Queensland University of Technology's Sebastian Eggert obtained his PhD in laboratory automation using the Opentrons OT-1 robot in his tissue engineering laboratory.
Unexpectedly, a simple order of equipment could contain treasures of inspiration that can lead to a doctorate! That's exactly what Queensland University of Technology (QUT), Australia >Sebastian Eggert's personal experience, he ordered an Opentrons OT-1 robot for the school's tissue engineering laboratory. It was this Opentrons OT-1 automated pipetting platform that allowed him to earn his PhD in laboratory automation. In this issue, he shares his experience using Opentrons.
“As an engineer, you often think about how many things can be automated.”
Sebastian, who was born and raised in southern Germany, received his master's degree in mechanical engineering from the Technical University of Munich and also worked in biology- and chemistry-based laboratories. In April 2017, he moved to Australia and started at the University of Queensland Center for Biomedical Engineering Pursue a Ph.D.
We are creating viscous gel biomaterials to mimic human cells, while also designing and constructing novel microenvironments that are physiologically relevant. These 3D models, such as breast and prostate cancer models, are used in drug screening to evaluate the impact of chemical, physical or biological factors to determine the possible effects of taking new drugs on humans.
However, it goes without saying that screening hundreds of drugs for even one drug can involve millions of tedious, time-consuming, and mind-numbing pipetting steps.
It didn't take a PhD or 10 years of professional education to perform these simple and repetitive pipetting tasks, and I told myself that wasn't what I wanted to do, and I wasn't going to waste all day pipetting. As an engineer, you often think about things that can be automated.
That's what he did. In December 2017, he received permission from his professor to purchase an OT-1 pipetting workstation for the laboratory to automate these routine tasks.
We can customize protocols based on application needs. At that time, I almost had no expectations or experience. PhD students don't typically order large lab equipment! But because I had an engineering background, it was relatively easy for me to understand automation technology and start experimenting with programming.
Adaptable coding is why Sebastian chose the older OT-1 pipetting platform over the just-released OT-2.
If we want a customizable device, the OT-1 is more suitable for DIY. With other robots, we have to stick with their software and API and have no access to their protocol parameters. However, Opentrons provides us with free, open source software so we can tailor the protocol to our application needs. The tutorials and videos on the Opentrons website are very intuitive. I generated my own API and changed the content to suit our application. It was an exciting moment when I saw a pipette that I normally use manually suddenly start dispensing and aspirating automatically.
Handling tough situations
However, handling thick, honey-like hydrogels with Opentrons robots is different from handling other regular liquids.
When using traditional air-pad pipettes, viscous liquids move slowly to the tip and create bubbles. Additionally, the tips tend to retain some material. You can buy handheld positive displacement pipettes that use a solid piston to reliably push viscous liquids out of the tip, but these devices are expensive. I customized and 3D printed a special pipette holder and optimized the OT-1 to integrate a positive displacement pipette, enabling automated pipetting of viscous liquids while ensuring pipetting efficiency and repeatability.
This innovation alone is already a significant achievement, but for Sebastian it is just the beginning of his creativity and PhD project.
When I started my PhD research, I conceived the concept of a modular open source workstation where pipetting was the basic module for pipetting and dispensing. We purchased the OT-1 based on my concept. Opentrons' open source vision inspired my PhD research from the moment I got my OT-1. I'm fascinated by the options for customizing hardware and software changes.
After Sebastian integrated the positive displacement pipette and became more familiar with programming methods, he contacted Toma Morris, a former Opentrons senior software engineer. Toma provides Sebastian with guidance on software navigation to complement his hardware expertise.
"I'm delighted to be able to help Sebastian inspire his PhD research so that he and the work he does can help more people." - Toma Morris
Many thanks to Opentrons for giving me access to all parameters and steps when developing a custom solution. Additionally, the open source nature of Opentrons allows me to integrate other custom modules to run simultaneously. In mid-2018, I was ready to incorporate an additional hardware module to build a more complex workstation. Through conceptualization, analysis, and protocol design, I finally came up with a simple research concept that could be more easily adopted by other laboratories. It took some time, but eventually, I found a way to incorporate this concept into my PhD research. Thanks to the OT-1, my PhD research has evolved to focus on the design and development of automated solutions for 3D cell culture workflows.
Exercise the right to assemble – automated
Sebastian's concept demonstrates a streamlined approach to performing the basic steps required by a laboratory in a user-friendly manner that can be easily adopted by other laboratories.
He independently crafted an enclosure using an aluminum frame and acrylic panels, doing the electrical engineering, welding and assembly himself. He then designed and developed interchangeable hardware modules, including a storage module to store well plates to be processed to increase throughput; a cross-linker module to initiate photopolymerization of hydrogels; and A transport module for moving and positioning orifice plates through the system.
Unlike stand-alone automated pipetting platforms, all components are fully assembled into the housing, and with the OT-1, the base can automatically transport samples to each module. (Click here to see the system in action.)
In a system, the combination of various modules can achieve a specific set of functions.
Now he's giving back.
The vision of Opentrons also inspires us, and we are willing to follow the same open source philosophy. All documentation on how to use a positive displacement pipette with the OT-1, including a revised software script, 10 lines of code for the "Get Tip" function, and a pattern for 3D printing or laser cutting the pipette holder , are now freely accessible via GitHub.
Opentrons has always been helpful and very supportive of my work.
Today, Sebastian is conducting the final experiment of his doctoral research. A summary of his findings has been published in HardwareX, a peer-reviewed open source scientific journal dedicated to the open source design and construction of scientific instruments, and will be part of his submission later this year A chapter of a doctoral thesis.
Hardware development for the second prototype has also been completed and is running well. At the conference, it was really exciting to see how enthusiastic other scientists were about the project and how enthusiastic other PhD students were about adopting the system in their own research. Opentrons has always been helpful and supportive of my work. During a visit to New York, I had the opportunity to present my concept to Toma, Will Canine (co-founder and chief product officer) and Alfie Umbhau (director of product). They were all enthusiastic and provided additional support and insight. Special thanks to Toma, who helped me integrate and develop my own API. Without his help, this project would not have reached the stage it is at now. I'm so grateful!
