## page was renamed from VirtualCompartment ## These are wiki comments - leave them in so that people can see them when editing the page ## This template may be useful for documenting use cases ## Developed in response to a hackathon request for formalized, detailed use cases ## to help direct implementation proposals || '''Use Case Name''' : ../VirtualCompartment || || '''For Feature''' : [[MIMEditor]] || || '''Editors''': DavidKane || ## EXAMPLE: ## Use Case Name: Representation of Protein Complex ## For Feature: Grouping Function ## Editors: Mr. Knowitall <> == Summary == ## Provide a one paragraph description of the use case A user wants to describe a large protein complex that has a behavior analogous to a compartment. == Step-by-Step User Action == ## Provide a step-by-step account of how the user would execute the use case. For example: (1) right click on node, (2) choose "expand" from context menu, (3) new view is created, etc... 1. User specifies a boundary to partition the virtual compartments 1. User optionally specifies a label for the virtual compartments == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) An icon for representing virtual compartments has not yet been settled. A draft concept would be to use a cloud icon, like the following: {{attachment:virtualcompartment1_061115_dwk.png}} == Requirements for Cytoscape == ## List the components/functions already in Cytoscape that are relevant to the use case and possible implementations (e.g., "current context menus can be used accomplish step 2 above") ## Also list components/functions that are needed in Cytoscape to execute the use case (e.g., "cytoscape needs to allow for multiple views of the same network for this to work") TBD == Importance == ## Describe whether this use case is critical and how frequently users would come across it. Describe common work flows that might involve the use case (e.g., "this use case comes up regularly, on a weekly basis, whenever we want to analyze our protein superfamily networks"). 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 == ## List other applications or relevant examples outside of Cytoscape that provide some or all of the desired functionality (e.g., "You can do this using the group function in PowerPoint"). == Comments == 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?