segrelab Goto Github PK

.github

biosynthetic_network_robustness

This repository contains the code used in Bernstein DB, Dewhirst FE, Segre D. (2019) Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. eLife. DOI: 10.7554/eLife.39733.

bm3-book

boundaryconditionsforancientmetabolism

Associated github repository for code and data from the article "Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism"

bowsaw

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-manual

Documentation for using the COMETS application and related tools

comets-matlab-gui

comets-toolbox

MATLAB scripts and utilities for the COMETS software for spatial DFBA

comets-virus

comets_examples_tests

A collection of setups ready to run in COMETS. Also this set can be used as a testing suite.

comets_protocols

COMETS simulations examples and protocols

comets_windows_install

cometsdatabase

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.

dolmn

Division Of Labor in Metabolic Networks

dukovski_et_al_2024

COMETS input file to reproduce the results and figures in Dukovski et al. (2024)

environmentalcomplexity

Scripts for analyzing multispecies microbial community yields and taxonomic composition as functions of environmental complexity. Includes code to run and analyze consumer resource model simulations.

escher-maps

Universal ModelSEED Escher maps

evolutionaryalgorithms

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

fprau-btheta-2018

gem-utilities

gem2cue

iamm-collection

learn-fba

Didactic materials for teaching FBA.

marine_heterotrophs

Phenotyping of marine heterotrophs collection

mass

Prediction of representative phenotypes using multi-attribute subset selection

micone

The Microbial Co-occurrence Network Explorer