• MesoRD

  • Referenced in 31 articles [sw18202]
  • Stochastic reaction-diffusion simulation with MesoRD. Summary: MesoRD is a tool for stochastic simulation ... chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method ... simulate the Markov process corresponding to the reaction-diffusion master equation. Availability: MesoRD is free...
  • EpiSimdemics

  • Referenced in 7 articles [sw36952]
  • certain class of stochastic reaction-diffusion processes. Straightforward simulations of such process do not scale...
  • URDME

  • Referenced in 25 articles [sw10400]
  • framework for stochastic simulation of reaction-transport processes in complex geometries. We have developed URDME ... flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular ... relies on the Reaction-Diffusion Master Equation formalism to model the processes under study...
  • PyURDME

  • Referenced in 2 articles [sw16723]
  • modeling and simulation of stochastic reaction-diffusion processes on unstructured, tetrahedral (3D) and triangular ... algorithm is based on the mesoscopic reaction-diffusion master equation (RDME) model. PyURDME was originally...
  • STEPS

  • Referenced in 18 articles [sw17866]
  • modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions ... Setting up such models is a complicated process that consists of many phases. Initial versions...
  • ReaDDy

  • Referenced in 4 articles [sw17865]
  • ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments. We introduce ... mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution...
  • TFPDE

  • Referenced in 6 articles [sw12622]
  • TαS process, we simulate the moment statistics of stochastic reaction-diffusion equations with additive TαS ... density by approximating the TαS processes as CP processes; second, we directly solve the tempered...
  • Morpheus

  • Referenced in 1 article [sw34557]
  • models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale ... simulation to visualization, archiving and batch processing. Availability and implementation: Binary packages are available...
  • pSpatiocyte

  • Referenced in 0 articles [sw15003]
  • particle reaction-diffusion systems. The program called pSpatiocyte was created bearing in mind reaction networks ... subdomain and tri-stage lockstep communication for process-level, and voxel-locking techniques for thread...
  • FIDAP

  • Referenced in 37 articles [sw00006]
  • FIDAP (A Fluid Dynamics Analysis Program). This paper...
  • BoomerAMG

  • Referenced in 170 articles [sw00086]
  • BoomerAMG: A parallel algebraic multigrid solver and preconditioner...
  • CGAL

  • Referenced in 370 articles [sw00118]
  • The goal of the CGAL Open Source Project...
  • Expokit

  • Referenced in 184 articles [sw00258]
  • Expokit provides a set of routines aimed at...
  • FEMLAB

  • Referenced in 56 articles [sw00274]
  • COMSOL Multiphysics, vormals FEMLAB, ist eine Software zur...
  • Gmsh

  • Referenced in 635 articles [sw00366]
  • Gmsh is a 3D finite element grid generator...
  • HSL

  • Referenced in 274 articles [sw00418]
  • HSL (formerly the Harwell Subroutine Library) is a...
  • LAPACK

  • Referenced in 1649 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • Maple

  • Referenced in 5199 articles [sw00545]
  • The result of over 30 years of cutting...
  • MATCONT

  • Referenced in 396 articles [sw00551]
  • MATCONT: Matlab software for bifurcation study of dynamical...
  • Mathematica

  • Referenced in 6090 articles [sw00554]
  • Almost any workflow involves computing results, and that...