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    47 repositories

    • metaCRM_SynCom

      Public
      Metabolomics-informed consumer-resource modeling of a 15-member synthetic microbial community.
      Python
      •
      MIT License
      •1•3•0•0•Updated Aug 26, 2026Aug 26, 2026

    • comets

      Public
      Computation of Microbial Ecosystems in Time and Space
      HTML
      •
      MIT License
      •15•28•24•1•Updated Aug 19, 2026Aug 19, 2026

    • Combined-Phenotyping-of-Carbon-and-Nitrogen-sources-2026

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 5, 2026Jun 5, 2026

    • cometspy

      Public
      Python interface for running COMETS simulations and analyzing the results
      Python
      •
      GNU General Public License v3.0
      •12•16•20•0•Updated May 19, 2026May 19, 2026

    • HOT5-strains-paper-2026

      Public
      Public repository for Osborne et al 2026 manuscript with code for wgs of HOT5 strains and code for for data analysis and figure generation
      R
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • string-chemistry

      Public
      Python
      •1•2•0•1•Updated Jan 21, 2026Jan 21, 2026

    • GEM-hot1a3

      Public
      Linear Programming
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • GEM-atcc27126

      Public
      Linear Programming
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • comets-virus

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • SNP23

      Public
      Variant Calling on Marine Strains (2023)
      HTML
      •0•0•4•0•Updated Nov 11, 2025Nov 11, 2025

    • waspgut

      Public
      These are python scripts to reproduce the reults of a publication.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • iamm-collection

      Public
      R
      •0•0•2•0•Updated Sep 23, 2025Sep 23, 2025

    • COMETS_Chemotaxis

      Public
      Jupyter notebooks associated with Shi et al. Methods in Molecular Biology, Springer Nature
      simulationschemotaxis
      simulationschemotaxis
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025

    • Dukovski_et_al_2024

      Public
      COMETS input file to reproduce the results and figures in Dukovski et al. (2024)
      MATLAB
      •
      Other
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • COMETS_Protocols

      Public
      COMETS simulations examples and protocols
      Mathematica
      •
      Creative Commons Zero v1.0 Universal
      •3•4•0•0•Updated May 6, 2025May 6, 2025

    • learn-fba

      Public
      Didactic materials for teaching FBA.
      Jupyter Notebook
      •1•1•0•0•Updated Apr 22, 2025Apr 22, 2025

    • MetabolicComplexityDivergence

      Public
      Code for "Metabolic complexity drives divergence in microbial communities"
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • microscopy-vault

      Public
      coordination of microscope experiment, initiated for the marine projects summer 2024
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

    • bm3-book

      Public
      Jupyter Notebook
      •0•1•2•0•Updated Apr 30, 2024Apr 30, 2024

    • MASS

      Public
      Prediction of representative phenotypes using multi-attribute subset selection
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Feb 28, 2024Feb 28, 2024

    • MiCoNE

      Public
      The Microbial Co-occurrence Network Explorer
      pipelinenextflowdata-analysis
      pipelinenextflowdata-analysismicrobiomenetwork-analysis16s-rrna
      Python
      •
      MIT License
      •4•21•1•1•Updated Oct 17, 2023Oct 17, 2023

    • MiCoNE-pipeline-paper

      Public
      The source code for the MIND pipeline paper
      data-analysismicrobiomeqiime
      data-analysismicrobiomeqiimeqiime216s-rrna
      HTML
      •0•1•0•0•Updated Aug 31, 2023Aug 31, 2023

    • escher-maps

      Public
      Universal ModelSEED Escher maps
      Python
      •0•0•3•0•Updated Aug 11, 2023Aug 11, 2023

    • .github

      Public
      0•0•0•0•Updated Aug 4, 2023Aug 4, 2023

    • vivarium-comets

      Public
      Jupyter Notebook
      •0•2•4•0•Updated Mar 21, 2023Mar 21, 2023

    • co_culture_device

      Public
      This repository contains code, data, and protocols related to the BioMe co-culture device
      MATLAB
      •3•2•0•0•Updated Jan 13, 2023Jan 13, 2023

    • comets-manual

      Public
      Documentation for using the COMETS application and related tools
      Python
      •2•2•0•1•Updated Dec 1, 2022Dec 1, 2022

    • Prochlorococcus_Model

      Public
      Materials for Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus paper
      HTML
      •4•7•1•0•Updated Oct 24, 2022Oct 24, 2022

    • moss

      Public
      Prediction of representative phenotypes using multi-output subset selection
      Python
      •1•0•0•0•Updated Jul 25, 2022Jul 25, 2022

    • marine_heterotrophs

      Public
      Phenotyping of marine heterotrophs collection
      R
      •0•1•0•0•Updated May 11, 2022May 11, 2022
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