• CompuCell3D

  • Referenced in 23 articles [sw34248]
  • species bacterial-biofilm growth using the Glazier-Graner-Ho-ge-weg model and the CompuCell3D ... environment. The CompuCell3D modeling environment provides a convenient platform for biofilm simulations using the Glazier ... determining biofilm morphology. In our simulations, which generalize the PLH model by treating cells ... shapes of biofilms. Our results agree with most features of the PLH model, although...
  • iDynoR

  • Referenced in 10 articles [sw11206]
  • paper ”iDynoMiCS: next-generation individual-based modelling of biofilms” by Lardon et al, published...
  • BacSim

  • Referenced in 22 articles [sw17261]
  • generic, quantitative, spatially explicit, individual-based model BacSim was developed to simulate growth and behaviour ... properties of macroscopic, complex systems such as biofilms. Here, the growth of a single Escherichia ... extension of Gecko, an ecosystem dynamics model which uses the Swarm toolkit for multi-agent...
  • BiofilmSim

  • Referenced in 7 articles [sw18050]
  • accurately captures the biomechanical response of bacterial biofilms and their associated extracellular matrix ... Immersed Boundary Method (hrIBM) and validating our model by comparison to experimental results. With this ... originally developed in Part I () to treat biofilms as viscoelastic fluids possessing variable rheological properties ... from our model to data from mechanical characterization experiments on Staphylococcus epidermidis biofilms. The experimental...
  • Matlab

  • Referenced in 13702 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 10196 articles [sw00771]
  • R is a language and environment for statistical...
  • XFEM

  • Referenced in 391 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 1616 articles [sw04215]
  • The Abaqus Unified FEA product suite offers powerful...
  • DIFSUB

  • Referenced in 106 articles [sw04370]
  • Algorithm 407 — DIFSUB for solution of ordinary differential...
  • spatial

  • Referenced in 365 articles [sw04502]
  • spatial: Functions for Kriging and Point Pattern Analysis...
  • lme4

  • Referenced in 262 articles [sw04515]
  • R package lme4: Linear mixed-effects models using...
  • KernSmooth

  • Referenced in 1018 articles [sw04586]
  • Kernel smoothing refers to a general methodology for...
  • ACADO

  • Referenced in 74 articles [sw04764]
  • ACADO Toolkit is a software environment and algorithm...
  • CVODE

  • Referenced in 65 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 61 articles [sw05611]
  • VisIt is an interactive parallel visualization and graphical...
  • ParaView

  • Referenced in 233 articles [sw06128]
  • ParaView is an open-source, multi-platform data...
  • ode23

  • Referenced in 335 articles [sw06600]
  • The MATLAB ODE Suite: ode23: Solve nonstiff differential...
  • ode45

  • Referenced in 331 articles [sw06762]
  • Matlab ode45. Solve nonstiff differential equations; medium order...