Opentrons Python Protocol API

Overview

The Opentrons Protocol API v2 lets you write liquid handling protocols as plain Python files that run on OT-2 or Flex robots. Every protocol defines a metadata dictionary, an optional requirements dictionary, and a run(protocol) function. The ProtocolContext object passed to run() exposes all deck setup, pipette operations, module control, and utility methods. Protocols can be simulated on any computer with opentrons_simulate before uploading to the robot through the Opentrons App or HTTP API.

When to Use

• Setting up PCR reactions: Distribute master mix from a tube rack into a thermocycler plate, add template DNA from individual tubes, then execute a PCR profile automatically.
• Running serial dilutions: Programmatically step a multi-channel pipette across a 96-well plate to create 2-fold or custom dilution curves with defined diluent volumes.
• Performing ELISA plate layouts: Add blocking buffer, primary antibody, secondary antibody, and substrate to defined wells with tip changes between each reagent.
• Automating magnetic bead cleanups: Engage/disengage the magnetic module, aspirate supernatant, wash with ethanol, and elute — in a fully automated loop.
• Plate reformatting and stamping: Transfer an entire 96-well plate to a destination plate with one command; reformat from tubes to plates.
• Integrating hardware modules: Coordinate temperature control, shaking, and liquid handling steps in a single protocol with precise timing.
• Use PyLabRobot instead when writing protocols that must run on Hamilton STAR, Tecan Freedom EVO, or other vendors without Opentrons-specific hardware; for Opentrons-only workflows the native Protocol API provides tighter integration and module support.
• For retrieving and parsing published protocols before automation, use protocolsio-integration to search protocols.io alongside this skill.

Prerequisites