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μGrowthDB: querying, visualizing, and sharing microbial growth curve data

Radev, A.; Casado Gomez-Pallete, J.; Monsalve Duarte, S.; Faust, K.; Zafeiropoulos, H.

2025-10-13 microbiology
10.1101/2025.10.13.682118 bioRxiv
Show abstract

Microbial growth curve data contain valuable information about microorganisms physiology and metabolism. However, they are currently reported in various formats scattered across publications. A generic resource that allows querying and comparing microbial growth curve data is currently missing. For this reason, we developed GrowthDB, an open repository designed to store, visualize, analyze, and share quantitative measurements of species abundances and metabolite profiles from monocultures and communities of known composition. GrowthDB is designed to accommodate a range of experimental designs and measurement techniques. In addition to querying microbial growth curves by organism or metabolite, GrowthDB supports comparative visualisation of growth curves and offers a guided data submission process intended to make data upload as easy as possible. GrowthDB is available at: https://mgrowthdb.gbiomed.kuleuven.be/.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.