VCML is the Virtual Cell Markup Language and the native Virtual Cell format. The Virtual Cell supports interoperability with other standard representations for biological systems modeling. Formats that can be imported into the Virtual Cell include SBML levels 1, 2, and 3 (limited) and VFRAP. For SBML imports, it is preferrable to use Level 2, since it is more comprehensive than Level 1 and better supported that Level 3.
To import a file into the Virtual Cell, choose File -> Import. This opens a "Choose File" dialog. Navigate to the folder where the file to be imported is stored. Click Open to import the file or Cancel to cancel the operation.
Unit conversions from SBML
While importing an SBML model into the Virtual Cell, the units are converted into Virtual Cell default units. Note that species in SBML can be represented in terms of substance units or concentration units, whereas Virtual Cell represents species only in terms of concentration. An SBML species which is defined in substance units is converted to concentration units in the Virtual Cell by dividing the quantity in substance units by the size of the compartment in which the species is located. Also, reaction rates in SBML are defined in terms of substance/time, which are converted to concentration/time while importing into the Virtual Cell.
The unit conversion factors for species concentration are not explicit to the user. However, conversion factors (of the form species_ConcFactor) may be found in the Species Specifications tab of an application. A multiplicative factor may be found along with the actual value specified in the SBML model, e.g., 0.01 * 1000000, which means that 1000000 is the unit conversion factor for the species.
Reaction rate unit conversion factors can be seen in the Reactions Properties Pane for a reaction. A factor sbmlRateFactor that represents the unit conversion for the entire reaction rate (from substance/time units to concentration/time) will be present in the list of reaction rates and defined parameters. For reaction rate expressions that include a species, a corresponding concentration factor is also present. For example, if a reaction rate expression contains species ‘s1’, ‘s1’ is multiplied by ‘s1_ConcFactor’ to appropriately convert the species units.
These conversion factors will also be visible under Parameters and Functions pane that can be accessed by navigating the tree structure in the top left pane of the VCell BioModel document. In both these places, these concentration and species factors mentioned above appear suffixed with the corresponding reaction name.
SBML models with multiple compartments
When importing an SBML (level 2 or 3) model with more than one compartment, it is important to verify that it has a specified relationship between the different compartments. For the Virtual Cell to specify the correct cellular structures to each compartment, the relationship between compartments must be indicated within the SBML file. This is achieved by specifying in SBML the 'outside' attribute for a compartment, and its spatial dimension. In the Virtual Cell, Features have a spatial dimension of 3, while membranes have a spatial dimension of 2.