This repository defines a local development workspace and orchestration layer for the OmniBioAI ecosystem, including workflow execution, tool services, LIMS integration, AI-driven bioinformatics applications, and developer-facing utilities.
All services are designed to run locally, without mandatory cloud dependencies, using a shared workspace layout and reproducible startup mechanisms.
Important
This repository does not vendor or embed core application source code. Each major component lives in its own GitHub repository and is referenced here explicitly. This repository acts as a local control plane and workspace coordinator.
Desktop/machine/
├── omnibioai/ # OmniBioAI Workbench (Django core platform)
├── omnibioai-tool-exec/ # TES – Tool Execution Service (local/HPC/cloud)
├── omnibioai-toolserver/ # FastAPI ToolServer (Enrichr, BLAST, etc.)
├── omnibioai-lims/ # Laboratory Information Management System (LIMS)
├── omnibioai-rag/ # RAG-based Bioinformatics Intelligence Service
├── omnibioai_sdk/ # Python SDK for OmniBioAI APIs
├── omnibioai-workflow-bundles/ # Workflow bundles (Nextflow, WDL, Snakemake)
├── aws-tools/ # Cloud & infrastructure helper tools (optional)
├── utils/
│ └── kill_port.sh # Utility to free busy ports
├── smoke_test_stack.sh # Health checks for the full local stack
├── start_stack_tmux.sh # One-command local stack launcher (tmux)
├── db-init/ # Database initialization dumps
│ ├── omnibioai.sql # OmniBioAI core DB
│ └── limsdb.sql # LIMS database
├── docker-compose.yml # Full OmniBioAI local stack (Docker Compose)
├── .env.example # Environment variable template
├── backup/ # Archived / experimental work
└── ai-dev-docker/ # AI & Docker experiments (optional)
Each component must be cloned independently.
| Component | Repository |
|---|---|
| OmniBioAI Workbench | https://github.com/man4ish/omnibioai |
| Tool Execution Service (TES) | https://github.com/man4ish/omnibioai-tool-exec |
| ToolServer | https://github.com/man4ish/omnibioai-toolserver |
| LIMS (OmniBioAI-LIMS) | https://github.com/man4ish/omnibioai-lims |
| RAG Service (OmniBioAI-RAG) | https://github.com/man4ish/omnibioai-rag |
| Workflow Bundles | https://github.com/man4ish/omnibioai-workflow-bundles |
| OmniBioAI SDK | https://github.com/man4ish/omnibioai_sdk |
This repository only orchestrates these projects.
omnibioai_sdk/ provides a lightweight Python SDK for interacting with OmniBioAI APIs, including:
- Object registry access
- Development APIs (
/api/dev/*) - Notebook-based analysis workflows
The SDK is published independently on PyPI and is intended for:
- Jupyter notebooks
- Python scripts
- Workflow tooling
- Programmatic access to the OmniBioAI platform
The SDK is a thin client and does not embed backend logic.
aws-tools/ contains experimental and optional utilities for:
- Cloud execution
- Infrastructure prototyping
- Deployment experiments
These tools are not required for local development and may change independently.
- Single workspace root
- Relative paths only
- No hardcoded absolute paths
- Service isolation via ports
- Restart-safe startup
- Docker ↔ non-Docker parity
This makes the workspace:
- Portable across machines
- Safe to rename or relocate
- Suitable for Docker, HPC, or VM environments
- Stable for long-running research workflows
| Service | Default Port | Description |
|---|---|---|
| OmniBioAI Workbench | 8000 | Django UI, plugins, agents |
| TES | 8080 | Workflow & tool execution |
| ToolServer | 9090 | FastAPI tool APIs |
| OmniBioAI-LIMS | 7000 | LIMS integration |
| MySQL | 3306 | omnibioai + limsdb |
| Redis | 6379 | Celery, Channels |
All ports are configurable via .env.
✅ Clean workspace ✅ Docker + non-Docker parity ✅ Multi-database MySQL ✅ No absolute paths ✅ Production-leaning architecture
This repository acts as the local control plane for the OmniBioAI ecosystem.