opentrons-integration

Opentrons Integration — Laboratory Automation Protocol Development Skills

Skill Overview

Opentrons Integration is a Python protocol development skill designed specifically for Opentrons Flex and OT-2 lab robots. It provides full Protocol API v2 support, helping researchers and automation engineers write efficient liquid-handling automation protocols.

Use Cases

1. PCR Experiment Automation

Use a thermocycler module to automatically prepare PCR reaction mixtures and control temperature cycling. It supports complex PCR temperature-varying programs and is suitable for high-throughput gene amplification experiments in molecular biology laboratories.

2. Continuous Dilution and High-Throughput Screening

Perform precise continuous dilution operations, with support for batch liquid handling in 96-well plates. It is suitable for scenarios such as drug discovery, biological activity screening, and enzyme kinetics studies that require processing large numbers of samples.

3. Multi-Channel Pipetting and Plate Handling

Use an 8-channel pipette to process an entire column of samples simultaneously, greatly improving experimental efficiency. It is especially suitable for parallel workflows such as ELISA detection, cell culture, and standard curve preparation.

Core Features

1. Full Support for Protocol API v2

Provides complete Opentrons Protocol API v2 interfaces, supporting protocol metadata definition, hardware loading, liquid-handling operations, and module control. All protocols are written in Python, with concise, intuitive syntax that is easy to learn and maintain.

2. Integrated Control of Hardware Modules

Integrate and control hardware modules such as the temperature module, magnetic module, heater-shaker, and thermocycler. It supports complex experiment workflow orchestration and enables end-to-end automation from sample preparation to detection.

3. Protocol Simulation and Validation

Built-in simulation mode allows virtual testing of protocols before running them on a real robot. It verifies pipetting paths, volume distribution, and timing schedules to avoid equipment collisions and liquid errors, ensuring safe and reliable experiments.

Frequently Asked Questions

What is an Opentrons protocol? How do I write one?

An Opentrons protocol is an automation experiment script written in Python that defines the robot’s sequence of actions. To write a protocol, first import protocol_api, define metadata including the protocol name, author, and API level, then in the run() function load hardware (pipettes, labware, modules) and execute liquid-handling operations. Protocols support simulation tests to verify the logic before real execution.

What’s the difference between Opentrons Flex and OT-2?

Flex is Opentrons’ next-generation robot, supporting a wider range of labware and more advanced module integration, using Flex-specific pipettes and API. OT-2 is a mature, stable platform with a wide selection of pipettes, making it suitable for migrating existing protocols. Both platforms support Protocol API v2, but hardware models and slot layouts differ; when writing protocols, you need to specify robotType in requirements.

How do I use Opentrons for PCR automation?

Use the thermocycler module to automate PCR experiments. First load the thermocyclerModuleV2 module and the PCR plate. Then use the pipette to distribute the master mix and samples into each well. Next, set the lid temperature and the PCR cycling program (denaturation, annealing, and extension temperatures and times). The API supports defining multiple cycling steps and hold times, enabling precise control of ramp rates and cycle counts to achieve fully automated PCR from reaction setup through amplification.