In this repository, you can find the scripts and data to reproduce the results of 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
The contents of the folders are as follows:
- Automatic_Law_detection - Scripts and data to reproduce the law detection of amino acid limitation and drug dose response.
- CoCultures_ODEs_system - Scripts and data for the decision tree example using data from "Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions".
- DT_antibiotics_interactions - Scripts and data for reproducing the data frames plotted in Figures 5 and 6. The data are from "High-throughput characterization of bacterial responses to complex mixtures of chemical pollutants".
- Diauxic_Phages - Data and scripts for the segmentation fits of data from "Fast phage detection and quantification: An optical density-based approach", as well as diauxic growth data from "Diauxic lags explain unexpected coexistence in multi-resource environments".
- EtOH_production - Fitting of multidimensional ODEs on data from "Mechanistic Modelling of Biomass Growth, Glucose Consumption, and Ethanol Production by Kluyveromyces marxianus in Batch Fermentation".
- synthetic_tests - Synthetic tests for SM and other related tasks.
- Notebooks - Notebooks containing compact versions of most of the main text analyses.
- Source_Data - The txt files of the data generated for the paper.
For stable documentation of the package and various examples, please consult the Documentation.