VCell Desktop Help

• Introduction
  • Overview
  • General Navigation and Window Setup
  • Top Menu
  • User Login
  • File
    • File -> New
    • File -> Open
    • File -> Save As
    • File -> Revert To Saved
    • File -> Permissions
    • File -> Field Data
    • File -> Import
    • File -> Import (BNGL files)
    • File -> Export
  • Account
    • Auth0 Overview
      • Auth0 Profile Page
        • Auth0 Existing User Account Linking
        • Auth0 Returning User (Forgot Password) Account Linking
        • Auth0 New User Account Creation
    • SetProxy
    • ViewSimStatus
  • Window
  • Tools
    • Launch VFRAP
    • Exported Data Viewer
    • Transform to Stochastic Capable
  • Help
• Overview of Rule-Based Features
  • Introduction to Rule-Based Modeling
  • How to create a rule-based model
  • How to simulate a rule-based model
  • Network-Free Application
• Physiology Overview
  • Reactions Diagram
  • Reactions Table
    • Reactions Properties Pane
    • Membrane Flux Properties Pane
    • Reactions Rules Editor Pane
    • Reactions Rules Kinetics Pane
    • Pathway Links
  • Physiology Structures Tabular View
    • Structure Properties Pane
  • Species Table
    • Species Properties Pane
    • Pathway Links
  • Molecules Table
    • Molecules Properties Pane
  • Observables Table
    • Observable Properties Pane
• Applications Overview
  • Geometry Overview
    • Creating analytic geometries in VCell
    • Creating image-based geometries in VCell
    • Creating Geometries from STL files
    • Geometry Structure Mapping
      • Structure Mapping for spatial geometries
      • Structure Mapping for non-spatial geometries
    • Kinematics
  • Specifications Overview
    • Species Specifications
      • Field Data - Using experimental or simulation data as initial conditions
    • Reactions Specifications
    • Network Specifications
    • Network-Free Specifications
  • Protocols Overview
    • Events
    • Electrical Mapping
    • Microscope Measurements
    • Rate Rules
    • Assignment Rules
  • Simulations Overview
    • Simulations
      • Batch Simulations
    • Simulations Editor
    • NFSim Simulations Editor
    • Output Functions
    • Generated Math
    • Numerical Solvers
    • Simulation Results
    • Spatial Simulation Results Overview
      • Spatial Simulation Results Slice/Surface View
      • Region of Interest Tools
      • Membrane Surface Viewer
      • Statistics
      • Simulation Results Viewer Plots
      • Post Processing Statistics Data
      • Post Processing Image Data
      • Exporting Spatial Simulation Results
      • FIJI/ImageJ VCell Simulation Results Viewer Plugin
      • Importing HDF5 files into FIJI/ImageJ
      • Specific Format Settings
    • 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 Overview
  • 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 Database
  • Pathway Commons Database
• Properties Panes
  • Application Properties Pane
  • VCell Database Info Panel
  • Annotations Panel
  • Point Location Process Kinematics Properties Pane
  • Point Object Kinematics Properties Pane
  • Surface Object Kinematics Properties Pane
  • Surface Process Kinematics Properties Pane
  • Volume Object Kinematics Properties Pane
  • Volume Process Kinematics Properties Pane
  • Membrane Flux Properties Pane
  • Molecules Properties Pane
  • Observable Properties Pane
  • Parameter Properties Pane
  • Pathways Object Properties Pane
  • Problems (Issues) Panel
  • Reactions Properties Pane
  • Reactions Rules Editor Pane
  • Reactions Rules Kinetics Pane
  • Species Properties Pane
  • Stoichiometry Tab
  • Structure Properties Pane
• Appendix
  • UID Providers for Annotations
  • Error List
  • Warnings