Use Case Name : ../VirtualCompartment

For Feature : MIMEditor

Editors: DavidKane

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A user wants to describe a large protein complex that has a behavior analogous to a compartment.

Step-by-Step User Action

  1. User specifies a boundary to partition the virtual compartments
  2. User optionally specifies a label for the virtual compartments

Visual Aides

An icon for representing virtual compartments has not yet been settled. A draft concept would be to use a cloud icon, like the following:


Requirements for Cytoscape



This is actually a feature that is not currently in the Kohn notation, but an area for which maps are actively being developed that need a suitable abstraction for this concept. However, this would take a lower priority than getting the existing concepts in the map implemented.

Other Examples


Shared ../MimEditorUseCaseComments

It is not clear how to represent the virutal compartments in BioPAX.

The complexes that would be modeled with virtual compartments, are large enough that they would distract from maps in which they would appear of modeled directly. Proteins that are attached to these complexes have different behaviors than when free from the complex.

AllanKuchinsky - 2007-01-22 05:26:11

At the Cytoscape model level, are all of compartment, protein complex, and virtual compartment just different instantiations of Groups?  Are there different semantics with respect to attribute assignment, membership criteria?

Molecular_Interaction_Maps/VirtualCompartment (last edited 2009-02-12 01:04:00 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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