Cloud Lab: Where robots do research

As a chemistry PhD student, Dmitro Kolodizny was used to running experiments. But in early 2018, his research advisors asked him to participate in a run run by robots instead.

They wanted Kolodizny, who was developing the intracellular fluorescent probe at Carnegie Mellon University in Pittsburgh, Pennsylvania, to spend a month trying to recreate his research at the Emerald Cloud Lab (ECL). The biotechnology company in South San Francisco, Calif., enables scientists to conduct wet-lab experiments remotely in an automated research environment known as the Cloud Lab. If the test goes well, it will help pave the way for widespread use of cloud labs in the university.

Unlike his Pittsburgh lab, where Kolodizny and his fellow students conducted their own experiments, the workhorse at ECL’s 1,400-square-metre headquarters were rows of machines powered by lines of code issued by researchers around the world, who were asked from the waist down. Sometimes there was help. White robots that walked around the room. There were hundreds of machines at work, but only one or two human technicians were needed to manage the entire process.

It took only a week for Kolodieznyi to replicate several years of his PhD research – everything from organic synthesis of fluorescent tags to advanced microscopy. He says they only scratched the surface of the company’s capabilities, which include cell culture, DNA synthesis, liquid chromatography and structural-analysis methods, such as mass spectrometry and nuclear magnetic resonance. But the experience made its mark: in 2020, after earning his PhD, he joined the company as a scientific developer.

Kolodieznyi’s positive response, along with research disruptions in 2020 as a result of the COVID-19 pandemic, led Carnegie Mellon University to invest US$40 million in partnership with ECL to create a Pittsburgh-based cloud lab – the first of its kind Facility built in an academic setting. Construction of the Carnegie Mellon University Cloud Lab began in November 2021, and is set to open in mid-2023. According to Rebecca Doerge, Glen de Vries dean of the university’s Mellon College of Science, the university’s faculty members, staff and students will have priority access to the lab, so every researcher there has a chance to access the technology.

Academia, small start-up firms and big pharma are increasingly turning to cloud labs, as part of a trend to outsource work. The approach is “a laboratory that is working 24/7,” says Germano Coppola, executive director of research and development at biotechnology firm CSL Behring in Melbourne, Australia, which is a client of ECL.

Cloud labs “offer tremendous potential for scientists to generate a lot of data without even entering the lab,” he says.

virtual bench

ECL co-founders Brian Frieza and DJ Kleinbaum weren’t ready to make the lab bench virtual. Friends as children, the pair attended Carnegie Mellon, and in 2010, they founded Emerald Therapeutics in South San Francisco to focus on developing antiviral drugs. But Frieza and Kleinbaum spent much of their time trying to get the machinery to work in their new lab. Their solution was an ever-expanding set of computer code to manage the equipment and run experiments round the clock. Frieza not only saw an increase in productivity from set-up, but also an increase in reproducibility.

“I was turning experiments into code,” Frieza says. “At the end of the day, there’s no ambiguity in this text, I can push a button and reproduce it.”

The pair realized that other laboratories could benefit from this virtual system, and that same year they formed ECL to sell subscription access to their equipment and software. The best way to think about it, Frieza says, is with streaming services like Netflix or Spotify for the Lab. Just as users of those services pay for access to a virtual library of digital content without purchasing a song or television episode, ECL and other cloud labs provide access to a vast warehouse of tools without investing any capital.

Researchers can log on to the ECL dashboard and specify which experiments they want to conduct and when; configure the equipment to their liking; make adjustments along the way; And get live progress updates on their experiments and watch the process on video. An artificial-intelligence-based ‘expert’ acts as a highly skilled technician, giving users the ability to change default values ​​and identify problems that prevent experiments.

Close up on the robotic arm at the Stratos San Diego Smart Lab.

One of the robots at the Stratos Lab facility.credit: Stratos, Inc.

ECL provides three levels of access depending on how many experiments users want to run at once. The lowest tier allows three to run in parallel and starts at $24,000 per month. It’s not cheap, Frieza admits, but compared to the cost of buying the equipment, he says it saves researchers money in the long run. Stratos, which has a cloud lab in Menlo Park, California, optimizes its access levels and pricing, allowing users to tailor their experience to their budget.

For Coppola and CSL Behring, Cloud Labs effectively provide 24-hour service. Coppola sends its samples and reagents to ECL’s headquarters or purchases them from its existing inventory, programs its orders into a point-and-click user interface and waits for the results to arrive. He can view and read his experiments on a webcam—outside in real time.

Cloud labs aren’t the only option for research teams that lack the infrastructure or expertise to conduct certain experiments: Contract research organizations (CROs) are another. But the two approaches are very different, says Daniel Raine, vice president of technology-enabled services, which is based at Stratos’ other facility in San Diego, Calif. With Cloud Lab, scientists do all their experiments on their own. You may be driving them from thousands of kilometers away, but they will remain your thoughts and your results.

In contrast, “CROs are very labor-driven,” Raine says, meaning they rely on humans to do most of the work. “What we are doing is using our robotic capabilities to industrialize science and make it more reproducible and reliable.”

Because of this, when experiments fail, cloud-lab users can go back to their data to find out what went wrong, without relying on anyone else. Kolodieznyi describes the process as having an army of highly talented, highly trained bachelors at your beck and call. They might not be able to design the study at first, but once they’re trained, they can run your experiments — and do it the same way every time, he says.

“I can’t remember how many times I’ve read something in a paper, tried it and not surprisingly, it didn’t work. But in Cloud Lab, if I just copy and paste my experiment , then it will work again, ”says Kolodizny.

Advocates of Cloud Lab say that along with reproducibility benefits, providing affordable access to the tools needed to do science helps democratize research. “It doesn’t matter who you are or where you are. You’re all using the same lab. It’s a big deal,” says Frieza.

Huaying Zhang, a bioengineer at Carnegie Mellon, has proposed using the university’s Cloud Lab by high-school students in a low-income district in Georgia state – for which he was awarded a grant by the US National Science Foundation. She points out that not all students interested in science may have access to sophisticated equipment, but running experiments in a cloud lab removes those barriers. Once the Carnegie Mellon Cloud Lab is up and running, she hopes to give students the chance to conduct real experiments on equipment normally reserved for PhD students and postdocs.

“You’re not just memorizing facts. You’re getting real data,” Zhang says. “Students can use tools they would not normally be able to access.”

At University College London, researchers have teamed up with London-based Synthes Life Sciences R&D Cloud to provide a no-code user interface that will let researchers automate tasks and create experimental workflows remotely. According to a statement from Synthes, this partnership will enable scientists to “future-proof” their experimental designs against unexpected disruptions to their work.

However, writing in Bulletin of Atomic Scientists, researchers Filippa Lentzos and Cédric Invernizzi note that, by reducing the barrier of expensive equipment, Cloud Labs could enable bad actors, such as terrorist groups, to abuse the technology to conduct “malicious” experiments (see go .nature.com/3nsbg9e). When asked for comment on the issue, spokespersons for both Stratos and ECL say that they use the highest-level data encryption, and that they have never had any security concerns, although they have no security concerns about their security. There is no active investigation. Contingencies.

For Doerge, the benefits of Cloud Lab outweigh such concerns — especially in the midst of the ongoing pandemic. She says most of the university’s research grounds came to a halt in early 2020 in the form of COVID-19. A cloud-lab facility would have allowed this research to continue, as well as several laboratory courses at the university.

“It was the change that science needed, like the cell phone, like the self-driving car,” Dorge says. “The process of science does not correspond to technology.”

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