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    • Codes for manuscript, "Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
      Jupyter Notebook
      0000Updated Oct 7, 2024Oct 7, 2024
    • gLV parameter estimation for Cdiff communities
      Jupyter Notebook
      MIT License
      0000Updated Jun 12, 2024Jun 12, 2024
    • Scripts used in DoTA-seq methods paper
      Jupyter Notebook
      2000Updated Dec 15, 2023Dec 15, 2023
    • Growth limitation via chemically complex carbohydrates reduces sensitivity of synthetic human gut communities to perturbations
      Jupyter Notebook
      MIT License
      0000Updated Aug 22, 2023Aug 22, 2023
    • Microbiome Recurrent Neural Network (MiRNN)
      Jupyter Notebook
      MIT License
      0000Updated Jul 20, 2023Jul 20, 2023
    • PyTorch Implementation of LSTM-based dynamical model for predicting species abundance and metabolite concentrations in a heterogeneous community
      Jupyter Notebook
      1200Updated Jul 10, 2023Jul 10, 2023
    • Tutorials

      Public
      Tutorials for programming in Python, model development, and parameter estimation
      Jupyter Notebook
      0000Updated Apr 28, 2023Apr 28, 2023
    • Scripts used in Bfragilis CPS paper
      Jupyter Notebook
      1000Updated Oct 31, 2022Oct 31, 2022
    • MATLAB
      GNU General Public License v3.0
      0000Updated Sep 29, 2022Sep 29, 2022
    • Microbial Interactions Impact Cdifficile Antibiotic Response
      Python
      1000Updated Sep 7, 2022Sep 7, 2022
    • Python implementation of methods described in "Pattern Recognition and Machine Learning" by Christopher Bishop to perform Bayesian Linear regression on synthetic data.
      Jupyter Notebook
      2000Updated Apr 14, 2022Apr 14, 2022
    • Jupyter Notebook
      0010Updated Mar 10, 2022Mar 10, 2022
    • MATLAB
      0000Updated Mar 10, 2022Mar 10, 2022