# Opentrons Integration

Official Opentrons Protocol API for OT-2 and Flex robots.

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: Writing
- License: Unknown
- Last updated: 2026-10-30
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill opentrons-integration -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill opentrons-integration -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill opentrons-integration -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill opentrons-integration -g -a gemini-cli -y`

## Description

Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Opentrons Integration

## Overview

Opentrons is a Python-based lab automation platform for Flex and OT-2 robots. Write Protocol API v2 protocols for liquid handling, control hardware modules (heater-shaker, thermocycler), manage labware, for automated pipetting workflows.

## When to Use This Skill

This skill should be used when:
- Writing Opentrons Protocol API v2 protocols in Python
- Automating liquid handling workflows on Flex or OT-2 robots
- Controlling hardware modules (temperature, magnetic, heater-shaker, thermocycler)
- Setting up labware configurations and deck layouts
- Implementing complex pipetting operations (serial dilutions, plate replication, PCR setup)
- Managing tip usage and optimizing protocol efficiency
- Working with multi-channel pipettes for 96-well plate operations
- Simulating and testing protocols before robot execution

## Core Capabilities

### 1. Protocol Structure and Metadata

Every Opentrons protocol follows a standard structure:

```python
from opentrons import protocol_api

# Metadata
metadata = {
    'protocolName': 'My Protocol',
    'author': 'Name <email@example.com>',
    'description': 'Protocol description',
    'apiLevel': '2.19'  # Use latest available API version
}

# Requirements (optional)
requirements = {
    'robotType': 'Flex',  # or 'OT-2'
    'apiLevel': '2.19'
}

# Run function
def run(protocol: protocol_api.ProtocolContext):
    # Protocol commands go here
    pass
```

**Key elements:**
- Import `protocol_api` from `opentrons`
- Define `metadata` dict with protocolName, author, description, apiLevel
- Optional `requirements` dict for robot type and API version
- Implement `run()` function receiving `ProtocolContext` as parameter
- All protocol logic goes inside the `run()` function

### 2. Loading Hardware

**Loading Instruments (Pipettes):**

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/opentrons-integration/SKILL.md