https://github.com/sysbiochalmers/raven

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

constraint-based-modeling gap-filling genome-scale-models human-metabolism metabolic-engineering metabolic-models metabolic-reconstruction sysbio systems-biology

Last synced: 19 Apr 2026

https://github.com/lcsb-biocore/cobrexa.jl

Constraint-Based Reconstruction and EXascale Analysis

cobra constraint-based-modeling exascale exascale-analysis high-performance hpc julia

Last synced: 31 Jul 2025

https://github.com/cdanielmachado/embl_gems

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

constraint-based-modeling genome-scale-models metabolism

Last synced: 17 Jan 2026

https://github.com/stelmo/escher.jl

Visualization of metabolic models in Makie.

cobra constraint-based-modeling julia visualization

Last synced: 16 Jul 2025

https://github.com/metexplore/miom

Constraint-based modeling of metabolism using Mixed Integer Optimization

cobrapy constraint-based-modeling flux-balance-analysis genome-scale metabolism milp modeling optimization python reconstruction

Last synced: 14 Oct 2025

https://github.com/christianlieven/memote-m-capsulatus

Genome-scale metabolic model of Methylococcus capsulatus.

c1 constraint-based-modeling genome-scale-models metabolic-models metabolic-reconstruction metabolism methanotrophy methylococcus systems-biology

Last synced: 05 Mar 2026

https://github.com/sysbiochalmers/yarrowia_lipolytica_w29-gem

Genome-scale model of Yarrowia lipolytica.

constraint-based-modeling genome-scale-models metabolic-engineering metabolic-models metabolic-network metabolic-reconstruction omics-data-integration stoichiometric-reactions systems-biology yarrowia-lipolytica

Last synced: 04 Jul 2025

https://github.com/htpusa/moomin

MOOMIN is a tool for analysing differential expression data

constraint-based-modeling differential-expression gene-expression matlab metabolic-network moomin

Last synced: 13 Oct 2025

https://github.com/metexplore/dexom

Diversity-based enumeration of optimal context-specific metabolic networks

cobra-toolbox constraint-based-modeling metabolic-engineering metabolic-network metabolic-pathways metabolic-reconstruction metabolism omics-data-integration optimization

Last synced: 14 Oct 2025

https://github.com/stelmo/equilibrator.jl

A lightweight interface to eQuilibrator and equilibrator_api through Julia.

constraint-based-modeling equilibrator julia thermodynamics

Last synced: 07 May 2025

https://github.com/htpusa/moomin.jl

From differential gene expression to metabolic changes

constraint-based-modeling differential-expression gene-expression metabolic-models transcriptomics

Last synced: 11 Apr 2025

https://github.com/spherotob/gcopt

Determination of product-growth-coupled strain designs employing stoichiometric metabolic models.

constraint-based-modeling metabolic-engineering systems-biology

Last synced: 31 Aug 2025

https://github.com/sysbiochalmers/rhto-gem

Genome-scale metabolic model of Rhodotorula toruloides

constraint-based-modeling genome-scale-models metabolic-engineering metabolic-reconstruction sysbio systems-biology yeast

Last synced: 26 Mar 2025

https://github.com/metexplore/dexom-python

diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library

cobrapy constraint-based-modeling metabolism omics-data-integration optimization python

Last synced: 24 Aug 2025

https://github.com/sysbiochalmers/gecko2_simulations

Collection of scripts for reproduction of simulation results in "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0".

constraint-based-modeling enzyme-constraints metabolism

Last synced: 24 Aug 2025

https://github.com/charlesrocabert/gbapy

Growth Balance Analysis for Python

constraint-based-modeling growth-balance-analysis metabolic-models non-linear-optimization systems-biology

Last synced: 03 Mar 2026

https://github.com/nyxflower/memo

Constraint-based metabolic modelling with sparse IPOPT

constraint-based-modeling interior-point-optimizer metabolic-models non-linear-optimization

Last synced: 07 Jun 2026

https://github.com/qwerty239qwe/pipegem

This is a package for visualizing and analyzing multiple metabolic models. It also allow users to integrate omic data, metabolic tasks, and medium data with genome-scale metabolic models (GEMs).

constraint-based-modeling genome-scale-metabolic-model metabolic-models omics-data-integration

Last synced: 20 Jan 2026

https://github.com/sysbiochalmers/cellfactory-ecyeastgem

Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.

cell-factory constraint-based-modeling enzyme-constraints yeast

Last synced: 29 Jul 2025

https://github.com/cnapy-org/efmtool_link

bioinformatics computational-biology constraint-based-modeling metabolic-pathways python stoichiometric-modeling

Last synced: 04 Apr 2026