If you are interested in how StochSS is designed, or want to see examples of how it can be used for modeling and simulation, we recommend the paper on StochSS published in PLOS Computational Biology:

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

(Download as PDF)

Basic Introduction to StochSS

  Creating Administrator and Standard User Accounts
  Importing a Model
  Creating a New Model
  Running a Simulation and Visualizing results
  Backup and Transfer your Data

Sensitivity Analysis

  Example: Michaelis-Menten

StochOptim: Parameter Estimation

  Example: Estimate parameters of a birth-death model

Spatial Stochastic Simulations

Example: Annihilation of two species in a cylinder

Cloud Computing

  Job Reproduction
  Cost Analysis

Parameter Sweeps


  Surface Renderings with Domain Clipping
  Colorized Wireframe Meshes
  Volume Rendering
  Visualization in Interactive Jupyter Notebook


Technical Documents
StochSS user auth system (March 2014)
Notes on using custom reaction-diffusion meshes in StochSS
OLD: Notes on using custom reaction-diffusion meshes in StochSS (March 2014)