cdanielmachado Goto Github PK

arfba

Allosteric Regulation FBA (simulation method)

carveme

CarveMe: genome-scale metabolic model reconstruction

carveme_paper

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

cooccurrence

Supplementary data for co-occurrence manuscript

designmc

Designing microbial communities

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

elin_msc_thesis

embl_gems

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

embo_mcd22

emsampler

Random sampling of Elementary Flux Modes

framed

framed: a metabolic modeling package for python

gprtransform

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

hiorco

Higher-Order Co-occurrence

jenny_msc_thesis

Supplementary information for MSc thesis in Biotechnology, NTNU, May 2022.

kefir_paper

Supplementary Material for Blasche et al

marieke_msc_thesis

Supplementary material to "Predicting metabolic fluxes from gene expression data using machine learning"

martin_msc_thesis

reframed

ReFramed: metabolic modeling package

smetana

SMETANA: a tool to analyse interactions in microbial communities

solver_benchmark

teaching

transcript2flux

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

tutorials

Tutorials on metabolic modeling

yeast_36_strains