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 models are listed in a tree structure as 'folders'. A "key" icon by the folder indicates that the models is shared with other users. a "globe" icon indicates a model that has been made public. The number of models stored in the database under each 'folder' is displayed in parenthesis.

• My BioModels - where the current user's models are listed with user name in parenthesis. The "lock" icon indicates these models are private to the user unless otherwise indicated. The example below shows a private model, one that was shared with another user and one that was marked as public.
  
  

• Shared With Me - where models shared by other users with current user are grouped by user name and listed as model name.
  
  

• Tutorials - list models that are designed to demonstrate specific components of VCell, such as FRAP (for spatial simulations), or Multiple Applications of a BioModel (MultiApp). These models can be used as starting models for modelers seeking to model similar problems.
• Public BioModels - list all VCell models available to the general public.

• The Published folder contains public Models created by users and used in a publications. Models are grouped by the publication citation and listed by user name and model name.
  
  

• The Curated folder contains VCell models created by the VCell team or collaborators to reproduce a model described in a publication. Curated models are listed by user name : model name
• The Uncurated folder contains public Models created by users that have not been peer reviewed.

Expanding a tree node displays all the models of relevant type. 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 (Associated Citations, Model Provenance, and Applications Provenance including Geometries and Simulations) in the Selected BioModel Summary in the Database File Info Properties Pane in the lower right of the window.

Right clicking any selected model brings up a pop-up menu.

• 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. An Archived BioModel or MathModel is protected from deletion or alteration by the owner.

  A description of the restrictions imposed on Archived documents is displayed. The current Archive restrictions: ARCHIVING cannot be undone without VCELL administrative assistance. ARCHIVED versions of documents cannot be deleted without VCELL administrative assistance. Press OK to set 'ARCHIVE' mode. Models can always be made public using Permissions without archiving, and archived models can have permissions set to either 'Private' or 'Public''. Models with results reported in publications should be made available to the public; see DocumentWindow->Help->'How to Publish a Model' for information on how to report publication information. Once information of the publication and the public model are provided to the Virtual Cell team, the model will be added to the "Published Models" folder and the model will be automatically archived. If the users wishes to continue developing the model, it can be copied into a new BioModel or MathModel name in the user's private model folder. The model and citation will also be listed on the VCell “Published Models” web page.

• Publish - Convenience link (same as DocumentWindow->Help->'How to Publish a Model') on how to identify a VCell model in a publication and how to associate a model with publication information in the VCell Database.
• 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.