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Opentrons Lab Automation Integration

Writes and validates Python protocols for Opentrons OT-2/Flex robots — pipetting, serial dilutions, PCR, and hardware module control.

AutomationIntermediate★ 368⑂ 39AI score 8/10Last updated: Sep 29, 2026

What it does

  • Generates protocols that follow the required Opentrons Protocol API v2 structure (metadata dict + run() function).
  • Produces correct labware/tip-rack/pipette loading plus transfer, distribute, consolidate, mix, air_gap, touch_tip patterns with exact API names.
  • Controls temperature, magnetic, heater-shaker and thermocycler modules, including multi-cycle PCR profiles.
  • Explains OT-2 vs Flex differences (deck slot naming, pipette models, module generations) so protocols stay hardware-compatible.
  • Ships a troubleshooting table for OutOfTipsError, deck collisions, volume overruns, and bad labware API names.

Who it's for

  • Life-science and chemistry lab staff running an Opentrons OT-2 or Flex
  • Grad students and researchers converting repetitive pipetting into code
  • Anyone who wants to dry-run protocols with opentrons_simulate before touching hardware
  • Multi-vendor labs (Hamilton, Beckman, Tecan) should pair this with a pylabrobot skill

Example uses

  1. "Build a serial dilution protocol across row A of a 96-well plate" → diluent distribution plus mix_after transfers.
  2. "Set up a 35-cycle PCR run on the thermocycler" → master-mix distribution, sample addition, and execute_profile.
  3. "Automate a magnetic bead cleanup" → engage/disengage sequence with repeated wash steps and a simulation command to verify it.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/jaechang-hits/SciAgent-Skills/HEAD/legacy/opentrons-integration/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the legacy/opentrons-integration folder from the GitHub repo jaechang-hits/SciAgent-Skills into my ~/.claude/skills/jaechang-hits-opentrons-integration/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/jaechang-hits/SciAgent-Skills.git && mkdir -p ~/.claude/skills && cp -r SciAgent-Skills/legacy/opentrons-integration ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repository: git clone https://github.com/jaechang-hits/SciAgent-Skills.git
  2. Create the Claude skills directory: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r SciAgent-Skills/legacy/opentrons-integration ~/.claude/skills/
  4. Install the Opentrons Python package: pip install opentrons
  5. Restart Claude Code and ask something like "write an Opentrons PCR protocol" to trigger the skill.
  6. Always validate generated files with opentrons_simulate my_protocol.py before uploading to a real robot.
View source on GitHub ↗License: NOASSERTION