Customer Interview | Emory University Assistant Professor Adam Ericsen’s OT-2 experience

Adam Ericsen studies HIV host-virus interactions using fully automated genotyping, microbial sequencing, and immunological assays.

Adam Ericsen is Emer Assistant Professor and Assistant Director of the Genomics Core Laboratory at the Yerkes National Primate Research Center. His focus is on studying modulators of the host immune response, a system consisting of many complex steps, and in April 2018 he began integrating three Opentrons pipetting robot was integrated into his laboratory toolkit to conduct experimental research in this innovative, automated way.

We spoke with Adam to learn how these robots can help automate his entire lab.

Opentrons: Please introduce your research background.

Adam Ericsen: I have a PhD in Pathology from the University of Wisconsin-Madison. An immunogenetics and infectious disease researcher by training, my current work focuses on understanding host-virus interactions in HIV infection. I primarily used macaque monkeys as a model for this study.

Opentrons: What does your research project look like?

Adam: For the past decade, I have been studying how genetic and environmental factors alter disease progression in virally infected animals.

Opentrons: What is your daily routine like in the lab?

Adam: Our lab runs a large number of genotyping, host and microbial sequencing, and immunological assays. From a macro perspective, we are committed to understanding how disease progression is influenced by genetic and non-genetic factors to find actionable biological pathways to slow or completely prevent the progression of AIDS in people living with HIV.

Our lab is very new, and it is difficult to train technicians to perform multiple types of testing independently. I need our lab to be good at whole blood processing, leukocyte and plasma separation, DNA isolation (from any and all sample types), quantitative molecular testing, and flow cytometry. This may sound ambitious? Maybe so...but in order to conduct meaningful research, I need my small lab to function like a large lab.

A common protocol for us is to spin the blood at high speed and separate it into several fractions. Getting to the level we are at now was not easy, but establishing a fairly routine blood processing workflow was essential. Training a new lab—my new team—to do a similar test was time-consuming and laborious. I kept reminding myself that the time spent training my team was worth it, but my determination only lasted so long.

This is where Opentrons robots come in: even if I can't be in the lab physically, I need my experience, my training, and my hands in the lab.

Opentrons: Why did you choose OT-2?

Training a new lab - my new team - to do tests "just like this" is extremely time-consuming and stressful... This is where Opentrons robots come in: Even if I can't be in the lab physically, I need My experience, my training and my hands are in the lab.

Adam: I had heard about Opentrons before the OT-2 came out. I was attracted to Opentrons' open-source program: I can add, modify, and enhance core functionality at any time, which allows my small lab to purchase a machine once and, through the magic of code, dramatically increase the efficiency of its experiments. As one of my technical staff described it, “We can write the code and watch it work.”

We ended up combining SQL, C++, PHP, JS, HTML5, and Python to build a custom web-based front-end interface that managed all interactions with our Opentrons protocol (without extended documentation for the API, we couldn't make it happen). I can sit in the airport in Portland and control one of our OT-2 pipetting robots in our lab in Atlanta. Might be a little fancy, but it's just an example of what we can accomplish.

Perhaps more importantly, the bot can interact with our inventory of samples and reagents, as well as call the Google Voice API. Ever since we started facing the efficiency dilemma, we've been, as my family says, "automating everything." Together we wrote a number of Python modules, and each completed protocol run sends a message to our lab server to ensure that all important items (such as labware definitions, rack locations, volumes, etc.) are up to date.

We have adopted the OT-2 platform to replace the manual inspection work that I would have had to train new technicians to perform. Now, our team has largely moved away from manual operations. I joke that once robots can write grant applications and manuscripts, we'll be able to do it all in the park.

We have embraced the OT-2 platform to perform every inspection job that would otherwise require training new technicians to do manually.

Opentrons: What exactly do you use the OT-2 for, and how does it fit into your workflow?

Adam: We fully automate the following processes, including PCR, Fluidigm, flow cytometry, blood processing (after centrifugation) and nucleic acid isolation testing. If the experiment requires it, we design custom labware ourselves and my wife prints the tools using 3D printing technology. All our labware is microchip controlled, and anything loaded onto the robot is scanned via barcode or RFID: the robot checks with the server to make sure the correct samples are where they should be.

We can even fully process whole blood samples that have been centrifuged first. Nathan Gullicksrud in my group figured out a way to fix the blood bottles at a specific height so we could easily extract the plasma and white blood cell layers. That means we can fractionate the plasma, separate the plasma, clean up the white blood cells, and that's it - they're ready to go. It became clear that we could handle up to 96 simultaneous vacutainers in a matter of hours with very little manual intervention. We quickly scaled to throughput that would have been unimaginable.

