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<?xml version='1.0' encoding='ISO-8859-1' ?>
<toc version="1.0">
<tocitem image="toplevelfolder" text="The Virtual Cell Help">
<tocitem target="GeneralOverview" text="Introduction">
<tocitem target="General" text="Overview"/>
<!-- <tocitem target="RuleBasedOverview" text="Rule-Based Features"/> -->
<tocitem target="GeneralNavAndWinSetup" text="General Navigation and Window Setup"/>
<tocitem target="Login" text="Logging into VCell"/>
<tocitem target="TopMenu" text="Top Menu"/>
<tocitem target="File" text="File Menu">
<tocitem target="New" text="File->New Menu"/>
<tocitem target="Open" text="File->Open Menu"/>
<tocitem target="SaveAs" text="File->Save As Menu"/>
<tocitem target="RevertToSaved" text="File->Revert to Saved Menu"/>
<tocitem target="CompareWithSaved" text="Compare With Saved"/>
<tocitem target="Permissions" text="File->Permissions Menu"/>
<tocitem target="FieldData" text="File->Field Data Menu"/>
<tocitem target="Import" text="File->Import Menu (SBML files)"/>
<tocitem target="ImportBNGL" text="File->Import Menu (BNGL files)"/>
<tocitem target="Export" text="File->Export Menu"/>
</tocitem>
<tocitem target="Account" text="Account Menu">
<tocitem target="Auth0ProfilePage" text="Login"/>
<tocitem target="SetProxy" text= "Set Proxy Window"/>
<tocitem target="ViewSimStatus" text="View Simulation Jobs"/>
</tocitem>
<tocitem target="Window" text="Window Menu"/>
<tocitem target="Tools" text="Tools Menu">
<tocitem target="LaunchVirtualFRAP" text="Launch Virtual FRAP Menu"/>
<tocitem target="ExportedDataViewer" text="Exported Data Viewer"/>
</tocitem>
<tocitem target="Help" text="Help Menu"/>
</tocitem>
<tocitem target="RuleBasedOverview" text="Rule-Based Features">
<tocitem target="RuleBasedTheory" text="Introduction to Rule-Based Modeling"/>
<tocitem target="RBCreate" text="How to create a rule-based model"/>
<tocitem target="RBSimulate" text="How to simulate a rule-based model"/>
<tocitem target="NFSimApp" text="Network-Free Application"/>
<!-- <tocitem target="SpringSaLaDTheory" text="Introduction to SpringSaLaD Modeling"/>
<tocitem target="LangevinApp" text="SpringSaLaD Application"/> -->
</tocitem>
<tocitem target="PhysOverview" text="Physiology">
<tocitem target="ReactDiagView" text="Reaction Diagram"/>
<tocitem target="ReactTabView" text="Reactions Table">
<tocitem target="PP_Reactions" text="Edit Reaction"/>
<tocitem target="PP_MemFlux" text="Edit Membrane Flux"/>
<tocitem target="PP_ReactionRulesEditor" text="Edit Reaction Rule"/>
<tocitem target="PP_ReactionRulesKinetics" text="Edit Kinetics for Reaction Rule"/>
<tocitem target="PathLink" text="Edit Pathway Links"/>
</tocitem>
<tocitem target="PhysStructTabView" text="Structures table">
<tocitem target="PP_Structures" text="Structures Properties Pane"/>
</tocitem>
<tocitem target="SpeciesTabView" text="Species Table">
<tocitem target="PP_Species" text="Edit Species"/>
<tocitem target="PathLink" text="Edit Pathway Links"/>
</tocitem>
<tocitem target="Molecules" text="Molecules Table">
<tocitem target="PP_Molecules" text="Specify Molecular Details"/>
</tocitem>
<tocitem target="Observables" text="Observables Table">
<tocitem target="PP_Observables" text="Edit Observable"/>
</tocitem>
</tocitem>
<tocitem target="ApplicationOverview" text="BioModel Applications">
