💎 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 with common 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.

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.

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

Constraint-based modeling of metabolism using Mixed Integer Optimization

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

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

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

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

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

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

An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.

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

KMG060 Systems Biology course - repo for students

COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae