 
Overview of Documentation and Tutorials

The download package includes documentation and tutorials that will help you get started using the various software components of Simmune.

The 'Manuals' directory contains instructions on how to use
* the Modeler (to specify models of signaling pathways based on molecular interactions)
* the Network Viewer (to visualize signaling models)
* the Simulator GUI (for performing spatially resolved simulations of cellular signaling processes)
* the Cell Designer (to create cell morphologies for spatially resolved simulations of cellular signaling processes)
* the Analyzer (to explore the effect of parameter variations on signaling pathway behavior)
* the Multi-Importer (to export and import models to and from SBML3 Multi)

The 'Tutorials' directory contains tutorials and example models, geometries (and simulation descriptions) for
* using the Analyzer
* simulating E-Cadherin mediated cell-cell interactions
* creating and exploring a model of G-protein coupled receptor signaling through spatially resolved simulations
* building a G-protein model with a focus on network visualization
* replicating the signaling studies on Yeast MAPK (Fus3) activation that was an example in Angermann et al. Nature Methods 2012.