Daniel Machado

carveme. CarveMe: genome-scale metabolic model reconstruction

smetana. SMETANA: a tool to analyse interactions in microbial communities

reframed. ReFramed: metabolic modeling package

embl_gems. EMBL GEMs: A collection of GEnome-scale Models for bacterial species

framed. framed: a metabolic modeling package for python

HiOrCo. Higher-Order Co-occurrence

cooccurrence. Supplementary data for co-occurrence manuscript

designmc. Designing microbial communities

SteadierCom. Microbial community simulation

carveme_paper. Data and scripts for the paper "Fast automated reconstruction of genome-scale metabolic models for microbial species and communities"

transcript2flux. Scripts and results from omics-based methods assessment paper in PLoS Comp Bio 2014

GPRTransform. Stoichiometric representation of GPR associations (transformation method and gene-based simulation methods)

tutorials. Tutorials on metabolic modeling

arfba. Allosteric Regulation FBA (simulation method)

solver_benchmark. Jupyter Notebook

embo_mcd22. Jupyter Notebook

kefir_paper. Supplementary Material for Blasche et al