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Opentrons Lab Robot Protocols

Write, review, simulate and troubleshoot Opentrons Flex and OT-2 lab-robot Python protocols

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
15 files

What it does

This skill teaches an AI agent how to write and check Python programs that control Opentrons lab robots, which move liquids between plates and tubes automatically. Once installed, the agent follows the official Opentrons Protocol API v2 rules for Flex and OT-2 robots, picks correct labware, pipettes and modules, uses runtime parameters, and simulates the protocol locally before any physical run. It also insists on a safety checklist (App analysis, operator review, dry run with nonhazardous liquid) before anything touches real hardware.

Great for

  • Lab automation engineers writing liquid-handling protocols for Opentrons Flex or OT-2
  • Researchers migrating older OT-2 scripts to newer API versions
  • Teams reviewing or troubleshooting existing Opentrons protocols before a run

Skip it if

  • Running a protocol on a physical robot without a trained operator: simulation cannot verify calibration, liquid behaviour, or collisions, and the skill says so explicitly
  • Multi-vendor lab workflows: the skill itself recommends PyLabRobot for those
  • Hazardous or clinical workflows without site biosafety review: the templates are examples, not validated methods

Try asking

  • “Write a Flex protocol that transfers 100 µL from a reservoir into a 96-well plate using a 1000 µL single-channel pipette”
  • “Migrate my OT-2 API 2.13 script to a current API level and explain what changed”
  • “Review this Opentrons protocol for tip, volume and deck-slot errors before I import it into the App”
  • “Create a runtime-parameter version of this PCR setup so my lab tech can change sample count”
Step-by-step guide: how to use Opentrons Lab Robot ProtocolsInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 15 original files, the MIT licence and an attribution note.

    opentrons-integration.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip opentrons-integration.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip opentrons-integration.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Always state your robot model, pipettes, modules and labware load names up front; the skill asks for them before writing final code
  • Simulate with the same pinned opentrons version you authored with, then import into the correct Opentrons App and confirm analysis succeeds
  • Treat template volumes, temperatures and cycle settings as placeholders and validate them with a nonhazardous dry run before any wet-lab use

What's inside

  • references/api_reference.md
  • references/liquid_handling.md
  • references/migration-api-2-19-to-2-29.md
  • references/modules_and_deck.md
  • references/protocol_authoring.md
  • references/sources.md
  • references/validation_and_operations.md
  • requirements-flex.txt
  • requirements-ot2.txt
  • scripts/absorbance_reader_template.py
  • scripts/basic_protocol_template.py
  • scripts/ot2_basic_protocol_template.py
  • scripts/pcr_setup_template.py
  • scripts/runtime_parameters_template.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.