## page was renamed from Molecular Interaction Maps/Competition ## page was renamed from Competition ## 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''' : ../ShowCompetition || || '''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 a species is involved in two or more binding reactions, and that these reactions are in competition for recruiting that species. == 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 reaction that will be one of those competing 1. User specifies a species in that first reaction that will recruiting by the competing binding reactions 1. User specifies another binding reaction involving the species being recruited by both 1. User optionally specifies the evidence for this competition == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) An example of the Kohn notation for this reaction follows: {{attachment:competition1_061115_dwk.png}} In this example, the protein A can be bound to either B or C, and that both reactions are competing to recruit A. == 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 a fairly frequent occurrence in the maps, although it is not necessary to support both variations of the layout immediately. The second of the two variants above is the more important version to support. == Variations == The angle where the reaction splits to the competing participants, should be less than 90º. This can be difficult from a layout perspective, and so the following form of the notation is usually easier to use: {{attachment:competition2_061115_dwk.png}} Each specific reaction can be involved in subsequent reactions. In addition, it is possible for the reaction to specify that either is a possibility. In this example, if the complex AB were necessary, then the node next to B would be used. If the complex AC were necessary, then the node next to C would be used. If either AB or AC could be used in a reaction, then the node next to A would be used. {{attachment:competition3_061115_dwk.png}} Competition can also occur with ../CovalentBinding, in which case similar notation is used, but with the double-line used for ../CovalentBinding, as in this example: {{attachment:competition4_061121_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 We are unsure how to best model competition under BioPAX. This typically is only modeled for noncovalent binding, however, the model has been occassionally used for covalent binding reactions as well. ---- AllanKuchinsky - 2006-12-11 03:21:31   At the model level, Should the competing reactions be represented by a Group, with the recruited species as the left side of the 'composite' reaction?  Might we approach this via analogy to a set protein isoforms, one if which participates in a reaction under certain conditions?   At the view level, would we need to show a less than 90-degree angle at the intersection of outgoing edges, i.e. an angle of pi/2*n, where n=number of competing elements?   In the second variation, what is meant by the term "node"?  Is it referring to the dot? ---- MiritAladjem - 2006-12-13 12:40:20   Allan, thank you for the comment.   Regarding the first question, in the example above and in the first two variations the object on the left has the potential to form a group with either one of the two objects on the right. Regarding the third question, yes node=dot in the paragraph describing the second example.