StochSS 1.9 Documentation

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 StochSS 1.9 (Legacy)

(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)