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man4ish merged 1 commit into from
Aug 8, 2026
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docs: fix stale org/repo links, correct plugin count #1

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15 changes: 8 additions & 7 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
> Full AI/Bioinformatics development environment for GPU/DGX machines.
> Built on NVIDIA PyTorch 25.10 with CUDA support.

[![Docker](https://img.shields.io/badge/ghcr.io-omnibioai--dev--env-blue?logo=docker)](https://ghcr.io/man4ish/omnibioai-dev-env)
[![Docker](https://img.shields.io/badge/ghcr.io-omnibioai--dev--env-blue?logo=docker)](https://ghcr.io/omnibioai/omnibioai-dev-env)
[![License](https://img.shields.io/badge/license-Apache%202.0-green)](LICENSE)
[![GPU Required](https://img.shields.io/badge/GPU-required-orange?logo=nvidia)](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html)

Expand Down Expand Up @@ -65,15 +65,15 @@ This is **not** part of the OmniBioAI production stack. It is not:

### Option A — Pull from GHCR (recommended)
```bash
docker pull ghcr.io/man4ish/omnibioai-dev-env:latest
docker pull ghcr.io/omnibioai/omnibioai-dev-env:latest
bash run_ai_dev.sh
```

### Option B — Build locally
```bash
git clone https://github.com/man4ish/omnibioai-dev-docker
git clone https://github.com/OmniBioAI/omnibioai-dev-docker
cd omnibioai-dev-docker
docker build -t ghcr.io/man4ish/omnibioai-dev-env:latest .
docker build -t ghcr.io/omnibioai/omnibioai-dev-env:latest .
bash run_ai_dev.sh
```

Expand Down Expand Up @@ -209,10 +209,11 @@ sc.pl.pca_variance_ratio(adata)
## Part of the OmniBioAI Ecosystem

This dev environment is designed to work alongside the
[OmniBioAI platform](https://github.com/man4ish/omnibioai) —
[OmniBioAI platform](https://github.com/OmniBioAI/omnibioai-workbench)
(checked out locally as `omnibioai/`) —
a unified AI-powered bioinformatics workbench supporting:

- 200+ bioinformatics plugins
- 231 enabled bioinformatics plugins
- RNA-seq, single-cell, spatial omics, variant calling
- TES workflow execution (Slurm, K8s, AWS Batch, Azure)
- RAG-powered literature search (PubMed + FAISS)
Expand All @@ -234,5 +235,5 @@ If you use this environment in your research, please cite:
```
OmniBioAI Dev Environment (2025)
Manish Kumar
https://github.com/man4ish/omnibioai-dev-docker
https://github.com/OmniBioAI/omnibioai-dev-docker
```