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Virtual Cell Release Notes
Versions and Version Features
VCell 4.7 (Current Beta)
Released 6-26-09
- 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 (Current Release)
Released 6-2-09
- 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.
VCell 4.5
Released 9-11-08
- 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
VCell 4.3
Released 9/19/2007
- 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 9/1/2006
- Parameter scans
- Faster surface visualization
- Automated GUI testing framework
- 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 4.1
Released 4/3/2006
- 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 10/03/2005
- Completely redesigned user interface.
- Multiple document interface (MDI).
- Multiple application viewing inside each BioModel.
- Database Manager for managing documents.
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