opentrons-protocol-agent

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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

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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

1. Protocol Generation: Creates valid .py files for OT-2/Flex.
2. Labware Validation: Checks compatibility of plates and tipracks.
3. Volume Calculation: Automates liquid transfer math (e.g., dilution factors).

Workflow

1. Describe: Provide the experiment details (source, destination, volumes).
2. Generate: The agent uses the opentrons_protocol_template.py or internal logic to draft the script.
3. 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