From legacy systems to data pipelines modernization in fermentation process

Developments in biotechnology using high throughput systems are increasingly and consequently the creation and consumption of data continue to grow rapidly. Data migration is an essential part of legacy system modernization in bioprocess. Migration process involves transferring data from outdated platforms or unknown data schemas to more advanced and secure systems. Data migration can be represented through data pipelines including data extraction, transformation and loading (ETL). The data pipelines are implemented in order to increase the overall efficiency of data-flow from the source (raw data) to the knowledge generation (Mohanty et al., 2013). Legacy systems in fermentation generally occur in bioreactor components as sensors, protocols, software or databases. These issues can limit the integration with modern tools and systems as Process Analytical Technology (PAT) instruments (Gerzon et al., 2022), avoiding real-time data on process parameters and thereby fail to assist operators in maintain optimal conditions for cell growth and production. The aim of this research is to present a guided process for designing data pipelines in bioreactors legacy systems. We present as use case a set of 24 mini-bioreactors of 50 mL. We conducted unit testing for components of the ETL process in order to ensure the integration and migration process of the legacy DB.