My phone is basically a portable computer. So is yours, unless you’re still a huge fan of the Nokia 3310. You might have a smart device at home that controls the lights, plays music, or even chats with you. Technology permeates every corner of our lives, but somehow biologists have been left behind. In labs around the world, many researchers still use pen and paper to design experiments and record data. Now computer aided biology (CAB) is revolutionizing the field, especially in the integrated field of synthetic biology.
Synthetic biology in the UK was in its infancy when Markus Gershater and Sean Ward founded Synthace as a spin-out from University College London in 2011. Fast forward to 2019 and Synthace is the go-to example of a successful UK synthetic biology company. The company attracted nearly $50M in investment from grant and private funding sources, with $25.6M coming from a Series B investment round led by Horizon Ventures in December last year.
In the age of engineered metabolic pathways and synthetic proteins, the true bottleneck in bioprocess development lies in carrying out the Design-Build-Test-Learn cycle. A scientist armed with a pipette and all the reagents in the world must design their experiments to suit human limitations. Automated platforms, however, can pipette faster and more accurately than any human. Advancements in microfluidics and sensor technology also allow ease of cell culture and fermentation, so the whole process from cloning to analysis can be performed with minimal human input. Synthace recognized the potential of this early on and began development on their integrated software platform, Antha.
Putting the power of computation in the biologist’s hand
Antha is a powerful software platform designed to improve experimental output by 100-fold. While synthetic biology training provides a truly interdisciplinary approach, not all of today’s biologists are up to speed with programing code. Antha’s user-friendly interface is the product of an interdisciplinary team of engineers, chemists, and biologists, allowing the user to design complex, multi-factorial experiments without worrying about the logistical effort in carrying it out.
“Antha uniquely enables flexible automation and diverse equipment integration,” says Dr. Markus Gershater, co-Founder and Chief Scientific Officer of Synthace. “For example, its rapid, flexible reprogramming of automation enables these pieces of equipment to be used for highly sophisticated, multifactorial experiments which are exceptionally demanding to carry out by hand, or with conventional ways of programing the robots.”
De-bottlenecking the process by coordinating automation from start to finish allows experiments to be performed in a fraction of the time. Crucially, this decreases overall costs, providing immediate return on investment in expensive automated systems. In addition to robots, Antha interfaces with analytical equipment. Antha uses its built-in tracking to record samples as they are prepared right through to analysis.
“We have seen the transformational effect of these capabilities in our own labs, and those of our customers, where people are able to do experiments they couldn’t imagine doing without Antha,” says Gershater.
Another major issue addressed by Antha is reproducibility. In biology especially, results are affected by natural variation in living organisms. Add to this the natural human variation, and the source of data outliers can be difficult to pin down. Automation largely mitigates the risks associated with human variation and has revolutionized the field of synthetic biology where an interdisciplinary approach to problem solving and process optimization is key. Antha communicates the protocol to the robotics and analytics machines, which carry out the work, and information is fed back into Antha for data analysis.
It’s in data acquisition that the superpower of Antha lies. Artificial Intelligence (AI) requires huge amounts of data to work with. Gershater explains, “Biological data are often fragmented and from [statistically] underpowered experiments. Antha produces highly structured, statistically powerful datasets, with high standards of metrology that can then be combined and interrogated though AI.”
Synthace have already taking advantage of this by making partnerships with companies from transformative start-ups like LabGenius to multinationals like Microsoft, who are using Antha to generate data for AI driven biological insight.
CAB is moving from strength to strength in synthetic biology. Synthace is currently working with Microsoft to bring the Antha platform to clients via cloud computing and improve upon their computer aided design, a topic on which they have released a well-received white paper. Riffyn’s Scientific Development Environment (SDE) platform is another integrative software allowing design and control of experiments with data analysis. Riffyn SDE is open source for non-profits and works well with third-party software. Desktop Genetics have developed software platforms for making CRISPR mutants. Their DESKGENTM AI platform accesses a vast CRISPR library to help design the best CRISPR guides for a given experiment.
Biology is catching up with the 21st Century fast. The range of CAB software available is expanding and can be controlled through standard computers, tablets and, in some cases, even your phone.11