flux-balance-analysis

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.

A Python package for "classic" Constraint-Based Reconstruction and Analysis (COBRA) and the new COBRA with kinetics (COBRA-k). Link to documentation and tutorials:

Python, modeling and Flux balance analysis tutorials for the undergraduate Systems Biology course in Amsterdam

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2022

Constraint-based modeling of metabolism using Mixed Integer Optimization

University of Cambridge Part III Systems Biology course, practical exercises for learning flux balance analysis

Python implementation of mgpipe

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.

Library to perform metabolic engineering tasks

Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002

Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2024

Dynamically load-balanced FVA through a hybrid MPI/OpenMP architecture.

KMG060 Systems Biology course - repo for students

Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines | Ewelina Węglarz-Tomczak, Thierry D.G.A. Mondeel, Diewertje G.E. Piebes, Hans V. Westerhoff | Biomolecules 2021

Constraint-based model vulnerabilities analysis - Python analysis tool http://contrabass.unizar.es

Machine learning pipeline for genome-scale metabolic engineering and intervention ranking in E. coli using COBRApy and FBA.