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Platform to Integrate Robotics, Synthetic Biology, A.I.

Microbes

(Department of Defense)

12 April 2018. Two companies are developing a new model for a cloud-based platform that makes possible automated collaborative research with artificial intelligence in synthetic biology. The project is undertaken by Transcriptic, in Menlo Park, California and Ginkgo Bioworks in Boston, under a $9.5 million contract from Defense Advanced Research Projects Agency, or Darpa, an agency of the U.S. Department of Defense.

Transcriptic and Ginko Bioworks aim to to overcome current limitations of biological design and modeling that the companies say rely on trial-and-error experimentation and imprecise measurement making it difficult to explore complex cellular systems with reproducible results. This initiative expects to address these limitations, say the companies, with more intensive application of engineering principles enabling large-scale collaborative experiments using robotics by geographically dispersed teams.

In this project, Ginko Bioworks is contributing its synthetic biology facilities and expertise that now develop engineered yeast and other microorganisms for industrial processes and consumer products. The company’s labs, what it calls foundries, design customized biological forms to meet specified properties, using computational techniques, analytics, and robotics. Ginko Bioworks says its foundries generate terabytes of data from genomic sequences, transcriptions, metabolomics, and proteomics.

Transcriptic develops science lab automation systems that bring together lab instruments and processes with Internet-of-Things or IoT technologies. The company offers a robotic cloud-based laboratory platform that it says can accelerate scientific discovery. Transcriptic also integrates these systems and processes into a single user interface called Transcriptic Common Lab Environment that makes it possible to conduct lab experiments from a remote laptop.

The companies plan to merge these capabilities with design and analysis algorithms driven by machine learning, a type of artificial intelligence. In addition to analyzing large quantities of data, the project team expects to apply machine learning to accelerate discovery and biological design as well as produce an open data exchange in the cloud could that can benefit research and academic communities in fields other than synthetic biology.

Ginko Bioworks is already using Transcriptic’s technology in its labs. In a five-year deal announced in October 2017, Ginko Bioworks began installing robotics systems in its Boston labs with the aim of doubling their output and providing more flexibility to meet customer needs in a growing biotech industry. The deal represents Transcriptic’s first licensing activity that involved on-site collaboration with customers.

Darpa is supporting this collaboration under its Synergistic Discovery and Design Program to encourage more data-driven methods like those used in aeronautics, automobiles, and integrated circuits to boost robust designs in disciplines where full-scale models for those designs are lacking. The agency cites synthetic biology as one of those fields, with biological systems that have millions of protein-metabolite interactions, yet still too often rely on manually-intensive analysis of small data sets.

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