• 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...
  • Matlab

  • Referenced in 13460 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 9810 articles [sw00771]
  • R is a language and environment for statistical...
  • XFEM

  • Referenced in 382 articles [sw01026]
  • An extended finite element library. This paper presents...
  • Gromacs

  • Referenced in 124 articles [sw04128]
  • GROMACS is a versatile package to perform molecular...
  • ABAQUS

  • Referenced in 1594 articles [sw04215]
  • The Abaqus Unified FEA product suite offers powerful...
  • DIFSUB

  • Referenced in 104 articles [sw04370]
  • Algorithm 407 — DIFSUB for solution of ordinary differential...
  • spatial

  • Referenced in 360 articles [sw04502]
  • spatial: Functions for Kriging and Point Pattern Analysis...
  • lme4

  • Referenced in 240 articles [sw04515]
  • R package lme4: Linear mixed-effects models using...
  • KernSmooth

  • Referenced in 978 articles [sw04586]
  • Kernel smoothing refers to a general methodology for...
  • ACADO

  • Referenced in 72 articles [sw04764]
  • ACADO Toolkit is a software environment and algorithm...
  • CVODE

  • Referenced in 62 articles [sw04947]
  • CVODE is a solver for stiff and nonstiff...
  • DAKOTA

  • Referenced in 77 articles [sw05202]
  • A Multilevel Parallel Object-Oriented Framework for Design...
  • VisIt

  • Referenced in 51 articles [sw05611]
  • VisIt is an interactive parallel visualization and graphical...
  • ParaView

  • Referenced in 204 articles [sw06128]
  • ParaView is an open-source, multi-platform data...
  • ode23

  • Referenced in 318 articles [sw06600]
  • The MATLAB ODE Suite: ode23: Solve nonstiff differential...