COBRApy is a package for constraint-based modeling of metabolic networks.

Computational synthetic biology: Predicting DNA edits for bioengineering

Infer metabolic directions from moment differences of mass-weighted intensity distributions

A python library for metabolic networks sampling and analysis

debugging biological networks to reach coherence, completeness and consistency

Curation and analysis of metabolic models

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL

Open source genome-scale metabolic models of human and model animals

Pathway Tools multiprocessing wrapper (for PathoLogic).

A Universal Modeling Language for Metabolic Flux Analysis

R codes for creating metamapp graphs and files

Genome-scale model of Yarrowia lipolytica.

MOOMIN is a tool for analysing differential expression data

🗺️ A repository of CNApy projects

Kinetic modeling of glucose and acetate metabolisms in E. coli

MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.

An R package to find the gaps in metabolic networks, and fill it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also include the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database.

Enzymatic Link Prediction

TRIMER is a package for building integrated metabolic–regulatory models base on Bayesian network. TRIMER can be used for knockout phenotype prediction and knock flux prediction.