opentrons-integration

Write Opentrons Protocol API v2 Python automation code for OT-2 and Flex liquid handling and module workflows.

4|Updated Mar 2, 2026
One-click install
npx skills add https://github.com/shushuzn/Rairos --skill opentrons-integration-shushuzn
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: opentrons-integration
Source: https://github.com/shushuzn/Rairos/tree/main/skills/opentrons-integration
Command: npx skills add https://github.com/shushuzn/Rairos --skill opentrons-integration-shushuzn

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill helps you write correct, production-ready Opentrons Protocol API v2 instructions so your Flex or OT-2 liquid-handling runs reliably without manual trial-and-error.

Core Features & Use Cases

  • Protocol API v2 structure: define protocol metadata, requirements, and a run() entry point that Opentrons can execute.
  • Deck, labware, instruments, and modules: load pipettes, labware, adapters, and hardware modules (temperature, magnetic, heater-shaker, thermocycler).
  • Liquid handling workflows: execute transfers, distributions, consolidations, mixing, aspiration/dispense flow control, and tip strategy patterns for common assays like serial dilution and PCR setup.
  • Simulation and operational safety: support simulation-aware comments and standard operational controls (pauses, delays, rail lights on Flex).

Quick Start

Use the opentrons-integration skill to generate an Opentrons Protocol API v2 Python protocol that runs a serial dilution on a 96-well plate using a single Flex pipette with efficient tip usage.

Frequently Asked Questions about opentrons-integration

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I write an Opentrons Protocol API v2 script for PCR setup?

To write an Opentrons Protocol API v2 script for PCR setup, define protocol metadata and a run(context) entry point, then load pipettes, labware, and thermocycler modules to execute liquid handling transfers and temperature cycling.

Can I control a heater-shaker and thermocycler in the same Opentrons protocol?

Yes, you can control a heater-shaker and thermocycler in the same Opentrons protocol by loading both hardware modules into your deck configuration and specifying their commands within the run() function.

What's the best way to automate serial dilution on an OT-2 robot?

The best way to automate serial dilution on an OT-2 robot is to use Protocol API v2 to program transfer and mixing steps across a 96-well plate with efficient tip management strategies.

How do I configure labware and pipettes for Opentrons Flex simulations?

You configure labware and pipettes for Opentrons Flex simulations by using Protocol API v2 to load instruments onto the deck and adding simulation-aware comments to verify the workflow without physical execution.

Does Opentrons Protocol API v2 support custom tip management during liquid handling?

Yes, Opentrons Protocol API v2 supports custom tip management during liquid handling by allowing you to define tip strategy patterns for transfers, distributions, and consolidations.

Why does my Opentrons protocol require a run(context) function?

Your Opentrons protocol requires a run(context) function because Protocol API v2 uses this entry point to execute automation commands, load labware, and control modules during the robot's operation.