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University of Connecticut Health Center - Know Better Care VCell - The Virtual Cell

VCell Release Notes

current VCell editions (released 2011-11-11).    Run VCell

VCell 5.1 (Beta) released 2011-11-11
  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 (Current Release)
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. Improved/updated 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)

recent VCell editions (2009-2011)

VCell 4.8
Released 2011-03-30
  • 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.
  • 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
  • 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.
  • 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.
  • 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
  • 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
  • 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.
  • Geometry
    • New assistant dialog for creating analytic shapes in geometry editor
    • Terminology: SubVolumes= subdomains
  • 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
  • Implementation of Global Parameters for BioModels.
  • Resources: Links to BioModels database
  • Protein Subcellular Location Image Database (PSLID) import and data handling in FieldData
  • Allow membrane field data from simulation results
  • Improved spatial data analysis for ROIs.
    • Predefined ROIs for existing spatial compartments.
    • ROIs  from user defined Boolean functions.
    • ROIs from user drawn polygons.
  • CVODE solver used for Optimization in parameter estimation.
  • Support for both Intel and G5 macs. Basic CellML import into MathModels.
  • Added sort and search functions to Math Viewer and Math Model editor.
  • 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
  • Hybrid Stochastic simulations (HySSS)
  • Differential Algebraic Solver for non-spatial "fast" systems
  • Math generation improvements (improved comparison)
  • Additional SBML improvements (e.g. libSBML 3.0.2)
  • Formalize VCML as XML document
VCell 4.4
Released 2008-04-01
VCell 4.3
Released 2007-09-18
  • BioNetGen@VCell
  • Copy/Paste parameters (initial conditions, math overrides, simulation results and parameter estimation values) amongst each other
  • Publish documents
  • Improvements in memory efficiency and resource utilization
  • Improvements in SBML import/export
VCell 4.2
Released 2006-10-06
  • Parameter scans
  • Faster surface visualization
  • Automated GUI testing framework
VCell 4.1
Released 2005-02-03
  • 2D/3D Membrane Diffusion added to BioModels and MathModels
  • 3D Surface Visualization for spatial simulation results
  • Reaction diagram draws faster for large networks, and easier to resize
  • Known molecular weights added to controlled vocabulary, and improved queries Species (from models or controlled vocabulary)
  • Model Editor layout improved
  • Additional simulation status is provided while running jobs
  • Stiff solver support for uniform output time step (useful for SBML support)
  • Added 2D/3D membrane diffusion and sensitivity analysis to numerical methods testing framework.
VCell 4.0
Released 2005-10-03
  • Completely redesigned user interface
  • Multiple document interface (MDI)
  • Multiple application viewing inside each BioModel
  • Database Manager for managing documents.

The Virtual Cell, a project of NRCAM, is developed by the Center for Cell Analysis & Modeling (CCAM)