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Opentrons Protocol Integration

Authors, reviews, migrates, and simulates Opentrons Python Protocol API v2 protocols for Flex and OT-2 lab robots.

AutomationAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Helps you write, review, migrate, and debug Python Protocol API v2 protocols for Opentrons liquid-handling robots (Flex and OT-2).

  • Correct requirements/metadata blocks per robot type plus an API-level gate table (2.15–2.29)
  • Explicit deck building: slot assignment, exact labware load names, adapters, trash bins and waste chute, modules (Thermocycler, Absorbance Plate Reader, Flex Stacker, gripper paths)
  • Pipette and tip selection, plus choosing the right liquid-handling layer (transfer, distribute, consolidate, liquid classes, dynamic mixing)
  • Runtime parameters (including CSV), and resource budgeting for tips, dead volume, and destination capacity
  • Layered validation: py_compile → pinned local opentrons_simulate → Opentrons App analysis → operator-reviewed dry run
  • A curated list of common failure modes (legacy pipette names, duplicated apiLevel, API 2.29 on OT-2, deprecated Well.load_liquid())

Six bundled template scripts (basic transfer, serial dilution, PCR setup, runtime parameters, plate reader) and seven reference documents ship with the skill.

Who it's for

  • Lab scientists and automation engineers operating Opentrons Flex or OT-2
  • Teams updating older protocols to current robot software
  • Reviewers who need a repeatable safety and code-review checklist

Example uses

  1. "Write an API 2.29 Flex protocol that distributes 100 µL of buffer from a 12-channel reservoir into a 96-well plate" → generates code with valid load names and an explicit trash bin.
  2. "Migrate this OT-2 API 2.13 protocol to 2.28 and give me the simulation command" → applies the migration reference plus uv run --with "opentrons==9.0.0" opentrons_simulate.
  3. "My plate reader read fails" → diagnoses the initialize()-before-read() sequence and other known pitfalls.

· · · Install guide · · ·

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 skills/opentrons-integration folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/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/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/opentrons-integration ~/.claude/skills/

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

  1. Install Python 3.10+ and uv for local simulation.
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills folder: mkdir -p ~/.claude/skills
  4. Copy the skill in: cp -r scientific-agent-skills/skills/opentrons-integration ~/.claude/skills/
  5. Restart Claude Code and ask something like "write an Opentrons Flex protocol for a serial dilution" to trigger the skill.
  6. Verify simulation: uv run --with "opentrons==9.1.1" opentrons_simulate protocol.py (use opentrons==9.0.0 for OT-2).
  7. Never run on hardware until the protocol passes analysis in the matching Opentrons App and you complete an operator-reviewed dry run.
View source on GitHub ↗License: MIT