Toolboxes (Matlab)

Nutrient Uptake - A model for the prediction of nutrient transport for acclimated, steady-state microbial growth. source

MSE - Microbial Simulation Environment. A platform for the simulation of microbial growth, physiology and metabolism in the natural environment. source

PanGEM - A pipeline for the reconstruction of strain-level genome-scale metabolic networks, using a pangenome as a template. source

Genome-scale models

Prochlorococcus MED4 SBML, BioOpt, Excel