18th Annual Virtual Cell Short Course
June 12 -14, 2017

Release Version – VCell 5.3

OS Download
Mac OS X 64-bit install guide VCell Installer* DMG Archive (104 MB)
Windows 64-bit VCell Installer* Executable Installer (90 MB)
Windows 32-bit VCell Installer* Executable Installer (90 MB)
Linux 64-bit VCell Installer* Executable Installer (56 MB)
Linux 32-bit VCell Installer* Executable Installer (55 MB)

Beta Version – VCell 6.1

OS Download
Mac OS X 64-bit install guide VCell Installer* DMG Archive (89 MB)
Windows 64-bit VCell Installer* Executable Installer (85 MB)
Windows 32-bit VCell Installer* Executable Installer (84 MB)
Linux 64-bit VCell Installer* Executable Installer (59 MB)
Linux 32-bit VCell Installer* Executable Installer (57 MB)
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VCell Release History

A comprehensive listing of the latest enhancements for each release version.

New Features in VCell 5.3, release

  • New general compartment topology that supports multicellular modeling.
  • Custom unit system allows user-defined units.
  • Improved support for SBML models.
  • Introducing new VCell installers created using the Install4J cross-platform installer builder.
  • VCell performance improvements supported by JProfiler.

New Features in VCell 6.1, beta

  • A new graphical user interface to build and visualize full molecular details of species and reaction rules. No need to learn a scripting language; visualization of full molecular details of species and visualization of reaction rules highlighting molecular components that participate in a rule.
  • Rule-based models can span multiple compartments.
  • Reactions and rules can be mixed and can both be visualized in the Reaction Diagram.
  • Full support for reactions and rules in all VCell Application types (spatial, nonspatial, deterministic, stochastic).
  • A set of rules can be simulated with Network-Free Simulator NFSim.
  • “Molecular Anchors” in rule-based models that keeps membrane-bound receptors attached to the membranes.

VCell source code is available on Sourceforge.

CCAM Software Downloads

A listing of additional computational tools developed at CCAM.

  • SpringSaLaD (Update released August 4, 2016. It fixes a minor bug in cluster size statistics. Go to CCAM Software to replace your current version.)
  • Microfilament Detector
  • BaSDI (Bayesian super-resolution drift inference)
  • Octane (Super-resolution imaging and single molecule tracking software.)

CCAM Publications

VCell is active in recognizing articles published by users and those from the VCell team itself. Please see the links below for a comprehensive listing of current and past publications.

Published VCell Models

NRCAM Publications

Publish a VCell Model

User Guides

Release version now has online help from within the VCell interface. From the Help top menu select “Help” to open the guide.

Quick Start guide for VCell Release.

Quick Start guide for Beta.

Rule Based guide for Beta.

VCell Help –  html version, also available from Help menu of VCell software.

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VCell Release History

Current VCell Editions

VCell 6.1 Beta

Beta 2016-10-14

  1. Graphical representation of rules and reactions in the Reaction Diagram.
  2. Enhanced visualization of reaction rules highlighting molecular components that participate in a rule.
  3. Full support for reactions and rules in all VCell Application types (spatial, nonspatial, deterministic, stochastic).
  4. "Molecular Anchors" in Rule-Based Models that keep any species that includes membrane-bound receptors attached to the membrane.
VCell 5.3 Release

Released 2015-06-09
Beta 2014-10-21

  1. General compartment topology (supporting multicellular modeling)
    • Prior to VCell 5.3, cellular compartments were strictly nested (e.g. extracellular-plasma membrane-cytosol-organelle membrane-organelle).
    • Any combination of volume compartments and membranes can now be specified - and optionally mapped to cellular geometry.
    • General compartment topology supported for electrophysiological models (for membrane potential polarity)
  2. Custom unit system.
    • Flexibility to choose the SI unit system which is appropriate for each model. A list of primary units (for concentration, time, length, etc) is specified.
    • If the unit system is changed, the model is automatically converted to the new unit system.
  3. Improved support for SBML models and biomodels.net database (rate rules, generalized topology, units).
    • Imported SBML models retain original unit system
    • Verified support for 323 (as of September 2014) curated models from biomodels.net database, up from 143 supported by VCell 5.2

Recent VCell Editions (2009 – 2014)

VCell 6.0

Rule-based modeling integration. Rule-based modeling involves the representation of species as structured objects consisting of molecules and molecular interactions as reaction rules for transforming the attributes of these objects. It allows one to systematically incorporate site-specific details about molecular interactions into a model.

