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 .py files 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.py or 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
1---2name: opentrons-protocol-agent3description: <!--4---5<!--6# COPYRIGHT NOTICE7# This file is part of the "Universal Biomedical Skills" project.8# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>9# All Rights Reserved.10#11# This code is proprietary and confidential.12# Unauthorized copying of this file, via any medium is strictly prohibited.13#14# Provenance: Authenticated by MD BABU MIA1516-->1718---19name: 'opentrons-protocol-agent'20description: 'Generates executable Python protocols for Opentrons OT-2 and Flex robots from natural language descriptions.'21measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.22allowed-tools:23 - read_file24 - run_shell_command25---262728# Opentrons Protocol Agent2930The **Opentrons Protocol Agent** bridges the gap between experimental design and physical execution by translating instructions into Opentrons Python API scripts.3132## When to Use This Skill3334* When you need to automate a liquid handling task (PCR prep, ELISA, serial dilution).35* When you have a text description of a lab protocol and need code for the robot.36* To validate if a requested protocol is feasible with available labware.3738## Core Capabilities39401. **Protocol Generation**: Creates valid `.py` files for OT-2/Flex.412. **Labware Validation**: Checks compatibility of plates and tipracks.423. **Volume Calculation**: Automates liquid transfer math (e.g., dilution factors).4344## Workflow45461. **Describe**: Provide the experiment details (source, destination, volumes).472. **Generate**: The agent uses the `opentrons_protocol_template.py` or internal logic to draft the script.483. **Review**: The user (or a simulator agent) reviews the code for safety.4950## Example Usage5152**User**: "Create a protocol for 1:2 serial dilution in a 96-well plate."5354**Agent Action**:55(Uses an LLM to fill in the template or generate code)56```bash57# Agent writes the file to disk58python3 -m opentrons.simulate generated_protocol.py59```606162<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add biotender-max/opentrons-protocol-agent in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.
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BioTender-max (@biotender-max) published this skill. Their other Agent Skills are listed on their SkillMD profile.
BioTender-max