Released 2024-July

New Features in VCell 7.6

VCell Features

• Single Sign On browser-based login for the VCell Desktop application and the new VCell web portal.
• New VCell web portal enables user account management.
• New ImageJ plugin for analyzing large spatial simulation results without downloading the entire dataset (via N5 data format).
• The model annotation tool now integrates search for terms across several biomedical repositories via the BioPortal API.
• New Export Viewer organizes recently exported simulation data.

Model interoperability

• Improved import and export of SBML with round trip validation of equations and cross validation with COPASI and Tellurium.
• Improved import and export of SEDML/COMBINE archives of complete BioModels with export of reaction diagrams, simulation results and publication citations.
• Improved support for SBML Spatial import and export.

Infrastructure

• Cross platform builds of VCell solvers ported to Github CI/CD.
• Secure user identity provide by Auth0.com via OpenID Connect.
• modern API technology based on Quarkus/OpenAPI and Java 17.
• VCell services ported from Docker Swarm to Kubernetes.
• New highly available on premise RKE2 Kubernetes cluster.
• Use PostgreSQL for development and tests, tested Oracle data migration. Production database updated from Oracle 11g to 19c.
• Maintain Java, Python and Typescript API libraries for secure access to VCell API services.

Released 2023-February

New Features in VCell 7.5

VCell Features

• Comprehensive support for SBML, SEDML and OMEX import, export, and execution, providing Math simplification on import.
• Increased quotas for ODE and PDE jobs.
• Allow parameter scans on local client-side simulation runs.
• Parameter Estimation upgraded to the latest version of COPASI and improved feedback during execution (new plot of objective function vs iteration)
• Greatly expanded VCell CLI, including archive conversion and validation. (try docker run -it ghcr.io/virtualcell/biosimulators_vcell:latest help)
• Improved support for external access to VCell solvers (containerized version with command line execution e.g. docker run -it ghcr.io/virtualcell/vcell-solvers:latest FiniteVolume_x64 to run our standalone PDE solver – contact us for more information)
• Improved BioModel unit system transformation Export to HDF5 file format for ODE simulations including parameter scans and for spatial applications from both the VCell client UI and the CLI.
• Exporting to .csv file the results of multiple runs of non-spatial stochastic simulations.
• Fixed numerous bugs and installation issues;
• GUI improvements

Model and software testing

• Significantly expanded automated Unit and regression testing
• Significantly expanded automated
• Integration testing
• Test equivalence of BioModel math generation with originally stored math for an extensive test suite of 1000 public models – identified and fixed several minor bugs.
• Test SBML/SEDML export and import against all public VCell models which are mappable to SBML with rigorous round-trip verification.
• Test SBML import from the official SBML test suite (1753 test cases), to identify and document unsupported SBML features (e.g. Delay, Algebraic Rules, XOR operator, 0D/1D compartments).

Infrastructure

• Pre-release support for PostgreSQL database as an alternative to Oracle.
• VCell API authentication and RBAC ported to standard JWT bearer tokens in preparation for future OIDC and single sign-on.
• updated VCell API security (TLS)
• improved docker and multi-platform native builds for VCell solvers in GitHub actions.
• improved structured logging and server metrics integrated with Elastic Stack.
• improved administrative CLI tools.

Released 2021-March

New Features in VCell 7.4:

• Geometry preview when searching the VCell database.
• Multiple trajectory stochastic simulations using the default Gibson-Bruck solver have been vastly accelerated, for both local runs and on the server.
• Unit display and automated unit conversions extended to include rate and assignment rules, plus miscellaneous improvements to unit system handling.
• Support for external access to a subset of VCell solvers (containerized version with command line execution).
• Support for export/import of all simulation/solver settings via COMBINE archive (.omex) format, including enhanced support for Simulation Experiment Description Markup Language (SED-ML), and Kinetic Simulation Algorithm Ontology (KiSAO).
• Multiple bug fixes and minor improvements.

Released 2020-November

New Features in VCell 7.3:

• Multiple trajectories with statistical analysis for non-spatial stochastic simulations.
• Export/Import models into Open Modeling Exchange (.omex) Standard file format, which encodes both model and simulation specifications. Support for OMEX complements VCell’s ongoing commitment to support the SBML and SEDML standards.
• Default behavior of reaction (RX connection) tool for multiple compartments simplifies units and optimizes compatibility with spatial geometries.
• User alerts icon for scheduled maintenance and system messages.
• Species that modulate a rate expression but are not created or consumed (e.g. catalysts) are automatically denoted in the reaction diagram with a dotted line to the yellow reaction icon.
• Redesigned internally consistent BioModel and VCellDB info panels.
• Numerous miscellaneous improvements and bug fixes.

Released 2019-December

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.

Released 2018-November

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.

Released 2018-March

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.

Released 2017-April

• 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).

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

• 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

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.

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)

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)

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

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)

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.