  1. Graphical editing of species patterns and reaction rules
  2. Support for mixed models of reaction networks and reaction rules for all simulations.
  3. Network free simulations with NFSIM: For situations where a reaction network is too large or is unbounded.
  4. Uses an integrated BioNetGen library and supports import and export of the BioNetGen Language (BNGL).
VCell 5.2

Released 2014-10-21
Beta 2013-9-12

  1. Hybrid spatial stochastic solver combines particle based dynamics of certain species with reaction diffusion equations of other species within a single simulation. (For example, local activation of channel activity may be modeled stochastically while the flux of ions through the channel may be simulated deterministically.)
  2. Constructive Solid Geometry (building a complex geometry from simple shapes)
  3. Understands arbitrary units for model parameters (without resorting to base SI units for unrecognized derived units).
  4. Parameter estimation bug fixes and improvements
  5. More compact user interface for smaller displays
  6. Improved Pathway Model usability and interoperability with Pathway Commons, BioModels.net, and SABIO-RK databases.
VCell 5.1

Released 2012-10-25

  1. Integrated Virtual FRAP - Simulation Assisted Analysis of FRAP Experiments
    • Modeling FRAP data under various assumptions (diffusion only, effective diffusion, reaction off rate)
    • Parameter estimation using spatial temporal informaiton
    • Parameter identifiability verification using profile likelihood
    • Intuitive wizard based work flow to manipulate FRAP data
  2. New Parameter Estimation Capability based on COPASI technology
    • Global and local solvers
    • Able to run through VCell interface
  3. Quick-run simulations on your computer
    • Nonspatial-deterministic simulation (local ODE solver)
    • Spatial-deterministic simulation (local PDE solver)
    • Nonspatial-stochastic simulation (local Gibson-Bruck and hybrid solvers)
    • Spatial-stochastic simulation (local Smoldyn solver)
  4. Support for surface-based 3D geometry import (STL format)
VCell 5.0

Released 2011-11-11

  1. Completely renovated, intuitive GUI
    • Add/Edit/Delete Reactions, Structures and Species in tabular or diagrammatic view
    • Real-time detect and report errors/warnings
    • New searchable view for all model parameters
    • Integrated searchable database manager including Bio-models/Math-models/Geometries/Biomodels.net models
    • Improved reaction diagram (Quick creation of model elements and multi-compartment layout)
    • Improved image segmentation and editing tools to create geometries
  2. New Modeling capabilities:
    • Spatial stochastic applications using Smoldyn (ver. 2.23) stochastic solver
      • Interactive local run with particle view or cluster run
      • Able to export using "VisIt" rendering
  3. BioPAX/Pathway Commons interface in VCell
    • Query Pathway Commons for pathway data
    • Download pathways (interactions and substances) from BioPAX
    • Convert/link pathway objects to/with VCell model elements
  4. Simulation results/data export
    • Export simulation results to QTVR format
    • Improved image/movie export GUI and user information
  5. NOTE to users: in spatial applications, all variables are specified with a domain (same species in different compartments are considered different variables in the results)
VCell 4.8

Released 2011-03-30

  1. New Modeling Capabilities
    • Ability to specify current clamp either as current density or whole cell current
    • Functionality for creating events within non-spatial models such that a variable or time-dependent expression can trigger a predefined reset or change in the value of other variables during simulation.
    • Support in MathModel framework for approximating diffusion coefficient as infinite for select species in spatial models
    • Variables for volume and area can be used in kinetic expressions.
    • Kinetic expressions in non-spatial models can include species that are located in a different compartment (non-local interactions) from where the reaction is defined.
  2. Database Linkages
    • Search and retrieve ready to run, fully MIRIAM annotated models from BioModels.net.
    • Species may be associated with live web links to appropriate entries in databases (e.g. UNIPROT, REACTOME, ChEBI, ENSEMBL...) via Pathway Commons
  3. Improved handling of geometries
    • Integration of convenient 2D and 3D image segmentation tools to directly convert experimental images into Virtual Cell geometries.
    • Predefined analytical expressions for geometric shapes to aid in the creation of idealized cellular geometries
    • Create, edit and save new geometries from within a BioModel Application or MathModel, including search tools for finding existing geometries within other VCell models.
  4. Simulation Results and Data Export
    • Output Functions: User defined functions for compartmental and spatial simulation data are saved with model and available for all simulations in a given Application.
    • Spatial Simulations: Time plots of multiple variables from spatial points.
    • Compartmental Simulations: Time plots of multiple variable over multiple parameter scan results.
    • Export spatial simulation data in two additional formats: AVS-UCD and VTK.
  5. Navigations, User Interface
    • New search function to find models by name in Database Manager and model "Open" dialog
    • New BioModel Application user interface: Specification Tab contains a handy tree directory of all elements required to specify an application before math generation
    • Improved messages during model construction in BioModels
VCell 4.7

