
MesoRD
 Referenced in 31 articles
[sw18202]
 Stochastic reactiondiffusion 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 reactiondiffusion master equation. Availability: MesoRD is free...

EpiSimdemics
 Referenced in 7 articles
[sw36952]
 certain class of stochastic reactiondiffusion processes. Straightforward simulations of such process do not scale...

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

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

STEPS
 Referenced in 18 articles
[sw17866]
 modeling and stochastic simulation of coupled reactiondiffusion systems with complex 3dimensional 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 ParticleBased ReactionDiffusion Dynamics in Crowded Cellular Environments. We introduce ... mechanisms of dynamical processes in the cell, based on reactiondiffusion dynamics with particle resolution...

TFPDE
 Referenced in 6 articles
[sw12622]
 TαS process, we simulate the moment statistics of stochastic reactiondiffusion 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 reactiondiffusion 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 reactiondiffusion systems. The program called pSpatiocyte was created bearing in mind reaction networks ... subdomain and tristage lockstep communication for processlevel, and voxellocking 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...