• 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 nanometer-scale 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 reaction-diffusion 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. Code-base has been completely...
  • StoSpa2

  • Referenced in 1 article [sw33817]
  • software package for stochastic simulations of spatially extended systems. Code-base has been completely refactored...
  • PISKaS

  • Referenced in 1 article [sw29283]
  • Parallel Implementation of a Spatial Kappa Simulator. PISKaS is a stochastic simulator for rule-based ... version of Kappa-Language, 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 well-mixed 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 discrete-time 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, full-field, turbulent-wind simulator. It uses a statistical model ... physics-based model) to numerically simulate time series of three-component wind-speed 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 rule-based 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 two-dimensional 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 entity-centered ... 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 high-order stochastic simulation algorithm for generating three-dimensional complex geological patterns ... three-dimensional high-order simulation algorithm HOSIM is developed to simulate complex non-linear ... based upon new high-order spatial connectivity measures, termed high-order 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 least-squares 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 auto-correlation within an attribute and cross...