Mathematical software

CompuCell3D
Referenced in 23 articles [sw34248]
Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Ho-ge-weg model ... modeling environment provides a convenient platform for biofilm simulations using the Glazier-Graner-Hogeweg ... growth of a single-species bacterial biofilm, and study the roles of cell-cell ... cell-field interactions in determining biofilm morphology. In our simulations, which generalize the PLH model...

BacSim
Referenced in 22 articles [sw17261]
properties of macroscopic, complex systems such as biofilms. Here, the growth of a single Escherichia...

BiofilmSim
Referenced in 6 articles [sw18050]
Variable viscosity and density biofilm simulations using an immersed boundary method, part II: experimental validation ... accurately captures the biomechanical response of bacterial biofilms and their associated extracellular matrix ... originally developed in Part I () to treat biofilms as viscoelastic fluids possessing variable rheological properties ... from mechanical characterization experiments on Staphylococcus epidermidis biofilms. The experimental setup is described...

COMSTAT
Referenced in 7 articles [sw28030]
program that analyzes image stacks of biofilms recorded by confocal microscopes. It can extract ... been one of the preferred tools for biofilm quantification. In 2008 Martin Vorregaard ported...

iDynoR
Referenced in 9 articles [sw11206]
iDynoMiCS: next-generation individual-based modelling of biofilms” by Lardon et al, published in Environmental...

CompuCell3D