Automated summary
Translates a natural-language description of a lab experiment into an executable Python script for Opentrons OT-2 and Flex robots.
Strengths
- Produces valid .py files targeting the Opentrons Python API for OT-2 and Flex
- Checks compatibility of the plates and tipracks you specify
- Automates liquid transfer math such as volumes and dilution factors
- Includes a review step and simulation through python3 -m opentrons.simulate
Limitations
- Script quality depends entirely on how precisely the experiment is described
- Validation is limited to the declared labware, with no physical check on the robot
- Does not replace a human safety review before real execution
When you need to automate a liquid handling task (PCR prep, ELISA, serial dilution) and quickly get a runnable script for OT-2 or Flex.
When the protocol relies on hardware Opentrons does not support or requires formal regulatory validation.
Security analysis
CautionThe skill is a legitimate lab automation helper and does not instruct destructive, exfiltrating, or obfuscated actions. However, it uses shell execution and simulates generated Python protocols, so it has meaningful execution risk and should be listed with caution.
- •Declares run_shell_command, allowing command execution in the agent environment.
- •Example runs python3 -m opentrons.simulate generated_protocol.py, which may execute generated Python protocol code.
- •No explicit constraints on where generated files are written or what shell commands are permitted.
- •Contains proprietary/confidential copyright notice and author signature metadata that are unusual for an open skill catalog but not directly malicious.
Examples
Create an Opentrons Flex protocol for a 1:2 serial dilution across a 96-well plate with 200 µL final volume, using a 200 µL tiprack, then simulate it to check labware compatibility.Write an OT-2 Python protocol that sets up 20 µL PCR reactions in a 96-well plate from a master mix and primers, and validate that the plate and tiprack are compatible.Generate a protocol for an ELISA plate prep on the OT-2: transfer samples from a 96-well source plate, add 100 µL of diluted antibody, and include a wash step.name: 'opentrons-protocol-agent' description: 'Generates executable Python protocols for Opentrons OT-2 and Flex robots from natural language descriptions.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:
- read_file
- run_shell_command
Opentrons Protocol Agent
The Opentrons Protocol Agent bridges the gap between experimental design and physical execution by translating instructions into Opentrons Python API scripts.
When to Use This Skill
- When you need to automate a liquid handling task (PCR prep, ELISA, serial dilution).
- When you have a text description of a lab protocol and need code for the robot.
- To validate if a requested protocol is feasible with available labware.
Core Capabilities
- Protocol Generation: Creates valid
.pyfiles for OT-2/Flex. - Labware Validation: Checks compatibility of plates and tipracks.
- Volume Calculation: Automates liquid transfer math (e.g., dilution factors).
Workflow
- Describe: Provide the experiment details (source, destination, volumes).
- Generate: The agent uses the
opentrons_protocol_template.pyor internal logic to draft the script. - Review: The user (or a simulator agent) reviews the code for safety.
Example Usage
User: "Create a protocol for 1:2 serial dilution in a 96-well plate."
Agent Action: (Uses an LLM to fill in the template or generate code)
# Agent writes the file to disk
python3 -m opentrons.simulate generated_protocol.py
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