OmniBioAI Launcher

A browser-based gateway to interactive analysis environments for the OmniBioAI platform. The launcher operates in two independent modes: opening a specific registry object in your preferred IDE, and starting/stopping long-running IDE services backed by Docker containers.

This repository is intentionally separate from omnibioai-sdk, the pure Python API client. The launcher is the browser entry point; the SDK is for programmatic use inside notebooks and scripts.

---

Overview

Mode	What it does
Object Launch	Browse the registry, select an object, open it in JupyterLab, VS Code, or RStudio with context pre-loaded
IDE Services	Start / stop containerised JupyterLab, RStudio, and VS Code Server from the Launcher UI

The two modes are independent — IDE Services can be used without an object context, and Object Launch works with any running JupyterLab instance.

---

Supported Environments

Environment	Description	Default port
JupyterLab	Full bioinformatics kernel (scanpy, DESeq2, scVelo, cellxgene …)	8888
RStudio	R with Bioconductor — Seurat, DESeq2, scran, monocle3, tidyverse	8787
VS Code Server	Python + R + Nextflow + WDL extensions, all packages from above	8080

---

Quick Start — IDE Services

The fastest way to get all three environments running locally:

# Clone and start
git clone https://github.com/man4ish/omnibioai-launcher.git
cd omnibioai-launcher
docker-compose up -d

Service	URL	Default credential
JupyterLab	http://localhost:8888	token: omnibioai
RStudio	http://localhost:8787	password: omnibioai
VS Code Server	http://localhost:8080	password: omnibioai

Stop all services:

docker-compose down

Override credentials or data paths with environment variables:

JUPYTER_TOKEN=mysecret OMNIBIOAI_DATA_DIR=/data/myproject docker-compose up -d

---

Quick Start — Object Launch

The Launcher UI is a React single-page app served on port 5190.

With a running backend:

cp .env.example .env    # fill in REACT_APP_OMNIBIOAI_BASE_URL and token
npm install
npm start               # dev server at http://localhost:3000

Via Docker:

docker build -t omnibioai-launcher .
docker run -p 5190:5190 omnibioai-launcher

Direct link from any page:

<a href="http://127.0.0.1:5190/?object_id=56d3fc3a-709b-4ed0-bf17-8cb73c6746b0">Analyze</a>

If no object_id is given, the app opens a searchable registry list. Selecting an object shows a detail view (metadata, lineage, job log) and a button to open it in an environment.

---

Pre-installed Packages

JupyterLab (docker/jupyter/Dockerfile)

Base image: jupyter/datascience-notebook:latest

Python — scanpy, anndata, scVelo, squidpy, pyDEA, gseapy, biopython, pysam, cellxgene, leidenalg, harmonypy, decoupler, pydeseq2, omnipath

R / Bioconductor (via conda) — DESeq2, edgeR, limma, Seurat

RStudio (docker/rstudio/Dockerfile)

Base image: rocker/rstudio:4.3.2

Bioconductor — DESeq2, edgeR, limma, Seurat, clusterProfiler, EnhancedVolcano, ComplexHeatmap, SingleCellExperiment, scran, scater, monocle3

CRAN — tidyverse, ggplot2, pheatmap, RColorBrewer, patchwork, cowplot

VS Code Server (docker/vscode/Dockerfile)

Base image: codercom/code-server:latest

Extensions — ms-python.python, REditorSupport.r, nextflow-io.nf-lang, broadinstitute.wdl

Python packages — scanpy, anndata, scVelo, pydeseq2, gseapy, biopython, pysam

---

Architecture

OmniBioAI Studio
      |
Launcher UI  (React, port 5190)
      |
  ┌───┴──────────────────────────┐
  │  Object Launch               │  IDE Services
  │  (registry object context)   │  (container lifecycle)
  └───┬──────────────────────────┘
      |                                  |
  Open object in:               docker-compose up/down
  - JupyterLab  (URL + token)   GET  /api/launcher/status/{tool}
  - VS Code     (env var copy)  POST /api/launcher/start/{tool}
  - RStudio     (.R download)   POST /api/launcher/stop/{tool}

The IdeCard component in the Launcher UI polls GET /api/launcher/status/{tool} every 5 seconds. Clicking Launch calls POST /api/launcher/start/{tool}, polls until the container reports running, then opens the service URL in a new tab. A Stop button appears while the container is running.

