## page was renamed from DefineProcess ## 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''' : ../DefineProcess || || '''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 add a high-level process to a map. == 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 that a process should be added 1. User labels the process 1. User optionally associates the process with other maps == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) A process is represented with a labeled box: {{attachment:defineprocess1_061115_dwk.png}} Process can serve as inputs as well as outputs in maps. For example exposure to a drug can be a process that originates an interaction (e.g. inhibition). == 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"). Many maps refer to processes that are important in the context of the map, even if the details of the process are not. A process is an abstraction of those activities. == 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 A process differs from a ../VirtualCompartment, in that species can go into a ../VirtualCompartment by way of binding. A process has no notion of inside or outside. ---- AllanKuchinsky - 2006-12-11 03:29:43 At the model level, should this be represented as a group? Probably not if it is not expandable. Should this just be represented as a CyNode of a certain type that has different visual characteristics? If so, then what are the implications for graph theoretic analysis, e.g. shortest path? At the other extreme, could this be represented as an arbitrary graphical annotation? Would it have attributes? Would a Process ever serve as a link to a separate map, i.e. perform some UI gesture such as double-clicking on the Process node and have a new map come up in a separate view? ---- MiritAladjem - 2006-12-13 12:30:39 Allan, thanks for the comments. It will be most useful to allo a process to be linked to another map. However, in the map where the process is represented as above, it will not be expandable.