An operating system for the biology lab

An operating system for the biology lab

Emerald Cloud Lab’s facility for running experiments will operate 24 hours a day and allows users to control instruments remotely.Credit: Emerald Cloud Lab

“Their approach is beautifully simple,” says Dhash Shrivathsa, founder and chief executive of Radix Labs. “They put into a room all the equipment needed to process and sequence the genetic material in a vial of human blood.” He’s describing a leading liquid-biopsy company that has raised hundreds of millions of dollars on the promise of early disease detection on the basis of drawing blood. Its machines are highly automated and engineered to run seamlessly — and can be painstaking to reprogram when the design of an experiment changes. The company was spending months at a time doing so. “It was like switching from one program to another on your computer without an operating system,” explains Shrivathsa.

To speed up that process, the company turned to Radix for help. The two-year-old start-up in Cambridge, Massachusetts, has developed a computer language that can be used to encode a customer’s biology experiments, a compiler that translates that code into a machine-readable language, and a set of drivers that enables instructions to be understood and executed by the customer’s equipment. Radix’s technology aims to free biologists from worrying about the details of the machines in their laboratories and how they execute an experiment. This enables — among other things — the rapid redesign of experiments without needing to manually reprogram (or even physically reposition) the equipment involved. “If two different robots in the biology lab are told to do the same thing, we’d like to be able to have our customers use the exact same program on either or both, without any code change or effort on their part,” says Shrivathsa.

Automation has been integral to biology labs for decades — for example, in the form of programmable centrifuges and mixers. These instruments ease repetitive tasks and speed up the execution of experiments. But Radix’s goal is more ambitious. Just as a software engineer writes code for an idealized and virtual computer, the location and details of which are irrelevant, Radix’s technology enables a biologist to plan experiments for a virtual biology lab. The procedures are still carried out using real-world equipment, but the scientist does not need to know its make and model, or how and where it is set up. This represents both a practical and conceptual shift in how biology is done. The hardware layer separating the biologist from his or her subject becomes slightly more transparent.

Virtualization of the biology lab is an ambitious project. “Coming to this as a biologist, my initial instinct was that it wasn’t amenable to this treatment,” explains Markus Gershater, chief scientific officer at Synthace, a biological-software firm that he co-founded in London in 2011 and a competitor to Radix. But he was attracted by the possibility of making it easier for biologists to perform experiments in which many variables are modified simultaneously, by freeing them from the proliferation of procedures and handling steps that such experiments usually require. Contrary to his expectations, he found that experimental biology is well-suited to virtualization, because its underlying procedures are so similar. “So much of the logic in biology is in moving liquids around,” explains Gershater, “whether you’re working on malaria or genetically modified products.”

Radix, Synthace and other companies that are pursuing the virtualization of biology labs have lofty goals, and have attracted tens of millions of dollars in investment and some well-funded customers. But these companies are also clear that the challenges they face are not just technical. Their industry will need both cultural acceptance and a set of global standards to reach its potential, just as happened with the software and semiconductor industries that have inspired it. But where these will come from is not entirely clear.

Run it again

Emerald Cloud Lab in South San Francisco, California, has also developed a computer language and set of drivers that are capable of translating complex experiments into machine-readable instructions. But unlike Radix, which aims to work with the existing infrastructure of its customers — and requires it to write drivers for many kinds of equipment — Emerald owns and maintains the hardware that is needed to run a customer’s experiments. After its facility is completed next year, customers will be able to upload a script that encodes their experiment and then simply hit ‘Run’. There will be people among Emerald’s machines, but they will mostly also be following software-generated instructions — shifting and scanning sample vials and agar plates. “It’s a bit like Amazon fulfilment,” says Emerald co-founder Brian Frezza.

Emerald’s approach, says Frezza, offers

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