August 31, 2018

Free Genes Project makes DNA freely available to the world

BioBricks Foundation

This article is brought to you by Opentrons. Through their OT-One and OT-2 laboratory robots and open source protocols, Opentrons is making synthetic biology accessible to any lab, anywhere.

“One of the fundamentals of bioengineering is just getting access to working DNA that is the sequence that you want. And it’s surprisingly hard to do that.” — Anton Jackson-Smith, PhD student in Drew Endy’s lab at Stanford University.

Soon it won’t be hard for any scientist, anywhere, to access the DNA sequences that they need for their studies. The BioBricks Foundation Free Genes Project, based out of Drew Endy’s lab at Stanford University, is working to make free, accessible, and reusable DNA available to everyone.

The project is simple: if you have a DNA sequence you want cloned, tell the Free Genes Project team. They’ll check your sequence to make sure it is compatible with their cloning technology (the MoClo system), ensure there are no sequence specific patents, and do a biosecurity check. The DNA sequence is then sent to Twist Bioscience for DNA synthesis. Twist sends synthesized DNA back to the Endy lab, which transforms and make clones for distribution to you and any other lab. If your sequence isn’t MoClo compatible, you’ll still receive an aliquot of the raw synthesized DNA instead of a ready clone.

The project has pledged to make 10,000 genes freely available via bionet, a project of the BioBricks Foundation.

Why are they doing this? Keoni Gandall, head of the Free Genes Project, says the motivation is simple: “To give everyone access to this wonderful biotechnology of the future.” This is certainly- an especially inspiring example of the increasingly open-access, collaborative nature of the modern generation of scientists. Gandall and his colleagues believe that science — and the benefits it brings — happens faster when we work together. And when no one “owns” the data, people focus on what really matters: meaningful results.

Keoni Gandall

Keoni Gandall, head of the Free Genes Project, was featured on a recent SynBioBeta Live event, where he discussed how Opentrons OT-2 robot enables the Free Genes Project.

The team’s motivating factor isn’t the only way the project imbues open collaboration. Not only has the team partnered with Twist Bioscience to synthesize 10,000 genes, but they are also utilizing the Opentrons OT-2 laboratory robot, which is itself based on free, open-access software and protocols.

When the project first started, researchers in the Endy lab did everything by hand. But according to Gandall, this led to an “unacceptable amount of failure due to human error.” It was also time consuming: Manually building 100 genes from synthesis plates took an entire day of planning and operating. And this didn’t include the hours needed for transformation, colony picking, and DNA sequencing to confirm the clones.

The solution to the problem came in the form of Opentrons robots, which brought the processing time for 100 genes down from one day to one hour. This is incredibly valuable to the Free Genes team. According to Anton Jackson-Smith, a graduate student in the Endy lab, one of the most frustrating things for him is to see highly-intelligent, PhD-trained people waste their time pipetting instead of thinking critically about their projects and results — and how to apply them.

But why the OT-2? A number of commercially available liquid handling robots could achieve the same time-savings for the Free Genes team. “There are two reasons why we use the Opentrons,” says Gandall. “Affordability and open source software.”

At only $4000, nearly every lab can afford an Opentrons. The OT-2 also helps labs reduce reagent costs because it can pipette extremely small volumes; the Endy lab has halved, and in some cases, fourthed, the costs associated with the Free Genes project. And, unlike other laboratory robots, the OT-2 isn’t limited to just a single task. It can extract DNA, perform sequencing library preps, and (with some hacking) even pick colonies from agar plates.

This versatility is a direct result of the open-access nature of the software — all code is available on Github — and the ability of researchers around the world to create and upload their protocols for use by any other lab that needs them. There are dozens of protocols in the open source library already, with more added every week, says Opentrons head of scientific development, Kristin Ellis. The colony picking ability is a direct result of the efforts of the open source community. Jackson-Smith even made the OT-One Alexa-compatible. Now, instead of using your laptop to send instructions to the machine, you can have a conversation with Alexa and she’ll tell the robot what to do.

Opentrons

Will Canine, Opentrons CPO and co-founder, and Kristin Ellis, head of scientific development, discussed how the OT-2 is helping teams like the Free Genes Project at a recent SynBioBeta Live event.

Gandall feels that open access protocol sharing like that facilitated by Opentrons is critical for the future of synthetic biology. “If you don’t have open source software, it’s very difficult to share your protocols and processes with your peers. Other companies have very closed-down software stacks that force you to go through the company if you want to get a protocol or process. Opentrons makes that open source so you can share directly with your peers, which is far more efficient and I believe the only scalable way to operate in the future,” he says.

Opentrons Co-founder and CPO Will Canine feels that the Opentrons-Free Genes partnership is a natural fit. “Free Genes shares Opentrons’ goal of increasing accessibility of this technology to everybody,” he says. Because the Free Genes protocols are being made openly available in the Opentrons library, anyone can replicate the Endy lab’s DNA assembly pipeline in their own laboratory. This allows researchers to immediately start developing their DNA designs, rather first than spending valuable time on developing their automated protocols from scratch.

In a world where much of science remains behind closed doors or a paywall, a project to create freely accessible DNA is both simple and revolutionary.

To learn more about how the Free Genes Project, Twist Bioscience, and Opentrons are working together to make synthetic biology affordable and accessible to any lab, anywhere, watch the August 8 SynBioBeta Live event featuring Opentrons’ Will Canine and Kristin Ellis here.

Will Canine will be speaking in the “Lab of the Future” session at SynBioBeta 2018, The Global Synthetic Biology Summit, in San Francisco on October 1–3, and Kristin Ellis will be presenting a workshop on affordable lab automation.

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