Automation

The Automation Team is part of the Biofoundry and specializes in developing custom automated workflows and protocols. Our team is made up of automation specialists and our primary goal is to significantly enhance throughput and data generation in research projects, aiming for orders of magnitude improvements. We collaborate closely with research groups, tailoring specific workflows to meet their unique requirements.

Our team possesses extensive expertise in a variety of liquid handling robots and automated systems. This includes proficiency with open-source systems like Opentrons and Chi.Bio and we contribute to the scientific community by open-sourcing code and protocols developed on these platforms. Additionally, we are adept in working with larger proprietary systems such as the Tecan Fluent, Agilent Bravo, and Labcyte Echo. Our capability to leverage diverse instruments with unique functionalities allows us to support a broad spectrum of projects and research endeavours.

We provide comprehensive services including workflow development, scripting, troubleshooting, and operation. Our approach emphasizes rapid deployment and iteration of workflows, facilitating swift progress in research projects. Our portfolio includes automation projects in areas like NGS library preparation, media optimization through Design of Experiments (DoE), laboratory-scale evolutionary experiments, automated cultivation and sampling, PCR clean up, and more. Our team also supports activities withing the Biofoundry, working closely with the Analytics Team to automate their sample preparation processes for HPLC, proteomics and LC-MS analysis.

We are also responsible for the in-house gene synthesis platform, SpeedyGenes, which is a fully automated system for generation of protein libraries for screening and selection. With this system, which combinatorically assembles the protein from small DNA fragments, we can make protein libraries of arbitrarily large diversity, with mutations targeted to specific sites. This system is especially useful in generating libraries for screening and selection in deep learning workflows.

Technologies

• SpeedyGenes
• Chi.Bio Adaptive Laboratory Evolution system
• Agilent Bravo
• Opentrons OT2 (x4)
• Tecan Fluent
• Labcyte Echo (for protocols not covered by DNA Foundry)
• Chi.Bio reactor (x8)
• Pioreactor (x4, incoming)
• Growth profilers (x3)
• MutationMaker / SpeedyGenes (Targeted gene variant library generation)

Links

• Database of transporter growth and Opentrons code for generating data: Github
• ChiBio with evolution function: Github

Selected Publications

1. Munro LJ, Kell DB (2022) Analysis of a library of E. coli transporter knockout strains to identify transport pathways of antibiotics. Antibiotics 11, 1129. DOI: 10.3390/antibiotics11081129.