Code

Toolboxes

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

PheArrMe - A pipeline to guide the gapfilling of models generated with CarveMe using phenotype microarray data, including time-series absorption measurements of ‘biolog-like’ plates. source

Genome-scale models

Prochlorococcus MED4 SBML, BioOpt, Excel