Pinned Repositories
co_culture_device
This repository contains code, data, and protocols related to the BioMe co-culture device
comets
Computation of Microbial Ecosystems in Time and Space
comets-toolbox
MATLAB scripts and utilities for the COMETS software for spatial DFBA
cometspy
Python interface for running COMETS simulations and analyzing the results
CostlessExchange
Contains scripts and data files for FBA-based computation of microbial costless cross-feeding.
MiCoNE
The Microbial Co-occurrence Network Explorer
networkExpansion
code for network expansion
Prochlorococcus_Model
Materials for Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus paper
string-chemistry
vivarium-comets
Segrè Lab's Repositories
segrelab/comets
Computation of Microbial Ecosystems in Time and Space
segrelab/MiCoNE
The Microbial Co-occurrence Network Explorer
segrelab/cometspy
Python interface for running COMETS simulations and analyzing the results
segrelab/Prochlorococcus_Model
Materials for Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus paper
segrelab/co_culture_device
This repository contains code, data, and protocols related to the BioMe co-culture device
segrelab/string-chemistry
segrelab/vivarium-comets
segrelab/bm3-book
segrelab/comets-manual
Documentation for using the COMETS application and related tools
segrelab/dolmn
Division Of Labor in Metabolic Networks
segrelab/learn-fba
Didactic materials for teaching FBA.
segrelab/marine_heterotrophs
Phenotyping of marine heterotrophs collection
segrelab/optima
Private repo containing scripts etc for the cellulase optima project
segrelab/Dukovski_et_al_2024
COMETS input file to reproduce the results and figures in Dukovski et al. (2024)
segrelab/GEM-utilities
segrelab/iamm-collection
segrelab/microscopy-vault
coordination of microscope experiment, initiated for the marine projects summer 2024
segrelab/.github
segrelab/BowSaw
segrelab/comets-virus
segrelab/escher-maps
Universal ModelSEED Escher maps
segrelab/EvolutionaryAlgorithms
Contains scripts to run evolutionary search algorithms for microbial community design.
segrelab/GEM2CUE
segrelab/MASS
Prediction of representative phenotypes using multi-attribute subset selection
segrelab/MetabolicComplexityDivergence
Code for "Metabolic complexity drives divergence in microbial communities"
segrelab/MiCoNE-pipeline-paper
The source code for the MIND pipeline paper
segrelab/MiCoNE-synthetic-data
Synthetic data and generation scripts for the MiCoNE manuscript
segrelab/moss
Prediction of representative phenotypes using multi-output subset selection
segrelab/nsAA_project
segrelab/SNP23
Variant Calling on Marine Strains (2023)