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How Sebastian Eggert Got His Ph.D. In Lab Automation With Opentrons

Sebastian Eggert of Queensland University of Technology got his PhD in lab automation using his tissue engineering lab’s Opentrons OT-1 robot. Here’s how.

Be careful the next time you open a package that you’ve ordered online; under all that packaging, you just might find compelling inspiration for your PhD. That’s exactly what happened to Sebastian Eggert of Queensland University of Technology when he ordered an Opentrons OT-1 robot for the school’s tissue engineering lab.

Sebastian Eggert. CREDIT: Sebastian Eggert
Sebastian Eggert. CREDIT: Sebastian Eggert

‘As an engineer, you always think things can be automated’

Born and raised in southern Germany, Sebastian earned his master’s degree in mechanical engineering from the Technical University of Munich, where he also worked on biology- and chemistry-based labs. In April 2017, he moved to Australia to begin his PhD research in biomedical engineering at Queensland’s Centre for Regenerative Medicine.

We’re creating viscous hydrogel biomaterials to represent human cells, and we’re also designing and engineering physiologically relevant, novel microenvironments. These 3D models, such as breast and prostate cancer models, are then used in drug screenings to assess the effects of chemical, physical, or biological influences and determine how taking new pharmaceuticals might affect humans.

However, conducting those screenings on hundreds of drugs, or even one drug, can involve literally millions of tedious, time-consuming, mind-numbing pipetting steps.

You don’t need to have a PhD or to have spent 10 years of education for these simple, repetitive tasks, and I told myself I wasn’t going to spend all day and night doing pipetting. As an engineer, you always think things can be automated.

And that’s what he did. In December 2017, he got permission from his professor to add an OT-1 liquid-handling robot to the lab for those routine tasks.

We can customize protocols to fit our applications. I had no expectations and almost no experience. PhD candidates don’t usually order big lab equipment! But because I have an engineering background, it was relatively easy to understand the technology and get into the coding.

The adaptable coding is why Sebastian chose the older OT-1 model, rather than the just-released OT-2.

We wanted customizability, and the OT-1 is more do-it-yourself. With other robots, we’d have to stick to their software and their API [application programming interface], with no access to their protocol parameters. But with Opentrons, we have access to free, open-source software, so we can customize protocols to fit our applications. The tutorials and videos on are straightforward. I generated my own API and changed things to fit our application. It was pretty exciting to see the pipette you usually use manually suddenly dispensing and plunging automatically.

Dealing with a sticky situation

However, pipetting sticky, honey-like hydrogels is not the same as pipetting the liquids that Opentrons robots typically handle.

With traditional air-cushion pipettes, viscous materials move slowly into the tip, and bubbles are created. Moreover, residues often remain in the tip. You can buy hand-held, positive displacement pipettes that use a solid piston to reliably push the viscous material out of the tip, but that equipment is expensive. Instead, I customized and 3D-printed special pipette holders, and optimized the OT-1 to integrate positive displacement pipettes and enable efficient and reproducible automated pipetting of viscous materials.

That innovation alone would be a noteworthy accomplishment, but for Sebastian, it was only the beginning – of his creativity, and of his PhD topic.

When I started my PhD research, I had conceptualized a modular, open-source workstation with the pipetting being a base module for aspirating and dispensing. We purchased the OT-1 based on my concept. Opentrons’ open-source vision inspired my PhD from the point I got the robot. I was fascinated by the option for customized hardware, as well as software changes.

After Sebastian integrated the positive displacement pipettes and got more used to the coding, he connected with former Opentrons Senior Software Engineer Toma Morris, who supplemented Sebastian’s hardware expertise with guidance on navigating the software.

Toma Morris
“I’m glad to have helped inspire Sebastian on his PhD, so he and his work can help others,” Toma says. CREDIT: Toma Morris

Thanks to Opentrons, I had access to all the parameters and steps to develop customized solutions. Moreover, the open-source character allowed the integration of additional customized modules to operate in a synchronized mode. In mid-2018, I was ready to integrate an additional hardware module for a more complex workstation. Running through concepts and analyses and designs, I finally came up with a simple concept for my own research that was also easy to adapt for other labs. It took some time, but in the end, I figured out how to incorporate that into my PhD, which, thanks to the OT-1, has evolved into focusing on the design and development of automation solutions for 3D cell culture workflows.

Exercising the right to assemble – automatically

Sebastian’s concept mirrors an assembly-line approach to execute fundamental steps required in the laboratory in a user-friendly way for easy adoption.

He used aluminum framing and acrylic plates – tackling the electrical engineering, and soldering and assembling it all himself – to fashion a housing. Then he designed and developed interchangeable hardware modules, including a storage module that holds well plates waiting for processing to increase throughput, a crosslinker module to initiate photopolymerization of hydrogels, and a transportation module that moves and positions the well plates through the system.

Fully assembled in the housing along with the OT-1, the base transports samples through the modules automatically. (Click here to see the system in action.)

In contrast to a stand-alone liquid handling robot, this enables the combination of modules to execute a specific set of functions, all within one system.

Now he’s paying it forward.

Opentrons’ vision also inspired us to follow the same open approach. All the files for using positive-displacement pipettes with the OT-1, including the 10 lines of code for the revised software script for the ‘get a tip’ function, and the patterns for 3D printing or laser-cutting the pipette holders, are now freely accessible via the GitHub repository.

Opentrons was always helpful and supported my work.

Today, Sebastian is running the last experiments for his PhD. A summary of his research findings has been published in HardwareX, a peer-reviewed open-access scientific journal dedicated to the open-source design and construction of scientific instrumentation, and will also be a chapter in his PhD thesis, which he plans to submit later this year.

The hardware development for a second prototype has also been finalized, and it’s running well. It’s exciting to see the enthusiasm about the project from scientists at conferences, and from other PhD students who are adopting the system for their own research. Opentrons was always helpful and supported my work. During a visit to New York, I had the opportunity to present my concept to Toma, Will Canine [Co-founder and CPO], and Alfie Umbhau [Director of Product]. They were enthusiastic and provided additional support and insights. Toma especially helped me with the integration and development of my own API. Without his help, the project would not be at the stage where it is now. I am very grateful!