## page was renamed from AsymmetricBinding ## 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''' : ../AsymmetricBinding || || '''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 protein binds to another and contributes a peptide that binds to a receptor site or pocket on another protein. == 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 protein to be involved in the interaction as a contributor 1. User specifies another protein to be involved in the reaction as a receptor 1. User specifies that there is an asymmetric binding reaction 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 Kohn notation for this reaction is the following: {{attachment:asymmetricbinding1_061115_dwk.png}} An example using this notation follows: {{attachment:asymmetricbinding2_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") This would be modeled similarly to a ../NonCovalentBinding, i.e. with a group, but with a specific edge type. The barbed arrow would require custom rendering. == 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 notation is fairly rare and is not as important as the other use cases. == Variations == If the bound proteins are used in a subsequent reaction, a dot is placed on the line, and that is used to anchor the edges for the subsequent reactions. (See ../CompoundBinding) {{attachment:asymmetricbinding3_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 The BioPAX representation of this binding could be a Conversion Object, i.e. with Participants = A,B, AB, Left = A,B, Right=AB, where A and B are Proteins, but AB is a complex with components A and B). It is not clear how to differentiate simple binding from asymmetric binding in BioPAX. * AllanKuchinsky - Does this mean that the dot notation is *only* used after a connection has been made to the reaction? This might require enhancements to the Vizmapper to support computed attributes -- or alternatively, enhancement to the editor to compute a hidden attribute on groups which would be used to conditionally render the dot. 2006-11-17 04:11:46 * AllanKuchinsky - Is there an implicit constraint on the edge between A and dot that the edge must *not* be of the type that would get the barbed edge in view? 2006-11-21 15:23:44