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opentrons-integration

Design and execute Opentrons Protocol API v2 workflows for OT-2 and Flex robots.

33.0k|3.2k|Updated Oct 19, 2025
Search Tags:#automation#lab-automation#pipetting#opentrons#protocol-design#protocol-api-v2
One-click install
npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill opentrons-integration-k-dense-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: opentrons-integration
Source: https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/scientific-skills/opentrons-integration
Command: npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill opentrons-integration-k-dense-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Opentrons Protocol API v2 automation enables scientists and developers to programmatically define and run pipetting workflows, module control, and lab automation with reproducible results.

Core Features & Use Cases

  • Protocol structure and metadata: define metadata, requirements, and a run(protocol) function for clean, repeatable workflows.
  • Hardware & modules: load and control pipettes, labware, temperature, magnetic, heater-shaker, thermocycler, and absorbance modules.
  • Liquid handling: perform aspirate, dispense, transfer, distribute, and consolidate operations with tip management and flow control.
  • Protocol templates: reuse templates (basic, PCR setup, serial dilution) to accelerate automation development.
  • Use case: convert a manual protocol into an OT-2 or Flex automation that executes a 96-well plate transfer automatically.

Quick Start

Write a simple protocol that transfers 50 µL from well A1 to B1 using a P300 and a 96-well plate.

Frequently Asked Questions about opentrons-integration

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

FAQPage Schema
How do I automate pipetting workflows using Opentrons Protocol API v2?▼

Automate pipetting workflows by defining protocol metadata and a run function that loads labware, instruments, and modules to execute precise liquid handling operations. This skill structures your code for OT-2 and Flex robots to ensure reproducible automation.

Can I control temperature, magnetic, and heater-shaker modules with Opentrons protocols?▼

Yes, you can control temperature, magnetic, heater-shaker, thermocycler, and absorbance reader modules. The skill configures these hardware modules within your protocol to manage complex lab automation orchestration and experimental conditions.

What is the best way to structure an Opentrons protocol for reproducible lab automation?▼

The best way to structure an Opentrons protocol is to define metadata, specify deck requirements, and implement a run(protocol) function. This API-compliant structure ensures clean, repeatable workflows and enables debugging across experiments.

Does Opentrons protocol design support aspirate, dispense, and transfer operations with tip management?▼

Yes, Opentrons protocol design supports aspirate, dispense, transfer, distribute, and consolidate operations. It handles tip management and flow control to perform precise liquid handling across your labware during automated experiments.

How do I convert a manual 96-well plate transfer into an OT-2 or Flex automation protocol?▼

Convert a manual 96-well plate transfer by loading a 96-well plate and a pipette, then programming the transfer operation in the run function. The skill provides templates like basic, PCR setup, and serial dilution to accelerate automation development.

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