File -> Import

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.

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.