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

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.

KMG060 Systems Biology course - repo for students

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!

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

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

This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function

Analysis of neutrophil metabolic activity during metastasis using single-cell RNASeq and COnstraint-Based Reconstruction and Analysis.

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

Constraint-based modeling of metabolism using Mixed Integer Optimization

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

Python implementation of FastSL

"Maps for when the living gets tough: Maneuvering through a hostile energy landscape" | Mondeel, Thierry D.G.A. Rehman, Samrina Zhang, Yanfei Verma, Malkhey Dürre, Peter Barberis, Matteo Westerhoff, Hans V. | 2016 | IFAC-PapersOnLine |

Shiny app for visualization of the toy GENREs

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.

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

EMILiO

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

A sequential gene scanner for both gene deletions and upregulations, based on flux balance analysis