Software system design to support scale in mammalian cell line engineering

Cell line engineering (CLE) is the process of gene editing living cell lines for various purposes such as protein production, fluorescent tagging, compound screening tools, reference standards or diagnostics. Manufacturing processes of the line were typically low throughput and we aimed to increase the capacity of the platform to meet market demand. Software is required to match any throughput and equally as important as any lab based manual or automated methods. To support this increased throughput, a Laboratory Information Management System (LIMS) was developed which contained a data model that represents the CLE process and tracks all projects at each stage. A connection was also made to our own internal ordering system to track projects and register engineering designs based on a markup language we developed called Genetic Engineering Markup Language (GEML). Additionally, we developed an ML based method for analysing clones using an automated imaging platform. The combined wet-lab and software approach allowed us to treble the capacity of the platform allowing us to reach the potential of engineering biology.