Introduction
          Overview
          General Navigation and Window Setup
          Top Menu
          File
               File -> New
               File -> Open
               File -> Save As
               File -> Revert To Saved
               File -> Permissions
               File -> Model Annotation
               File -> Edit Annotation
               File -> Field Data
               File -> Import
               File -> Export
          View
          Server
               User Login
               Change User
               Update Registration Information
               New User Registration
          Tools
               Launch BioNetGen
                    BioNetGen Rules editor tab
                    BioNetGen Messages tab
                    BioNetGen Output tab
                    BioNetGen Help tab
               Launch VFRAP
               Transform to Stochastic Capable
          Help
     Physiology Overview
          Reactions Diagram View
          Reactions Table View
          Physiology Structures Tabular View
          Species
          Pathway Links
     Applications Overview
          Geometry Overview
               Creating analytic geometries in VCell
               Creating image-based geometries in VCell
               Creating Geometries from STL files
               Structure Mapping
               Structure Mapping for non-spatial geometries
               Structure Mapping for Legacy Non-Spatial Geometries
          Specifications Overview
               Species Specifications
                    Field Data - Incorporating experimental data in simulations
               Reactions Specifications
          Protocols Overview
               Events
               Electrical Mapping
               Microscope Measurements
          Simulations Overview
               Simulations
               Simulations Editor
               Output Functions
               Generated Math
               Numerical Solvers
               Simulation Results
                    Spatial Simulation Results Overview
                         Spatial Simulation Results Slice View
                         Region of Interest Tools, Data Plots and Statistics
                         Spatial Simulation Results Overview
                         Simulation Results Spatial Region of Interest (ROI)
                         Kymographs
                         Post Processing Statistics Data
                         Post Processing Image Data
                         Exporting Spatial Simulation Results
                         Exporting Quicktime Movies
                    Compartment Simulation Results Viewer
                         Compartmental Simulation Results Plot Settings
                         Stochastic Simulation Results Histograms
          Parameter Estimation Overview
               COPASI Optimization Methods Overview
               How to use parameter estimation in Virtual Cell
     Parameters and Functions
          Parameters and Functions
          Predefined Constants and Math Functions
          VCell Model Units
     Biological Pathways Overview
          Pathway Commons Database
          Pathway Preview
          Pathway Diagram View
          Pathway Objects Table View
          BioPAX Summary
          BioPAX Tree
          Pathways Object Properties Pane
          Entities Management Toolbar
     Database Sources
          VCell Database
          BioModels.net Database
          Pathway Commons Database
          SABIO-RK - Biochemical Reaction Kinetics Database
     Properties Panes
          Structure Properties Pane
          Species Properties Pane
          Reactions Properties Pane
          Membrane Flux Properties Pane
          Stoichiometry Tab
          Parameter Properties Pane
          Pathways Object Properties Pane
          Problems Tab
     Appendix
          Error List
          Warnings