Matlab code and data to reproduce results from "Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM" by Dreyfuss, Zucker, et al.

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.

EMILiO

Core cancer metabolism model of Palsson et al: https://rdcu.be/Olwc

Source code and information for journal article Social dynamics and modeling of chrono-nutrition

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

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

Figure 5 - Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters

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

"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 |

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

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

iJV803: a genome-scale metabolic model for Methylomicrobium album BG8

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

A RMosek optimization interface for the Sybil package

Shiny app for visualization of the toy GENREs

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