HTGAA: Remote Lab Automation

Typically in HTGAA, we combine exciting lectures with extensive lab work to better understand the building blocks of synthetic biology. This year, in many ways, is different. While we cannot have students back in the lab just yet, we have come up with a novel approach that would hopefully give you a taste of molecular biology workflows and also learn about the trending field of lab automation.

As far as we know, this is one of the first attempts of hands-on, remote wet-lab education. We appreciate any feedback and suggestions, even during the weekly work.

We will be using the OpenTrons OT-2, and open-source, user-friendly lab automation robot.

This week, we will focus just on the mechanics of operating the OpenTrons remotely. The exercise involves using food dyes to create a pattern into a 96-well plate. While this isn't a conventional synthetic biology workflow, the same commands would allow you to later execute exercises involving enzymatic reactions such as PCR, Gibson Assembly and more.

Instructions

• Only one student at a time can work on the machine, so first, go to the slack channel #opentron-users and post a message that you are starting a session. Do this every time you plan to connect to the machine, even if it's just for taking an image.

• You will need to connect to the remote machine using Remote Desktop software. This process is only for registered students, although if you do have access to an OpenTrons machine, feel free to follow along.
  • Windows users: in the search bar type Remote Desktop and run it
  • Mac users: download Microsoft Remote Desktop from the app store and run it
  • Linux users: use any RDP client of your choice.

• Login to: opentrons.media.mit.edu
  • Username and Password will be given to the registered student over Slack

• Click on the OpenTrons icon in the lower bar. You should see a single Robot in the list. Connect to it by hitting the toggle switch next to it

• Scroll down over the list of options on the right until you see the Robots Controls > Light toggle. Turn the lights on if they're off. This is also useful to scare labmates.

• Minimize the OpenTrons app. You should see two windows open:
  • On the right, Chrome browser shows the live OpenTrons cameras. When you turned the lights off/on, you should see the live feed changing. If for some reason you cannot see this window, open Chrome and in the address bar type localhost and hit Enter
  • On the left, a Microsoft Edge window with the Jupyter notebook. This wondow is where you will execute code to run experiments. If for some reason you cannot see this window, open the OpenTrons app, and scroll to Advanced Settings > Jupyter Notebook, click Open. And then go to HTGAA Logo > Warmup Exercise. Clicking it should open the notebook

• It's time to execute! But first, Make a Copy of the Jupyter notebook by going to File > Make a Copy. A new tab should appear, change the title of the file so it contains your name, and work only on your file.

• Now, follow the instructions in the notebook.