Released 2010-04-28

  1. Solvers
    • New combined CVODE/IDA solver for compartmental simulations.
    • New fully implicit finite volume solver for spatial simulations.
    • Improved solvers to handle user-defined discontinuities.
    • Terminology: Finite Volume solver= Semi-implict finite volume solver
  2. Initial Conditions
    • Advection (Velocity) added to Initial conditions in BioModels
    • Initial conditions can be specified in terms of other model parameters, reserved symbols and species.
  3. Geometry
    • New assistant dialog for creating analytic shapes in geometry editor
    • Terminology: SubVolumes= subdomains
  4. User Interface
    • Expression editors: Improved with auto-complete text
    • Data Export: Variables separated into membrane and volume variables
    • Simulation Editor/Advanced: New output option for semi-implicit solvers
    • Applications: Application menu added to main menu
    • Applications: Display of application methods (deterministic/stochastic) and geometric dimensions (compartmental/1D/2D/3D)
Vcell 4.6

Released 2009-05-28

  1. Implementation of Global Parameters for BioModels.
  2. Resources: Links to BioModels database
  3. Protein Subcellular Location Image Database (PSLID) import and data handling in FieldData
  4. Allow membrane field data from simulation results
  5. Improved spatial data analysis for ROIs.
    • Predefined ROIs for existing spatial compartments.
    • ROIs from user defined Boolean functions.
    • ROIs from user drawn polygons.
  6. CVODE solver used for Optimization in parameter estimation.
  7. Support for both Intel and G5 macs. Basic CellML import into MathModels.
  8. Added sort and search functions to Math Viewer and Math Model editor.
  9. Feature and Membrane sizes available for use in expressions in non-spatial models.

Older VCell Editions (2005 – 2008)

VCell 4.5

Released 2008-09-11

  1. Hybrid Stochastic simulations (HySSS)
  2. Differential Algebraic Solver for non-spatial "fast" systems
  3. Math generation improvements (improved comparison)
  4. Additional SBML improvements (e.g. libSBML 3.0.2)
  5. Formalize VCML as XML document
VCell 4.4

Released 2008-04-01

  1. Nonspatial stochastic modeling
  2. Field data (using images data as input to simulations)
  3. Annotations (MIRIAM compliant)
  4. Better SBML support
VCell 4.3

Released 2007-09-18

  1. BioNetGen@VCell
  2. Copy/Paste parameters (initial conditions, math overrides, simulation results and parameter estimation values) amongst each other
  3. Publish documents
  4. Improvements in memory efficiency and resource utilization
  5. Improvements in SBML import/export
VCell 4.2

Released 2006-10-06

  1. Parameter scans
  2. Faster surface visualization
  3. Automated GUI testing framework
VCell 4.1

Released 2005-02-03

  1. 2D/3D Membrane Diffusion added to BioModels and MathModels
  2. 3D Surface Visualization for spatial simulation results
  3. Reaction diagram draws faster for large networks, and easier to resize
  4. Known molecular weights added to controlled vocabulary, and improved queries Species (from models or controlled vocabulary)
  5. Model Editor layout improved
  6. Additional simulation status is provided while running jobs
  7. Stiff solver support for uniform output time step (useful for SBML support)
  8. Added 2D/3D membrane diffusion and sensitivity analysis to numerical methods testing framework.
VCell 4.0

Released 2005-10-03

  1. Completely redesigned user interface
  2. Multiple document interface (MDI)
  3. Multiple application viewing inside each BioModel
  4. Database Manager for managing documents.