NUFEB: A massively parallel simulator for individual-based modelling of microbial communities
Fig 2
An example of (partial) input script for NUFEB simulation.
A list of “fix” commands defines IbM processes that apply to the simulation, which includes Monod-based growth (k1), nutrient mass balance (k2), cell division (d1), and EPS production (e1). Each fix command may require one or more parameters for the model specification, such as EPS density (EPSdens), division diameter (divDia), and HET reduction factor in anoxic condition (etaHET). The last parameter is introduced due to the fact that the observed growth rate of HET in anoxic condition was always smaller than that in aerobic condition.