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LeonChaoX
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opentrons-integration

Generate Opentrons Protocol API v2 scripts for Flex and OT-2 liquid handling.

783|65|Updated Feb 27, 2026
Search Tags:#thermocycler#lab automation#opentrons#liquid handling#pcr setup#protocol api v2#robot protocol
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill opentrons-integration-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: opentrons-integration
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/13-%E5%AE%9E%E9%AA%8C%E5%AE%A4%E8%87%AA%E5%8A%A8%E5%8C%96%E4%B8%8E%E9%9B%86%E6%88%90/opentrons-integration
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill opentrons-integration-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill helps you write correct, robot-ready Opentrons Protocol API v2 scripts that reliably automate liquid handling on Flex and OT-2 hardware, reducing manual protocol development and runtime surprises.

Core Features & Use Cases

  • Protocol API v2 templates and structure: Create metadata, requirements, and a proper run(protocol) entrypoint for ProtocolContext.
  • End-to-end labware + instrument + module control: Load pipettes, labware, adapters, and modules (temperature, magnetic, heater-shaker, thermocycler).
  • Safe liquid handling patterns: Implement transfers, distributions, serial dilutions, mixing, air gaps, flow-rate tuning, and tip management for common assay workflows like PCR setup.

Quick Start

Ask your AI agent to generate an Opentrons Protocol API v2 (Flex or OT-2) protocol that performs a 96-well serial dilution on a labeled deck layout, including tip strategy and a simulation-first workflow.

Frequently Asked Questions about opentrons-integration

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

FAQPage Schema
How do I generate an Opentrons Protocol API v2 script for serial dilutions on the OT-2?▼

To generate an Opentrons Protocol API v2 script for serial dilutions, define metadata, load pipettes and labware, and use distribution and mixing commands with proper tip management. This ensures accurate liquid handling workflows on OT-2 hardware.

Can I use the Opentrons thermocycler module for PCR setup in my protocol?▼

Yes, you can use the Opentrons thermocycler module for PCR setup. Protocol API v2 supports loading and controlling hardware modules, enabling thermocycler cycling, temperature control, and magnetic separation within your automated liquid handling scripts.

What is the best way to structure a production-grade robot protocol for Flex and OT-2?▼

The best way to structure a production-grade robot protocol is to start with ProtocolContext requirements, define metadata, load instruments and adapters, and implement validated pipetting commands including flow-rate tuning and air gaps for reliable Flex and OT-2 automation.

Does Opentrons Protocol API v2 support heater-shaker and temperature modules?▼

Opentrons Protocol API v2 supports heater-shaker and temperature modules. You can load these hardware modules onto the deck layout and integrate their execution steps with liquid handling commands for comprehensive assay automation.

Why does my Opentrons protocol fail during tip management and liquid transfers?▼

Opentrons protocols often fail during liquid transfers due to incorrect tip strategy or missing air gaps. Implementing safe liquid handling patterns, including proper tip pickup, flow-rate tuning, and disposal, prevents runtime surprises and ensures accurate pipetting.

Do I need Python to automate lab workflows with Opentrons Flex and OT-2?▼

Yes, you need Python to automate lab workflows with Opentrons Flex and OT-2. Protocol API v2 scripts are written in Python, requiring specific metadata, dependencies, and a run(protocol) entrypoint to execute validated pipetting commands on the robot.

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