VCell Database

The Virtual Cell Database repository stores all the models created using the Virtual Cell software. The current user has access to the models created by him/her, models that are shared with the current user by other VCell users and those that are public.

The Virtual Cell Database can be accessed from 'Database' panel on the lower left corner of any VCell document window. The first tab in this panel is the VCell Database tab. Choosing this tab displays another set of 3 tabs - BioModels, MathModels, and Geometry that display the accessible models of that document type.

The VCell DB tab has a Search section that allows the user to search for models by name (and annotations). Under Advanced searches can also include date modified and models that contain 1 or more species names. The models are listed in a tree structure as 'folders'. The number of models stored in the database under each 'folder' is displayed in parenthesis. The possible folders that are listed include:

• My BioModels - where the current user's models are listed with user name in parenthesis.
• Shared BioModels - where models shared by other users with current user are listed (as "userName : modelName").
• Public BioModels - where VCell models created by users and used in their publications are listed (as "userName : modelName").
• Tutorials - list models that are designed for specific modeling problems, such as FRAP binding or Calcium diffusion. These models can be used as tutorials for modelers seeking to model similar problems.
• Education - lists simple models that have been created to demonstrate the VCell functionality to train new users of the VCell.

Expanding a tree node displays all the models of the user stored in the VCell database. Each model, when expanded, will list all the versions/editions of the models stored. Selecting any model or one of its versions lists a summary of the model (about its applications, geometries, simulations, annotations, etc) in the Selected BioModel Summary in the lower panel of the window.

Right clicking any selected model brings up a pop-up menu. The options available are:

• Open - opens the selected model. Please refer to the section File ->Open.
• Delete - allows user to delete the selected models (only the current user's models). To access the delete function, the user should make sure the document he/she is interested in deleting is closed prior to deleting it. A warning message is displayed asking if user wants to continue with the delete operation.
• Permissions... - allows user to share his/her models with other users. Please refer to the section File -> Permissions.
• Archive - this option is designed for use when models are used in publications or need to be saved in a final state.

  This maybe useful when models are a requirement for publication in a journal or associated with textbook examples. Models can always be made public through Permissions without archiving. When model results are reported in publications, it is ideal to make the model public. Once information of the publication and the public model are provided to the Virtual Cell team, they will be added to the VCell “Published Models” web page. An Archived BioModel or MathModel is protected from deletion or alteration by the owner. Their permissions can be set to either 'Private' or 'Public''. Users may wish to 'Archive'' the public model and 'Create a New Edition' to continue model development. A description of the restrictions imposed on Archived documents is displayed. Press OK to set 'ARCHIVE' mode. Current Archive restrictions: ARCHIVING cannot be undone without VCELL administrative assistance. ARCHIVED versions of documents cannot be deleted without VCELL administrative assistance.

• Publish - this option is currently disabled.
• Compare With - allows user to compare models. In the dialog that appears, the user can select the model he/she wishes to compare against the selected baseline model and press the Open button. Please refer to the section Compare With.

Selecting a model of any document type in the VCell Database displays the database information for the model in the Database File Info tab in the 'Properties' panel on the lower right hand corner of any VCell document. See Database Info for more information.