Synthetic biology’s DNA factories can now churn out genetic sequences faster than any human can track, but the software to manage that torrent of data is missing. This project builds the digital backbone for Imperial College’s DNA Foundry—a high-throughput facility that assembles custom genes and engineered genomes. The hardware already exists: liquid-handling robots, automated synthesizers, and sequencing machines. What is lacking is an integrated software system to log each step, link design to assembly, and make sense of the millions of data points generated per run. Without it, the Foundry cannot operate at full capacity or learn from its own output. If successful, the team will deliver an open-source operating system that connects every machine and database in the workflow, plus a “Knowledge Centre” that stores, analyses, and models the resulting data. This would let researchers design a genetic circuit on a computer, have it built and verified automatically, and receive feedback on performance—all within a single digital pipeline. The system will also screen every DNA sequence against biosecurity watchlists, preventing accidental or deliberate misuse of synthetic genes. The impact is largely invisible to the public: faster development of engineered microbes for medicines, biofuels, and biodegradable materials, underpinned by infrastructure that keeps the process safe and reproducible.
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Synthetic biology has the tremendous potential for enabling the design and implementation of sophisticated biochemical mechanisms for sensing, computing, control, production, and activation. This approach is anticipated to lead to many breakthrough applications in biotherapeutics, bioremediation, biomaterials, and in vivo-sensing and activation and self-assembly. The hardware available to exploit synthetic biology has evolved to deliver the many protocols for synthesizing DNA and verifying its assembly. Advances in liquid handling, automation, miniaturization, microfluidics and spectroscopy have collectively combined to make possible the rapid construction of synthetic genes, engineered pathways and synthetic genomes. The initial capital funding of this technology at the Centres of DNA Synthesis (The Foundries) has made possible the development of automated workstations organized to synthesize DNA components and assemblies designed to meet defined biofunctional performance parameters. As a direct consequence of the automation of DNA synthesis and assembly there has been a massive increase in throughput, size and complexity of experimental space covered. The research challenge now faced is the lack of an integrated suite of software tools to support DNA synthesis at the Foundry scale. This is part logistical, in the management of the process and data, and part statistical in the interpretation and modeling of the massive amounts of data generated by the Foundry. Similar to the automation of DNA sequencing, automation of synthetic biology in the Foundry will result in the generation and processing of huge amounts of data. The aims of this proposal: - Maximize the efficiencies of the Foundry by developing an open source operating system to support an integrated engineering design workflow allowing seamless inter-tool communication for hardware and software. - Develop a 'Knowledge Centre' capable of providing storage, processing, analysis and predictive modeling of the data coming from DNA design, sequencing, characterization and process metrics generated by the Foundry. - Build the computational infrastructure to comply with the International Gene Synthesis Consortium (IGSC) to prevent the misuse of synthetic genes. Sequences of DNA synthesized will be screened and users vetted to ensure vigilance and biosecurity of the Foundry.
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