## page was renamed from Molecular Interaction Maps/Transport ## page was renamed from Transport ## 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''' : ../ShowTransport || || '''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 the possibility that protein is transported across a membrane from one compartment into another. == 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 species to be transported 1. User specifies a starting compartment 1. User specifies a destination compartment 1. User optionally specifies the evidence for this relationship == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) An example of Kohn notation for transportation: {{attachment:transport1_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"). Being able to specify a compartment for a reaction, and to move species between compartments is critical for many maps. == Variations == Membranes are rendered with a thick double line. (See ../DefineCompartment) {{attachment:transport2_061115_dwk.png}} If the protein is involved in reactions after being transported across the membrane, then edges for those reactions, connect to the small black dot. {{attachment:transport3_061115_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 Some previous Kohn maps used a single line as well, but that convention does not need to be supported by the [[MIMEditor]]. The BioPAX representation of this binding could be a Transport object, but it is not clear how to specify the compartments the species is being transported from and to. Transport is a special case of ../StoichiometricConversion – converting one molecule in one compartment to one molecule in another compartment without net change in the number of molecules overall. ---- AllanKuchinsky - 2007-01-19 03:07:58   see comments on DefineCompartment.  At the model level, the concept of a Group in Cytoscape should support compartments.   At the view level, we need to consider whether compartments are placed on the network canvas or should be on a background canvas.