monitoring		monitoring
scripts		scripts
src		src
tests/integration		tests/integration
.coverage		.coverage
.dockerignore		.dockerignore
.env.example		.env.example
.gitignore		.gitignore
CONTRIBUTING.md		CONTRIBUTING.md
DEPLOYMENT.md		DEPLOYMENT.md
LICENSE		LICENSE
README.md		README.md
docker-compose.release.yml		docker-compose.release.yml
docker-compose.yml		docker-compose.yml
docker-compose.yml.bak.20260605_154518		docker-compose.yml.bak.20260605_154518
electron-builder.json		electron-builder.json
index.html		index.html
package.json		package.json
postcss.config.js		postcss.config.js
slurm_results.json		slurm_results.json
tailwind.config.js		tailwind.config.js
test_integration.sh		test_integration.sh
vite.config.js		vite.config.js

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OmniBioAI Studio

✨ What's New in v0.2.0-beta

v0.1.0-beta.1

📦 Downloads

🔐 Security Control Plane

🖥 Services

Plugin images (pulled on-demand by TES)

🧰 Bioinformatics Tools (500+)

HTTP API Tools (350)

Slurm/HPC Tools (144)

🧬 Bioinformatics Modules

Core Platform

Workflows

Omics Analysis

AI & Intelligence

Learn

📋 Requirements

🚀 Quick Start

Stack only (headless / no Electron)

Linux (AppImage)

From source

🔑 License & Access

Getting a License

License Key Format

First Launch Flow

Offline Grace Period

🔑 Environment Variables

🔗 GHCR Authentication

🐛 Error Reporting

☁️ Execution Backends

Local

HPC

Cloud

LLM

🏗 Architecture

⚙ Configuration

🔗 OmniBioAI Ecosystem

🗺 Roadmap

🖥 Platform Notes

🐛 Known Issues (Beta)

📄 License

👤 Author

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