Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2
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16 octobre 2023
- handle: 10670/1.3tbnew
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Mateusz Jundzill et al., « Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2 », Digitale Bibliothek Thüringen, ID : 10670/1.3tbnew
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With the rapidly growing amount of biological data, powerful but also flexible data management and visualization systems are of increasingly crucial importance. The COVID-19 pandemic has more than highlighted this need and the challenges scientists are facing. Here, we provide an example and a step-by-step template for non-IT personnel to easily implement an intuitive, interactive data management solution to manage and visualize the high influx of biological samples and associated metadata in a laboratory setting. Our approach is illustrated with the genomic surveillance for SARS-CoV-2 in Germany, covering over 11 600 internal and 130 000 external samples from multiple datasets. We compare three data management options used in laboratories: (i) simple, yet error-prone and inefficient spreadsheets, (ii) complex and long-to-implement laboratory information management systems and (iii) high-performance database management systems. We highlight the advantages and pitfalls of each option and outline why a document-oriented NoSQL option via MongoDB Atlas can be a suitable solution for many labs. Our example can be treated as a template and easily adapted to allow scientists to focus on their core work and not on complex data administration.