
HRSSA
 Referenced in 6 articles
[sw18041]
 HRSSA  efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks. This paper introduces HRSSA ... Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA ... built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds...

Smoldyn
 Referenced in 23 articles
[sw23962]
 individually to capture natural stochasticity and to yield nanometerscale spatial resolution. It treats other ... molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes...

sbioPN
 Referenced in 6 articles
[sw11725]
 sbioPN: sbioPN: Simulation of deterministic and stochastic spatial biochemical reaction networks using Petri Nets. sbioPN ... perform simulation of deterministic and stochastic systems of biochemical reaction networks with spatial effects. Models...

MOLNs
 Referenced in 2 articles
[sw16724]
 biology using pyurdme. Computational experiments using spatial stochastic simulations have led to important new biological ... barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological ... spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation ... stochastic reactiondiffusion models. MOLNs is based on IPython and provides an interactive programming platform...

InterSpread Plus
 Referenced in 1 article
[sw33832]
 InterSpread Plus: a spatial and stochastic simulation model of disease in animal populations. We describe ... spatially explicit, stochastic simulation model of disease spread, InterSpread Plus, in terms of its epidemiological...

CDFSIM
 Referenced in 5 articles
[sw13367]
 CDFSIM: efficient stochastic simulation through decomposition of cumulative distribution functions of transformed spatial patterns. Simulation...

MUI
 Referenced in 12 articles
[sw18209]
 coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example ... coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study...

pystospa
 Referenced in 1 article
[sw33818]
 software package for stochastic simulations of spatially extended systems, StoSpa2. Codebase has been completely...

StoSpa2
 Referenced in 1 article
[sw33817]
 software package for stochastic simulations of spatially extended systems. Codebase has been completely refactored...

PISKaS
 Referenced in 1 article
[sw29283]
 Parallel Implementation of a Spatial Kappa Simulator. PISKaS is a stochastic simulator for rulebased ... version of KappaLanguage, which we call Spatial Kappa (see the wiki of this repository ... computing architecture. To run a spatial simulation you need to use the mpirun tool ... accurate simulation and a large value, a fast but unaccurate simulation. It is recomended...

StochSS
 Referenced in 6 articles
[sw24921]
 visualization of models and results. Scale your simulations to the cloud with a click ... models from ODE, to wellmixed stochastic, to spatial stochastic. Supports parameter estimation and parameter...

Cell++
 Referenced in 2 articles
[sw35406]
 Cell++  simulating biochemical pathways. Motivation: With the generation of a wealth of information, detailing cellular ... within spatial and dynamic contexts. Here, we introduce Cell++, a novel stochastic simulation environment with ... wide variety of biochemical processes within a spatial context. Results: Focusing on three case studies...

Eir
 Referenced in 1 article
[sw39005]
 researchers simulate the spread of epidemics, mainly focusing on discretetime Markovian spatial models ... user to conduct stochastic simulations of epidemics, primarily using spatial models. With this software...

TurbSim
 Referenced in 9 articles
[sw34447]
 tools. TurbSim is a stochastic, fullfield, turbulentwind simulator. It uses a statistical model ... physicsbased model) to numerically simulate time series of threecomponent windspeed vectors ... space. Spectra of velocity components and spatial coherence are defined in the frequency domain...

PISKa
 Referenced in 1 article
[sw29285]
 Parallel Implementation of Spatial Kappa, based on KaSim, a stochastic simulator for rulebased models...

STOCHSIM
 Referenced in 6 articles
[sw32181]
 biomolecular processes. Summary: StochSim is a stochastic simulator for chemical reactions. Molecules are represented ... written in Perl/Tk. A simple twodimensional spatial structure has also been implemented, in which...

HSIM
 Referenced in 2 articles
[sw18272]
 systems. The stochastic simulation algorithm and its enhanced versions are adapted to simulate the behaviour ... well stirred mixture of reactants when spatial localisation is not relevant; Conversely, in entitycentered ... methods, the causes and consequences due to spatial localisation are well handled. In terms ... optimised algorithm for approximate stochastic simulation...

HOSIM
 Referenced in 8 articles
[sw38402]
 HOSIM: A highorder stochastic simulation algorithm for generating threedimensional complex geological patterns ... threedimensional highorder simulation algorithm HOSIM is developed to simulate complex nonlinear ... based upon new highorder spatial connectivity measures, termed highorder spatial cumulants. The HOSIM...

Stochastic kriging
 Referenced in 1 article
[sw12891]
 sampling uncertainty inherent in the stochastic simulation; it accomplishes this by incorporating trend models that ... common in leastsquares regression, spatial correlation modeling to account for inadequacies of the trend ... which is also based on spatial correlation concepts. Stochastic kriging facilitates adaptive, sequential experiment designs...

spup
 Referenced in 1 article
[sw27794]
 Uncertainty Propagation Analysis. Uncertainty propagation analysis in spatial environmental modelling following methodology described in Heuvelink ... functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo ... numerical and categorical data types are handled. Spatial autocorrelation within an attribute and cross...