<tocitem target="GeometryOverview" text="Geometry">
<tocitem target="geom_Analytic" text="Analytic Geometry"/>
<tocitem target="geom_from_images" text="Image-based Geometry"/>
<tocitem target="geom_from_surface" text="Geometry from Surface"/>
<tocitem target="geom_struct_mapping" text="Geometry Structure Mapping">
<tocitem target="geom_spatial_mapping" text="Spatial"/>
<tocitem target="geom_nonspatial_mapping" text="Non-Spatial"/>
</tocitem>
<tocitem target="Kinematics" text="Kinematics"/>
</tocitem>
<tocitem target="SpecificationsOverview" text="Specifications">
<tocitem target="SpeciesSpecifications" text="Species">
<tocitem target="fieldData" text="Field Data"/>
<!-- <tocitem target="SSSpeciesSpecifications" text="SpringSaLaD Species"/> -->
</tocitem>
<tocitem target="ReactionsSpecifications" text="Reactions">
<!-- <tocitem target="SSReactionsSpecifications" text="SpringSaLaD Reactions"/> -->
</tocitem>
<tocitem target="NetworkSpecifications" text="Network"/>
<tocitem target="NetworkFreeSpecifications" text="Network-Free"/>
</tocitem>
<tocitem target="ProtocolsOverview" text="Protocols">
<tocitem target="Events" text="Events"/>
<tocitem target="Electrical" text="Electrical Mapping"/>
<tocitem target="MicroscopeMeasurement" text="Microscope Measurements"/>
<tocitem target= "RateRules" text ="Rate Rules"/>
<tocitem target= "AssignmentRules" text ="Assignment Rules"/>
</tocitem>
<tocitem target="simulations_overview" text="Simulations">
<tocitem target="simulations" text="Simulations">
<tocitem target="BatchSimulations" text="Batch Simulations"/>
</tocitem>
<tocitem target="simulationEditor" text="Simulation Editor"/>
<tocitem target="NFSimSimulationEditor" text="NFSim Simulation Editor"/>
<tocitem target="output_functions" text="Output Functions"/>
<tocitem target="generated_math" text="Generated Math"/>
<tocitem target="numerical_solvers" text="Numerical Solvers"/>
<tocitem target="SimulationViewerOverview" text="Simulation Results"/>
<tocitem target="SpatialSimResultsOverview" text="Spatial Simulation Results">
<tocitem target="SimResSpatialSliceView" text="Spatial Simulation Results Slice View"/>
<tocitem target="SpatialSimResultsDrawingTools" text="Region of Interest Tools, Data Plots and Statistics"/>
<tocitem target="SimResultsSpatialSurfaceView" text="Spatial Simulation Results 3D Membrane View"/>
<tocitem target="SimResultsSpatialROIandStatistics" text="Statistics"/>
<tocitem target="SimResultsKymograph" text="Plots"/>
<tocitem target="PostProcessingStats" text="Post Processing Statistics Data"/>
<tocitem target="PostProcessingImage" text="Post Processing Image Data"/>
<tocitem target="ExportingSpatialSimResults" text="Exporting Spatial Simulation Results"/>
<tocitem target="ImageJDataViewerPlugin" text="FIJI/ImageJ VCell Simulation Results Viewer Plugin"/>
<tocitem target="OpenHDF5ImageJ" text="Importing HDF5 files into FIJI/ImageJ"/>
<tocitem target="SpecificFormatSettings" text="Specific Format Settings"/>
</tocitem>
<tocitem target="SimCompartmentResults" text="Non-spatial (Compartmental) Simulation Results">
<tocitem target="SimResultsNonSpatialPlotSettings" text="Plot Settings"/>
<tocitem target="SimResultsNonSpatialStochHistogram" text="Stochastic Results Histograms"/>
</tocitem>
</tocitem>
<tocitem target="PEOverview" text="Fitting">
