omicOS User Guide
A single-cell / spatial-omics analysis workbench —— powered by multi-agent LLMs, built on top of OmicVerse
What is this
omicOS is a workbench that brings together "multi-agent large language models" and "single-cell / spatial-omics analysis." You describe your analysis intent in natural language, and omicOS's team of agents automatically calls tools like OmicVerse and scanpy to produce real code, charts, and results inside a shared IPython kernel.
It is made up of three parts, and this guide is organized around them:
| Module | Address | Corresponding part of this guide |
|---|---|---|
| omicos-core | Local command line / daemon (Rust binary) | Part 1: Setup and Usage |
| omicOS UI | app.omicos.cn | Part 2: Illustrated Walkthrough |
| omicOS Server UI | auth.omicos.cn | Part 3: Account and Server-Side Management |
How to read this guide
- Part 1 shows you how to install omicOS on your own computer or server: installation, configuring environment variables, signing in to your cloud account, running remotely over SSH / HPC, and advanced usage of every command-line option. If you want to run an analysis, start here.
- Part 2 uses plenty of application screenshots to walk you through every feature of the app.omicos.cn web interface, step by step.
- Part 3 uses screenshots to explain how to configure and use the account and server-side management pages at auth.omicos.cn.
📌 This preview release includes Part 1 (English) only, for review. Parts 2 and 3 will be filled in over time as illustrated, screenshot-based walkthroughs.
Quick start in three steps
# 1. Install omicos (via npm, the easiest way)
npm install -g @omicverse/omicos
# 2. Sign in to your cloud account
omicos login
# 3. Start the server and open the web interface
omicos serve
# the browser opens https://app.omicos.cn automatically
For the details of each step, other installation methods, and server scenarios, head to Part 1.