## 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''' : ../DnaSite || || '''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 DNA site that is involved in a pathway == 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 there is a DNA site 1. User labels the DNA site == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) The notation for a DNA site is the following: {{attachment:dnasite1_061117_dwk.png}} An example using this notation follows: {{attachment:dnasite2_061117_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"). TBD == 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 12:12:38 This is related to the general problem of representing sequence features in the context of a network. BioPAX Level 2 has basic support for describing sequence features (taken from PSI-MI), however Level 3 will add support for stating which sequence features are bound to others (related to describing topology of a complex). ---- GaryBader - 2006-12-26 12:13:16 Also, this is related to the sub-gene use case by the GenMAPP group at http://cytoscape.org/cgi-bin/moin.cgi/groupAPI/UseCase_3A ---- AllanKuchinsky - 2007-01-19 03:37:08 What is the formal relationship between A and A'? ---- MiritAladjem - 2007-02-01 08:58:10 In answer to Alan's comment: A' is a variant of A that has the binding site but not the acting site. There are real examples of such molecules (e.g. splicing variants). In the depicted case, A or A' can both bind DNA but they compete on the same site so just one of those two molecules can bind to the site at a specific time.