Repositories list

• csdR

  Public
  Efficient CSD implementation in R

  R

  •

  GNU General Public License v3.0

  •1•7•0•0•Updated Jan 16, 2026Jan 16, 2026

• elixir-galaxy-tools-systemsbiology

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• AutoKEGGRec

  Public
  AutoKEGGRec is an automated tool that creates first draft metabolic network reconstructions of single organisms, community reconstructions based on a list of or…

  MATLAB

  •

  GNU General Public License v3.0

  •2•8•0•0•Updated Mar 21, 2024Mar 21, 2024

• autopacmen

  Public
  Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method

  HTML

  •

  Apache License 2.0

  •8•0•0•0•Updated Jul 7, 2023Jul 7, 2023

• BayesianGEM

  Public
  This repository contains code and data needed to replicate the analysis carried out in the manuscript Pettersen J and Almaas A. 2023.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •4•1•0•0•Updated Jun 21, 2023Jun 21, 2023

• T66-GEM

  Public
  GEM for Aurantiochytrium sp. T66

  standard-gemgenome-scale-modelthraustochytrid+ 1aurantiochytrium

  Python

  •

  Creative Commons Attribution 4.0 International

  •0•1•0•0•Updated Jun 13, 2023Jun 13, 2023

• BiGMeC

  Public
  BiGMeC - Biosynthetic Gene cluster Metabolic pathway Constructor

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3•16•0•0•Updated May 14, 2023May 14, 2023

• acidFBA

  Public
  MATLAB

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 22, 2022Jul 22, 2022

• micInt

  Public
  R package for analyzing microbial co-occurences

  rdata-manipulationco-occurence+ 2microbiome-analysisphyloseq

  R

  •0•1•0•0•Updated Mar 10, 2022Mar 10, 2022

• SystemsBrewology

  Public
  0•0•0•0•Updated Jun 18, 2021Jun 18, 2021

• CarveFungi

  Public
  Python

  •

  GNU General Public License v3.0

  •4•0•0•0•Updated Feb 10, 2021Feb 10, 2021