Introduction

Opentrons is working with the Open Medicine Institute to automate COVID-19 diagnostics on a fleet of OT-2 robots.

This is our development repository. Welcome! Here, you'll find:

• The scripts that run on the robots, written with the OT-2 Python Protocol API.
• Labware definition files.
• Some of our experimental notes and reports.

We're actively developing and testing these protocols, so things might be a little messy. We're publishing our works in progress here so that other labs might benefit from them as quickly as possible.

How it works

We're automating a RT-qPCR based diagnostic protocol. We split it into 3 parts, intended to be run on 3 separate robots:

• Station A: Sample intake
• Station B: RNA extraction
• Station C: qPCR setup

See the Python files for more details.

Reagent preparation and handling

Instructions for the manual part of this protocol (how to prepare reagents, how to set up labware, and so on) are hosted on protocols.io.

Directory structure

• /experiments contains the exact Python scripts that were used for certain validation experiments, so we don't get confused about which experimental results correspond to which versions of our Python code.
• /labware contains the custom labware definitions necessary to run these protocols. After cloning this repository, you should configure the Opentrons App to look in this directory. (Go to More > Custom Labware > Labware Management > Custom Labware Definitions Folder.)
• /notebooks is for stashing random Jupyter Notebooks that we're using for developing and debugging.
• /protocols is for the uploadable protocols themselves.

Where to ask questions

If you have a question about what you see in this repository, please post it as a GitHub issue.

If you have a more general question about using OT-2s for COVID-19 protocols, please email covid-19@opentrons.com.