In this repository, you can find the scripts and data to reproduce the results of the Kinbiont paper.
The contents of the folder 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.
For stable documentation of the package and various examples, please consult the Documentation.