VCell & COPASI
21st Annual Workshop
Computational Cell Biology
June 8-1 0, 2020
VCell Short Course 2020
Release Version – VCell 7.2
|Windows 64-bit||Windows 32-bit||Mac OS X 64-bit||Linux 64-bit||Linux 32-bit|
New Features for VCell 7.2
Please acknowledge the VCell Resource in all publications. VCell is supported by NIH Grant Number R24 GM134211 from the National Institute for General Medical Sciences. And please reference the appropriate citations.
The VCell source code is available under the most permissive MIT license and can be downloaded at GitHub.
VCell uses Install4J, a multi-platform installer builder to create our executables.
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.
Release version now has online help from within the VCell interface. From the Help top menu select “Help” to open the guide.
VCell Release History
Current VCell Editions
New Features in VCell 7.2:
- Redesigned VCell Database Panel, with separate folders for curated and published public models annotated with source publications and model provenance.
- Ability to import over 90% of curated SBML models from the repository at http://www.ebi.ac.uk/biomodels/ (available under the BMDB tab), preserving units and annotations.
- Rate rules and assignment rules are now supported in VCell BioModel ODE Applications.
- ImageJ – VCell interface: VCell's FIJI (ImageJ) service allows scripts running in FIJI to communicate with VCell allowing query, control, and transfer of model/simulation data between VCell and ImageJ.
- New interface for adding and maintaining annotations of model components allowing permanent identifiers linking to public databases such as PubMed and UniProt.
- Reactions from the VCell database can be searched and inserted within a BioModel reaction diagram; appropriate associations with existing species and compartments can be made during the insert operation.
- Individual reactions can be copied from a reaction diagram and pasted into the same or a different BioModel; appropriate associations with existing species and compartments can be made during the paste operation.
- New reaction diagram visualization options allowing variably sized icons to represent the properties of species in a network.
- Optional variable reduction. In earlier versions, math generation in ODE compartmental Applications automatically reduced the system, using mass conservation, to solve the minimal number of ODEs for a minimal set of variables; the rest of the variables (i.e. species) were determined from algebraic mass conservation relations. At the expense of slightly longer simulation times, users may now turn off variable reduction. This makes the generated math easier to understand and can avoid occasional numerical simulation issues.
- Updated BioFormats Library for microscope image import.
- Math Equation renderer to complement the Math Description Language displayed under the “Generated Math” tab.
- General bug fixes and performance improvements.
Recent VCell Editions
New Features in VCell 7.1:
- Ability to explore public and tutorial models in the VCell database without registration (using a Guest login); also, create models and run simulations locally.
- New VCell database folder for Published Models to identify models used within publications.
- Improved model database info panel with clickable Pubmed links and DOIs , annotations and model provenance.
New Features in VCell 7.0:
- 2D kinematics modeling and simulation for reaction-diffusion in moving boundaries.
- Improved usability for rule-based modeling, simulation, and data visualization.
New VCell 7.0 Design enhances developer collaborations:
- New reusable VCell software modules (e.g. vcell-core, vcell-client, vcell-server, vcell-solvers).
- Cloud hosted software development process supporting external collaboration and extensibility (GitHub, Travis-CI, DockerHub).
- Reproducible and portable server and solver deployments using Docker and Singularity container technologies.
- 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.
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.
- Graphical editing of species patterns and reaction rules
- Support for mixed models of reaction networks and reaction rules for all simulations.
- Network free simulations with NFSIM: For situations where a reaction network is too large or is unbounded.
- Uses an integrated BioNetGen library and supports import and export of the BioNetGen Language (BNGL).
- 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)
- 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.
- 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
- 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.)
- Constructive Solid Geometry (building a complex geometry from simple shapes)
- Understands arbitrary units for model parameters (without resorting to base SI units for unrecognized derived units).
- Parameter estimation bug fixes and improvements
- More compact user interface for smaller displays
- Improved Pathway Model usability and interoperability with Pathway Commons, BioModels.net, and SABIO-RK databases.
- 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
- New Parameter Estimation Capability based on COPASI technology
- Global and local solvers
- Able to run through VCell interface
- 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)
- Support for surface-based 3D geometry import (STL format)
- 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
- 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
- Spatial stochastic applications using Smoldyn (ver. 2.23) stochastic solver
- 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
- Simulation results/data export
- Export simulation results to QTVR format
- Improved image/movie export GUI and user information
- 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)
Older VCell Editions
- 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
- 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.
- 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)
- 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.
- 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
- Nonspatial stochastic modeling
- Field data (using images data as input to simulations)
- Annotations (MIRIAM compliant)
- Better SBML support
- 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
- 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.
- Completely redesigned user interface
- Multiple document interface (MDI)
- Multiple application viewing inside each BioModel
- Database Manager for managing documents.