---

API Endpoints

Object registry (existing)

Method	Endpoint	Purpose
GET	/api/dev/objects/	Paginated object list (search, type filters)
GET	/api/dev/objects/{id}/	Single object detail
GET	/api/dev/objects/?parent_id={id}	Children / siblings for lineage view
POST	/api/dev/launch/rstudio/	Signal backend to open RStudio after R script download

IDE services (new)

Method	Endpoint	Purpose
GET	/api/launcher/status/{tool}	Container status (running / starting / stopped)
POST	/api/launcher/start/{tool}	Start the IDE container
POST	/api/launcher/stop/{tool}	Stop the IDE container

{tool} is one of jupyter, rstudio, vscode.

All requests carry Authorization: Bearer <token>.

---

Docker Images

Pre-built images are published to the GitHub Container Registry:

ghcr.io/man4ish/omnibioai-jupyter:1.0
ghcr.io/man4ish/omnibioai-rstudio:1.0
ghcr.io/man4ish/omnibioai-vscode:1.0

To rebuild and push:

export CR_PAT=$(gh auth token)
echo $CR_PAT | docker login ghcr.io -u man4ish --password-stdin

for tool in jupyter rstudio vscode; do
  docker build \
    -t ghcr.io/man4ish/omnibioai-${tool}:1.0 \
    -f docker/${tool}/Dockerfile docker/${tool}/
  docker push ghcr.io/man4ish/omnibioai-${tool}:1.0
done

---

Environment Variables

Launcher UI (baked in at build time, prefixed REACT_APP_)

Variable	Default	Purpose
REACT_APP_OMNIBIOAI_BASE_URL	http://127.0.0.1:8000	OmniBioAI backend API base URL
REACT_APP_OMNIBIOAI_TOKEN	dev	Bearer token for all API requests
REACT_APP_JUPYTER_BASE	http://127.0.0.1:8890	JupyterLab host for object-launch URL
REACT_APP_JUPYTER_TOKEN	devtoken	JupyterLab auth token (?token=)
REACT_APP_USE_MOCK	false	Use hardcoded mock data without a backend

docker-compose services (runtime)

Variable	Default	Purpose
JUPYTER_TOKEN	omnibioai	JupyterLab authentication token
RSTUDIO_PASSWORD	omnibioai	RStudio login password
VSCODE_PASSWORD	omnibioai	VS Code Server login password
OMNIBIOAI_DATA_DIR	./data	Host path mounted as /data in all containers
OMNIBIOAI_WORK_DIR	./work	Host path mounted as /work in all containers

---

Development

cp .env.example .env    # edit variables for your local setup
npm install
npm start               # dev server on http://localhost:3000

The proxy field in package.json forwards /api/* calls to http://127.0.0.1:8000, so the OmniBioAI backend must be running locally during development.

Production build:

npm run build
# serve the build/ output with any static file server
npx serve -s build -l 5190

Launcher Docker image (nginx, port 5190):

docker build -t omnibioai-launcher .

# Override backend at build time
docker build \
  --build-arg REACT_APP_OMNIBIOAI_BASE_URL=https://api.omnibioai.com \
  --build-arg REACT_APP_OMNIBIOAI_TOKEN=mytoken \
  -t omnibioai-launcher .

docker run -p 5190:5190 omnibioai-launcher

---

Mock Mode

Set REACT_APP_USE_MOCK=true (or pass ?object_id=test in the URL) to run entirely on hardcoded data without a backend. Useful for UI development and screenshots.

---

Project Structure

omnibioai-launcher/
├── docker/
│   ├── jupyter/
│   │   └── Dockerfile          — JupyterLab + bioinformatics packages
│   ├── rstudio/
│   │   └── Dockerfile          — RStudio + Bioconductor stack
│   └── vscode/
│       └── Dockerfile          — VS Code Server + Python/R/workflow extensions
├── src/
│   ├── App.jsx                 — View logic: list, detail, launcher
│   ├── App.css                 — Dark-theme styles
│   ├── index.js                — React root mount
│   └── components/
│       ├── EnvCard.jsx         — Clickable environment tile (object launch)
│       ├── IdeCard.jsx         — IDE service card with status polling
│       ├── ObjectCard.jsx      — Object metadata display
│       ├── InstallModal.jsx    — Fallback modal when desktop app not found
│       └── Toast.jsx           — Ephemeral status notification
├── public/
│   └── index.html
├── docker-compose.yml          — IDE services orchestration
├── .env.example
├── package.json
├── nginx.conf
└── Dockerfile                  — Launcher UI (React → nginx)

---

License

Apache License 2.0