Building a digital foundation for synthetic biology research

Embriette Hyde

Just a stone’s throw from Hyde Park lie Imperial College London and the London Biofoundry. In the midst of tourist London, it is one of the global hotspots for synthetic biology. In other words, it’s a place where the greatest minds come together to combine biology and engineering to find solutions to problems like making biodegradable clothing, improving disease diagnostics, and, most recently, developing a high-throughput reagent-agnostic COVID-19 test.

The place is home to world-class problem-solving innovation because of the unique combination of academics, entrepreneurs, and the tools enabling them to liaise and turn some of the best academic research into the best commercial products.

“It really is a unique place,” says Tabasum Farzaneh, Senior Industrial Officer at SynbiCITE, the U.K.’s Innovation and Knowledge Centre for the adoption and use of synthetic biology by industry. “I work with research professionals with a range of skills and experiences in a really creative environment to drive innovation in engineering biology.”

Imperial College has earned its spot as the source of some of the best biotechnology research and product development in the world. Now, a partnership with Riffyn, the company that created the process data system called Riffyn Nexus, will help the College’s researchers, staff, and students further advance Imperial College as a global leader in accelerated biotechnology innovation. Riffyn Nexus has already enabled industry giants like Novozymes bring products to market twice as fast as ever before. And it helped Imperial and the NHS develop and deploy a robust high-throughput COVID assay in 9 weeks. The magic behind Riffyn Nexus is its ability to automatically integrate experimental data for machine learning in real time, and share that data seamlessly for collaboration across the globe.

A collaboration is born

The partnership started last year when Paul Freemont, Imperial College professor and co-director of the London Biofoundry and Farzaneh with her colleagues from the London Biofoundry and the IC Centre for Synthetic Biology (IC-SynB) hosted Timothy Gardner, CEO of Oakland-based Riffyn on a visit to London. Farzaneh had met Tim at SynBioBeta, San Francisco, earlier that year and knew he was on to something. Riffyn Nexus uses R&D processes as the organizing principle for its data storage, analysis, and user interface. It has enabled Riffyn customers — leaders in food, ag, and biopharma — to save thousands of error-prone man hours a year preparing and analyzing data. But last year Gardner was looking not for another industry partner, but for an academic one. In fact, he already had an idea in his mind for how a collaboration between a company developed with industrial R&D in mind and an academic institution might work.

“Science is suffering from a reproducibility issue that ultimately results from poor experimental design, outdated data analysis tools, and cumbersome sharing mechanisms,” says Gardner. “I envisioned a partnership with an academic institution that would bring the principles of computer-aided design and manufacturing quality to scientific experiments to reduce flawed research and increase reuse of scientific results. And the problem is not just technology, it’s also education.”

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Tabasum Farzaneh. Image source: Tabasum Farzaneh

To do this, he envisioned a multi-faceted approach that would enable all Imperial research labs access to Riffyn Nexus, establish a Center of Excellence that would introduce an educational curriculum focused on measurement systems analysis, statistical design of experiments, and the methods of data science — the century of best-practices upon which Riffyn Nexus functions.

This is the plan that Gardner presented to Freemont and his colleagues last year, and it wasn’t a difficult sell. In fact, according to Farzaneh, it was a no brainer for the team to agree to a partnership with Riffyn.

“Everyone in the room that day naturally connected and gelled, and we bounced around some really insightful challenges we were facing with sharing and pooling our data. We pretty much agreed there and then that we would go forward and work together via a multi-faceted partnership,” she says.

Building better science

The partnership kicked off with the first graduate student from Imperial College, Michael Crone, spending two weeks in Oakland, California with the Riffyn science team to learn the new technology. And from there, the partnership blossomed faster and more dramatically than anyone could have anticipated. Enroute to the San Francisco airport to return to London, Michael got a call from Fremont to begin developing a COVID assay immediately upon touching down. He used his new skills and the Riffyn technology to help make it happen.

Now Riffyn Nexus will be made available to all IC research labs and to all Imperial students at no cost — Riffyn’s contribution to the mission of better science and open science. And together with the Center for Excellence, Imperial and Riffyn will develop an educational curriculum supporting the training on research quality, process science, and use of Riffyn Nexus. And, through its intimate connection with U.K.-based start ups, the Biofoundry will help young entrepreneurs access the training and technology to speed their own product development efforts.

Farzaneh believes that Riffyn Nexus can benefit many departments at Imperial College, however, not just the synthetic biology groups. She remembers first meeting her colleagues in the Biofoundry, and being blown away by how much scientific infrastructure and capabilities had advanced since the days she worked in a lab — and that yet some of the problems that existed years before still plagued the field.

“Back then I was frustrated that there was a relatively low reuse of scientific results, especially those involving animals. It was just shocking that science still suffered from the problem of low reuse and low interoperability,” she says, adding, “Just imagine what we could achieve at Imperial by rolling out Riffyn Nexus across other departments, especially in medicine and life sciences.”

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The London Biofoundry. Image source: Tabasum Farzaneh

Indeed, there is a precedent for what Farzaneh envisions. One Riffyn customer was able to reduce the amount of animals they used in experiments by 80%, with no increase in personnel effort and with much cleaner data more appropriate for statistical analyses.

Farzaneh views the collaboration as “a really good case study for implementing open, transparent partnerships on a large institutional scale.” She sees it as an example moving forward for establishing similar partnerships at Imperial with other companies and organizations, with endless benefits for the Imperial community.

Following a stunningly successful beginning, with the partners working together to fight the global pandemic, Farzaneh looks forward to the day when the Biofoundry can reopen its doors and fully begin realizing the power of Riffyn Nexus.

“I’ve thoroughly enjoyed interacting with the Riffyn team to help implement this unique partnership; this will benefit the IC synthetic biology community at large and also the various commercial partners that we work with through the London Biofoundry,” she summarizes. “I look forward to collaborating on the various training and research projects unique to this partnership, including the integration of Riffyn Nexus into my Biofoundry colleagues’ COVID testing platform."

Like Farzaneh, I can’t wait to see the transformation awaiting the U.K. synthetic biology (and beyond) research landscape. Keep your eyes on London — I know I will be.