Repositories list

• SNP23

  Public
  Variant Calling on Marine Strains (2023)

  Shell

  •0•0•6•0•Updated Nov 25, 2024Nov 25, 2024

• MetabolicComplexityDivergence

  Public
  Code for "Metabolic complexity drives divergence in microbial communities"

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• comets

  Public
  Computation of Microbial Ecosystems in Time and Space

  Java

  •

  MIT License

  •10•19•22•1•Updated Nov 7, 2024Nov 7, 2024

• learn-fba

  Public
  Didactic materials for teaching FBA.

  Jupyter Notebook

  •1•1•0•0•Updated Sep 25, 2024Sep 25, 2024

• iamm-collection

  Public
  R

  •0•0•1•0•Updated Sep 6, 2024Sep 6, 2024

• cometspy

  Public
  Python interface for running COMETS simulations and analyzing the results

  Python

  •

  GNU General Public License v3.0

  •9•11•18•0•Updated Aug 14, 2024Aug 14, 2024

• 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

• GEM2CUE

  Public
  Python

  •

  MIT License

  •0•0•5•0•Updated May 10, 2024May 10, 2024

• bm3-book

  Public
  Jupyter Notebook

  •0•1•2•0•Updated Apr 30, 2024Apr 30, 2024

• 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 Apr 1, 2024Apr 1, 2024

• MASS

  Public
  Prediction of representative phenotypes using multi-attribute subset selection

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Feb 28, 2024Feb 28, 2024

• MiCoNE

  Public
  The Microbial Co-occurrence Network Explorer

  pipelinenextflowdata-analysis+ 3microbiomenetwork-analysis16s-rrna

  Python

  •

  MIT License

  •4•19•0•1•Updated Oct 17, 2023Oct 17, 2023

• MiCoNE-pipeline-paper

  Public
  The source code for the MIND pipeline paper

  data-analysismicrobiomeqiime+ 2qiime216s-rrna

  HTML

  •0•0•0•0•Updated Aug 31, 2023Aug 31, 2023

• comets-virus

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 18, 2023Aug 18, 2023

• escher-maps

  Public
  Universal ModelSEED Escher maps

  Python

  •0•0•3•0•Updated Aug 11, 2023Aug 11, 2023

• GEM-utilities

  Public
  Python

  •0•0•21•1•Updated Aug 11, 2023Aug 11, 2023

• .github

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

• string-chemistry

  Public
  Python

  •1•2•0•1•Updated Jul 6, 2023Jul 6, 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

  •2•2•0•0•Updated Jan 13, 2023Jan 13, 2023

• comets-manual

  Public
  Documentation for using the COMETS application and related tools

  Python

  •2•1•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

• optima

  Public
  Private repo containing scripts etc for the cellulase optima project

  Forth

  •0•1•0•0•Updated Mar 28, 2022Mar 28, 2022

• nsAA_project

  Public
  MATLAB

  •0•0•0•0•Updated Feb 25, 2022Feb 25, 2022

• MiCoNE-synthetic-data

  Public
  Synthetic data and generation scripts for the MiCoNE manuscript

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Jan 18, 2022Jan 18, 2022

• BowSaw

  Public
  R

  •1•0•0•0•Updated Jun 8, 2021Jun 8, 2021

• EvolutionaryAlgorithms

  Public
  Contains scripts to run evolutionary search algorithms for microbial community design.

  MATLAB

  •1•0•0•0•Updated Apr 27, 2021Apr 27, 2021

• dolmn

  Public
  Division Of Labor in Metabolic Networks

  MATLAB

  •

  MIT License

  •2•1•0•0•Updated Mar 26, 2021Mar 26, 2021