## 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''' : ../TranscriptionInhibitionShorthand || || '''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 one species can inhibit transcription of a protein, without showing in detail, all of the mechanisms. == 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 as the inhibitor 1. User specifies a transcription reaction to inhibit 1. User specifies that there is a ../TranscriptionInhibitionShorthand relationship between the two 1. User optionally specifies the evidence for this reaction == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) The symbol for ../TranscriptionInhibitionShorthand follows: {{attachment:transcriptioninhibitionshorthand1_061120_dwk.PNG}} An example showing A inhibiting the transcription of B follows: {{attachment:transcriptioninhibitionshorthand2_061121_dwk.PNG}} There are two right angles near the head. This can be more clearly seen when there is a longer edge. {{attachment:transcriptioninhibitionshorthand4_061121_dwk.PNG}} This use case differs from ../ShowInhibition in that the mechanism represented by ../TranscriptionInhibitionShorthand is inhibition of transcription, where as ../ShowInhibition can represent any mechanism of 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"). This has been used infrequently, and so is of a lower priority. ../ShowInhibition is usually sufficient. == 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 BioPax representation TBD ---- GaryBader - 2006-12-26 12:27:17   BioPAX - part of gene regulation proposal for next level. ---- AllanKuchinsky - 2007-01-22 05:18:58   can be handled by a new Edge type and associated rendering? would require modifications to vizmapper for edge rendering, or custom edge graphics? ---- AllanKuchinsky - 2007-05-25 10:12:53   Actually, since the bend is hear the head of the target node, couldn't we just support it with a new type of arrowhead?  Or is it best handled as an edge with anchor points and right-angle constraints?