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
Tutorials
(Download as PDF)
Basic Introduction to StochSS
Prerequisites
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
StochOptim: Parameter Estimation
Example: Estimate parameters of a birth-death model
Spatial Stochastic Simulations
Example: Annihilation of two species in a cylinder
Cloud Computing
Credentials
Job Reproduction
Cost Analysis
Parameter Sweeps
Visualization
Surface Renderings with Domain Clipping
Colorized Wireframe Meshes
Volume Rendering
Visualization in Interactive Jupyter Notebook
References
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)