Kinbiont.jl

Ecological and evolutionary processes of microbes are characterized by observables like growth rates and biomass yield, inferred from kinetics experiments.
Across conditions, these observables map response patterns such as antibiotic growth inhibition and yield dependence on substrate.
But how do we extract ecological and evolutionary insights from massive datasets of time-resolved microbial data? Here, we introduce Kinbiont — an ecosystem of numerical methods combining state-of-the-art solvers for ordinary differential equations, non-linear optimization, signal processing, and interpretable machine learning algorithms.
Kinbiont provides a comprehensive, model-based analysis pipeline, covering all aspects of microbial kinetics data, from preprocessing to result interpretation.

Documentation

For documentation please consult Documentation.

Publication

Please cite the Kinbiont paper.

Angaroni F., Peruzzi A., Alvarenga E. Z., Pinheiro F., Translating microbial kinetics into quantitative responses and testable hypotheses using Kinbiont, 2025, Nature Communication, 6440, 16, 1, https://doi.org/10.1038/s41467-025-61592-6

Data and scripts to reproduce the paper results at Kinbiont utilities