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opentrons-integration

Generate Opentrons Protocol API v2 Python protocols for OT-2 and Flex robots.

Updated May 24, 2026
Search Tags:#python#thermocycler#lab automation#opentrons#liquid handling#protocol api v2#robot deck layout
One-click install
npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill opentrons-integration-estrella-231
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: opentrons-integration
Source: https://github.com/Estrella-231/Mathematical_modeling_tongmeng/tree/main/.agents/skills/opentrons-integration
Command: npx skills add https://github.com/Estrella-231/Mathematical_modeling_tongmeng --skill opentrons-integration-estrella-231

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Writing reliable, production-ready Opentrons liquid-handling protocols is hard because you must correctly coordinate robot API v2 metadata, deck layout, labware definitions, modules, and tip/liquid handling while avoiding runtime errors.

Core Features & Use Cases

  • Official Opentrons Protocol API v2 workflow: Generates executable Python run() protocols for OT-2 and Flex that include proper protocol metadata and requirements.
  • Liquid handling + module control: Supports pipetting operations (transfer/distribute/consolidate, mixing, air gaps, flow rates) and integrates modules like thermocyclers, heaters/shakers, temperature, and magnetic modules.
  • Deck setup at scale: Manages labware, adapters, multi-channel pipetting patterns, and deterministic simulation-oriented development for validation before running on hardware.

Quick Start

Use this skill to write an Opentrons Protocol API v2 Python protocol for a Flex robot that sets up a thermocycler PCR workflow and performs master-mix distribution followed by sample loading.

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 Python script for a Flex robot?▼

This Skill generates executable Opentrons Protocol API v2 Python protocols for OT-2 and Flex robots by structuring a run(protocol) entry point with correct metadata, deck layout, and pipette transfer primitives for liquid handling workflows.

Can I integrate a thermocycler and heater-shaker module in the same Opentrons protocol?▼

Yes, you can integrate a thermocycler and heater-shaker in the same Opentrons protocol by orchestrating module operations alongside pipetting commands, coordinating hardware modules within the Protocol API v2 framework for automation workflows.

What is the best way to set up deck layout for multi-channel pipetting in Opentrons?▼

The best way to set up deck layout for multi-channel pipetting in Opentrons is to manage labware definitions and adapters programmatically within Protocol API v2, ensuring deterministic simulation-oriented development for validation before hardware execution.

Does Opentrons Protocol API v2 support master-mix distribution and sample loading?▼

Opentrons Protocol API v2 supports master-mix distribution and sample loading through built-in liquid handling primitives including transfer, distribute, and consolidate, with configurable flow rates, mixing, and air gap settings.

Why does my Opentrons liquid handling protocol fail during runtime execution?▼

Opentrons liquid handling protocols fail during runtime execution when protocol API v2 metadata is missing, deck layout is misconfigured, or tip and liquid management settings are incorrectly coordinated with hardware module orchestration.

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