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.