## page was renamed from StateCombination ## 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''' : ../StateCombination || || '''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 specify a condition that is the combination of two previously specified conditions. The two previous conditions may exist in separate species or within the same molecule. == 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 to be combined 1. User specifies another species to be combined 1. User specifies that the two species are to be combined 1. User optionally specifies the evidence for the relationship == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) The combination is represented with an arrowless line between the two species: {{attachment:statecombination1_061117_dwk.PNG}} State combinations can occur intramolecularly, for example, two different modifications on two different residues within the same molecule might be required for a specific activity. In the example below a phosphorylation reaction and an acetylation reaction are both required for stimulation: {{attachment:statecombination2_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") 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 is of moderate importance. A situation in which a reaction is contingent upon several requirements is common in biology. Examples include enzymes that need to be modified on several residues (phoshphorylation, acetylation) in order to catalyze specific reactions, or molecules that need to bind several other molecues in an unspecified order to participate in a process. == 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 ---- AllanKuchinsky - 2006-11-21 14:58:17   Model: the example of phosphorylation/acetylation could be handled in the model using the same constructs as A--.--B The user would need a way to specify the constraint that A and B must consist of phosphorylation and acetylation, or vice versa.   How would the user specify the constraints?  What variety of constraints would we want to give the user?  The most straightforward case would be 'type checking' of the nodes and edges.  Is this sufficient for the majority of usage?  Do we need to supply a more general constraint handling mechanism and 'language'? View: do we need a library of 'view' templates to handle views such as the phosphorylation/acetylation example? ---- MiritAladjem - 2007-02-01 09:27:16   Allan, in answer to your third question, in the Kohn annotation the depiction above is sufficient to determine that there are constraints.   In the example above, the node between the phosphorylated state of the molecule and the acetylated state of the molecule is the outcome of combining the two states. This is sufficient for the majority of cases. In answer to the fourth question, yes, in a "MIM tool" it will be nice to have a library of commmon reactions such as covalent binding with the common agents such as phosphorylation, methylation etc.