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.
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.
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.
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.