Cypher AI Documentation

This documentation covers CLI setup, instrument connection, Protocol Engine usage, and REST API integration. If you are evaluating Cypher AI for your lab, start with the Quickstart — you can run a protocol end-to-end in under 10 minutes if your instrument data is ready.

What is Cypher AI?

Cypher AI is an operating system for life-science research laboratories. It gives labs a single AI layer that replaces the patchwork of LIMS, ELNs, and custom scripts. The three core modules are:

AI Agent — writes and runs analysis tools on demand from plain-language prompts
Protocol Engine — generates version-controlled, reproducible experimental protocols
Data Fabric — connects instrument outputs and research results into one queryable, traceable layer

Quick navigation

Quickstart

Install the CLI, connect an instrument, and run your first protocol in under 10 minutes.

API Reference

Full REST API documentation: endpoints for protocols, experiments, and agent tasks.

Protocol Engine

Learn how the Protocol Engine works and how to generate, branch, and version protocols.

AI Agent

How to prompt the AI Agent to write and execute analysis tools, and manage the team library.

Prerequisites

Before you begin:

An early access account — request one here; we review applications personally and follow up within 2 business days
Python 3.10+ (for CLI and agent tool execution)
Your instrument's data export path or format (CSV, JSON, or instrument-native; supported connectors listed in Quickstart)

CLI installation

Install the Cypher CLI via pip:

shell

$ pip install cypher-ai
Collecting cypher-ai
Successfully installed cypher-ai-0.4.1

After installing, authenticate with your API key:

shell

$ cypher auth login
Enter your API key: ••••••••••••
Authenticated. Welcome to Cypher AI.

Next steps

Follow the Quickstart guide to connect your first instrument and run a protocol end-to-end. For integration questions, contact the team.