## page was renamed from Molecular Interaction Maps/Compartment ## page was renamed from Compartment ## 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''' : ../DefineCompartment || || '''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 membrane-enclosed 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 compartments 1. User optionally specifies a label for the compartments == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) A membrane boundary is represented with a thick, double-walled line. It can either partition the entire map, as in this example: {{attachment:compartment1_061115_dwk.png}} Alternately, the compartment can completely enclose a region on a map, as in this example: {{attachment:compartment2_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 We are unsure to what degree components in the map need to be aware of what compartments they appear in. == 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"). Compartments play an important role in describing transportation functions. They also interact with other elements in the ../ShowTransport and ../ProteinDomains use cases. == Variations == Some earlier maps used a pattern instead of shading to describe the membrane as in this example: {{attachment:compartment3_061117_dwk.png}} == 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 compartments in BioPax. ---- AllanKuchinsky - 2006-11-26 05:41:17 Do compartments need to be aware of what components are in them? For example, if a compartment is moved or resized, do positions of components need to move with them or shift arrangement to accommodate resizing? This requires further discussion, as there are a number of alternative ways that compartments could be represented: 1. as Groups, in which case components would be members. This raises the issue of whether Groups can intersect, e.g. for trans-membrane proteins. Since Groups are networks, this ought to be feasible, since nodes and edges can be shared across groups. But how would it affect intersecting groups if, for example, a compartment is moved or resized? 2. as arbitrary graphical annotations. Flexible, but doesn't accommodate the association of components with the compartment. 3. as a specialized type of Cytoscape Node. This seems as if it would require extensive changes and specialized processing in the Cytoscape core, probably not advisable. ---- MiritAladjem - 2007-02-01 08:53:38 Yes. Subcompartments and anything in the compartment needs to move when compartments are moved or resized.