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Robotic Programming Language Devised for Bio Labs

Nathan Hillson, center, with the PaR-PaR development team, from left: Nina Stawski, Changhao Bi, Sean Poust, and Gregory Linshiz. (Roy Kaltschmidt, Lawrence Berkeley National Lab))

Nathan Hillson, center, with the PaR-PaR development team, from left: Nina Stawski, Changhao Bi, Sean Poust, and Gregory Linshiz. (Roy Kaltschmidt, Lawrence Berkeley National Lab)

Researchers at the Joint BioEnergy Institute of Lawrence Berkeley National Laboratory in California created a programming language for robotic devices in biology labs. The high-level language called PaR-PaR — short for Programming a Robot — is described this month in the journal ACS Synthetic Biology.

Par-Par is written to help train robotic devices perform repetitive tasks in biological labs and, according to its developer biochemist Nathan Hillson, combines principles of computer science and a deep understanding of biological workflows. But the language is also designed to be easy to learn by bio lab staff. “After minimal training,” says Hillson, “a biologist should be able to independently write complicated protocols for a robot within an hour.”

Many biological lab routines, such as construction and cloning of DNA molecules, involve a many labor-intensive multi-step biological tasks, where robotics can increase research productivity and lower costs by reducing experimental error rates and providing more reliable and reproducible experimental data. Robotics developers have, up to now, however, generally targeted their software for high-volume industrial labs that require professional programmers to maintain or customize.

Hillson and colleagues in the synthetic biology program (pictured at top) at the Joint BioEnergy Institute saw a need for flexible easy-to-use programming tools for dynamic research environments that would let bio lab workers write the instructions for their own devices, rather than relying on professional programmers. They also wanted a single programming language that would work across robotics platforms in labs, rather than requiring staff to learn a separate language for each piece of equipment.

“Our vision was for a single protocol to be executable across different robotic platforms in different laboratories,” says Hillson, “just as a single computer software program is executable across multiple brands of computer hardware.” Another requirement was for robotics devices to interact with other lab software, which can enhance the value of that connected software.

PaR-PaR uses an object-oriented design common in modern software where physical laboratory objects — e.g., reagents, plastic consumables, laboratory devices — are represented as virtual objects. Associated with each object are properties, such as a name and a physical location, and multiple objects can be grouped together to create a new composite object with its own properties.

Actions performed by robotic devices on these objects can be constructed into sequences of actions, then entire procedures, which Par-Par translates into commands for the devices to perform. Collections of these commands can be stored and imported into Par-Par as external modules.

Par-Par, says Hillson, is “intended to benefit a broad segment of the biological research community, including non-profits, government agencies and commercial companies.” The software and documentation for Par-Par are available with an open-source license for downloading from the Joint BioEnergy Institute Web site.

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