Section: Software

JPADE

Participant : Nabil Mabrouk.

JPADE is a simulator for two-dimensional biofilms grown on a planar surface. The simulator is written in Java and solves a system of three diffusion-reaction equations for the substrate, the bacteria and a product excreted by the bacteria [23] .

The substrate consumption rate is modeled using a Monod equation. A fraction of the consumed substrate is supposed to be released back in the form of a product whereas the remaining part is transformed to biomass. The biomass, the substrate and the excreted product are allowed to diffuse. The diffusion factors may be constant or may depend on other variables. For instance, the simulator has been used for simulating the spatial patterns that arise for Pseudomonas Aeruginosa biofilms grown in flow chamber when the diffusion of the biomass is reduced by the accumulation of the self-excreted product.

The model parameters and the simulation results are displayed using a Graphical User Interface. JPADE is available on demand under the General Public License issued by the Free Software Foundation.