hammerlab / opentrons

Python API for writing protocols and running them on Opentrons robots

Opentrons Platform

• Overview
• Opentrons API
• OT-App
• Contributing/Building

Overview

Opentrons makes robots for biologists.

Our mission is to provide the scientific community with a common platform to easily share protocols and reproduce each other's work. Our robots automate experiments that would otherwise be done by hand, allowing our users to spend more time pursuing answers to the 21st century’s most important questions, and less time pipetting.

This repository contains the source code for the Opentrons API and OT App. We'd love for you to to explore, hack, and build upon them!

Opentrons API

The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.

We've designed it in a way we hope is accessible to anyone with basic computer and wetlab skills. As a bench scientist, you should be able to code your automated protocols in a way that reads like a lab notebook.

pipette.aspirate(tube_1).dispense(tube_2)

That is how you tell the Opentrons robot to pipette its max volume from one tube to another. Learn more here:

• Documentation
• Source code

OT App

Easily upload a protocol, calibrate positions, and run your experiment from your computer.

• Documentation
• Source code

Contributing

We love contributors! Here is the best way to work with us:

1. Filing a bug report. We will fix these as quickly as we can, and appreciate your help uncovering bugs in our code.

2. Submit a pull request with any new features you've added to a branch of the API or App. We will reach out to talk with you about integration testing and launcing it into our product!

Using BETA versions

If you want to build the platform and play with the latest development version we are working on before it is launched, here are the steps:

Set up your development environment

• Python 3.5.3 (pyenv is optional, but recommended)
  • On Linux, when using pyenv, run export PYTHON_CONFIGURE_OPTS="--enable-shared" before pyenv install ...
• Node 6.11.0 (nvm is optional, but recommended)
• OS X 10.11+, Linux, Windows 10 with Cygwin
  • On Ubuntu Linux, install libgconf-2-4, graphicsmagick, icnsutils packages via apt-get
• GNU Make: both API and OT-App are using Makefiles

Start the Opentrons API

Clone the repository to get started.

git clone https://github.com/OpenTrons/opentrons.git

Install the dependencies and API itself.

cd api
make install
# Verify
python -c 'import opentrons; print(opentrons.__version__)'
2.4.2

(Optional) test, lint and build API server executable (needed for the app)

make test
make exe

OT-App

Our app is built with Electron. The structure and configuration of bundling, testing and packaging are based on this great repo.

You can read great coverage of some tools that are used in our stack here. Note, our front-end framework of choice is Vue.js which dictates our choice of test tools: Karma, Mocha, Chai and Istanbul

Build

Install OT-App dependencies.

cd app
make install

Build and package the app

make build package
# Optionally test
make test
# For end-to-end click-through test
make test-e2e

Develop

If you want to play with the code base and make some changes, feel free to do so.

Start Python API Server (in a separate terminal):

cd api
export ENABLE_VIRTUAL_SMOOTHIE=true; python opentrons/server/main.py

Install dev tools:

cd app
# Install development tools that are not part of package.json
npm i electron-debug
npm i vue-devtools

Run OT-App in development mode. This will open development tools and connect to the API Server already running (instead of starting it from app/bin/opentrons-api-server):

make dev

Enjoy!