We quickly scaled to throughput that would have been unimaginable. With the OT-2, we save a lot of time.

Opentrons: How do you customize the OT-2 to suit your desired workflow?

Adam: I wrote a complete interface to connect to the OT-2. We also made several hardware modifications—including drilling holes and placing microchip scanners and photoelectric sensors at each plate location. The robot will prompt: "Attention. Attention. The run has been paused. For your safety, please close the front window", or "Transfer DNA from column X on the DNA input plate to..." So we can do almost anything - From whole blood and all its outputs, to fully automated DNA testing.

My goal is to empower my team members to engage in more meaningful activities. Instead of sitting in front of a biosafety cabinet for hours every day...technical expertise in a research laboratory can go far beyond that. The Opentrons platform inspired me to be ambitious, even a little overly ambitious, and I was willing to carry out research work on a larger scale and scale as a new PI.

Opentrons: What is your real experience using OT-2?

Adam: Opentrons are the first freely customizable liquid handling robot I have used. I write the core Ericsen Lab code on top of the Opentrons API, and when we encounter bugs or issues, we consult the Opentrons support team and they help us push the issue forward, and I modify or re-architect our approach as needed, and Work closely with the support team.

I have a great team. As a new researcher, I feel very lucky. However, no one on my team had programming expertise. I told them that I wanted to build an automated, intelligent, and active research program. I put them in front of the robot and said, "We're going to solve this problem together." Instead of training on the manual aspects of traditional inspection, we wrote code to let the OT-2 perform these operations. The training process for the lab changes from training with the robot to successfully perform basic inspections to being able to perform complex experiments. This gives my team the expertise we need in testing. My goal is to build a team of passionate and hard-working creatives who can successfully execute complex assays or experimental projects that have never been attempted before. I believe using Opentrons will save me more time as they will learn from the robots and the connectivity of the lab will protect research data, records and ensure we can support the work we produce.

If the robot I'm using in my lab isn't open source, it's just a replacement hand -- something I wouldn't have to spend as much to buy.

Opentrons: What are your expectations for laboratory automation processes?

Adam: I never considered failure. Buying a robot for a research lab is not the same as buying a popular consumer-focused device. Initially, I met a lot of frustrated researchers who had no idea how long it would take to get the Opentrons robot up and running. Indeed, using Opentrons robots requires a certain learning process. But with Python controlling lab robots, young labs with limited resources can go beyond at a lower cost. My robot sits right next to the flow cytometer in my lab, and the flow cytometer costs 10 times as much as the OT-2.

Opentrons: What are the advantages or disadvantages of your OT-2?

Adam: OT-2 is great! The OT-2 can do simple things, but it can also do things that no other platform can do.

Opentrons: Did you use any laboratory automation equipment before using the OT-2?

Adam: Actually not. But when I heard you were using a Python backend, I thought, "I can do that!" My wife and I are 3D printing, and we were surprised at how similar the learning curves were.

Opentrons: Do you have any other new automation research plans?

Adam: Well, we just ordered two more OT-2s, so it must be! OT-2 supports the speed and integrity of what we are doing. The fact that OT-2 is open source is very attractive to me given the limitations that exist with many proprietary platforms. If the robot I'm using in my lab isn't open source, it's just a replacement hand -- something I wouldn't have to spend as much to buy.

The OT-2 has become an integral part of daily life in the lab since we received it 18 months ago. It was an important early investment - I could have spent the money on training staff, but I think the robot and its platform are a more valuable use of our resources. We do a very advanced assay; we use a robot to do it and we just change a few pipettes.

Opentrons: What other interesting things can you share with everyone about OT-2?

Adam: One of the really fun and incredible things we’ve done is we’ve incorporated the Google Voice API to let the robot announce, like when it’s out of liquid, or when it needs suction. header, and what test it starts with. It can be announced with this gentle female voice. I was very pleasantly surprised by this!

OT-2 is not a robot that takes my job. Instead, it turned my job into something more fulfilling. We also invested in a benchtop flow cytometer alongside the OT-2. Startup labs don't typically invest this much money in new equipment, but I was able to get all of these features through the robot, so it wasn't expensive. Training a person to use a cytometer can take months, but with the OT-2 we can easily train people to do blood sampling in a more efficient way.

OT-2 has quickly become an integral and valued member of our lab team.

Considering the length of the article and to give you a better reading experience, this interview has been edited.