<tocitem target="parameterEstimationMethods" text="Parameter Estimation Methods"/>
<tocitem target="parameterEstimationUsage" text="How to use Parameter Estimation"/>
</tocitem>
</tocitem>
<tocitem target="ParametersAndFunctionsOverview" text="Parameters and Functions">
<tocitem target="ParametersAndFunctions" text="Parameters And Functions"/>
<tocitem target="PredefinedConstAndMathFns" text="Predefined Constants and Math Functions"/>
<tocitem target="ModelUnits" text="Model Unit System"/>
</tocitem>
<tocitem target="PathwayOverview" text="Biological Pathways">
<tocitem target="PathwayCommonsPanel" text="Pathway Commons Database"/>
<tocitem target="PathwayImportTable" text="Pathway Preview"/>
<tocitem target="PathwayDiagramView" text="Pathway Diagram"/>
<tocitem target="PathwayObjectsView" text="Pathway Objects"/>
<tocitem target="BiopaxSummaryView" text="BioPAX Summary"/>
<tocitem target="BiopaxTreeView" text="BioPAX Tree"/>
<tocitem target="PP_Pathways" text="Pathway Object Properties Pane"/>
<tocitem target="GroupOperationsPanel" text="Operations on Pathway Entities"/>
</tocitem>
<tocitem target="DatabaseOverview" text="Database Sources">
<tocitem target="VCellDatabase" text="VCell Database"/>
<tocitem target="BioModelsNet" text="BioModels Database"/>
<tocitem target="PathwayCommonsPanel" text="Pathway Commons Database"/>
</tocitem>
<tocitem target="PropertiesPaneOverview" text="Properties Panes">
<tocitem target="PP_ApplicationProps" text="Application Properties Pane"/>
<tocitem target="PP_VCellDatabaseInfo" text="Database Info Panel"/>
<tocitem target="PP_Annotations" text="Annotations Panel"/>
<tocitem target="PP_KinematicsPointLocationProcess" text="Point Location Process Kinematics Properties Pane"/>
<tocitem target="PP_KinematicsPointObject" text="Point Object Kinematics Properties Pane"/>
<tocitem target="PP_KinematicsSurfaceObject" text="Surface Object Kinematics Properties Pane"/>
<tocitem target="PP_KinematicsSurfaceProcess" text="Surface Process Kinematics Properties Pane"/>
<tocitem target="PP_KinematicsVolumeObject" text="Volume Object Kinematics Properties Pane"/>
<tocitem target="PP_KinematicsVolumeProcess" text="Volume Process Kinematics Properties Pane"/>
<tocitem target="PP_MemFlux" text="Membrane Flux Properties Pane"/>
<tocitem target="PP_Molecules" text="Molecules Properties Pane"/>
<tocitem target="PP_Observables" text="Observables Properties Pane"/>
<tocitem target="PP_Parameters" text="Parameter Properties Pane"/>
<tocitem target="PP_Pathways" text="Pathway Properties Pane"/>
<tocitem target="PP_Problems" text="Problems (Issues) Panel"/>
<tocitem target="PP_Reactions" text="Reactions Properties Pane"/>
<tocitem target="PP_ReactionRulesEditor" text="Reaction Rules Editor Pane"/>
<tocitem target="PP_ReactionRulesKinetics" text="Reaction Rules Kinetics Pane"/>
<tocitem target="PP_Species" text="Species Properties Pane"/>
<tocitem target="PP_Stoichiometries" text="Stoichiometries Properties Pane"/>
<tocitem target="PP_Structures" text="Structures Properties Pane"/>
</tocitem>
<tocitem target="AppendixOverview" text="Appendix">
<tocitem target="AnnotationProviders" text="UID Providers for Annotations"/>
<tocitem target="Definitions" text="Definitions"/>
<tocitem target="Errors" text="Errors"/>
<tocitem target="Warnings" text="Warnings"/>
</tocitem>
</tocitem>
</toc>