## page was renamed from EnzymaticStimulation
## 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''' : .../EnzymaticStimulation ||
|| '''For Feature''' : [[MIMEditor]] ||
|| '''Editors''': DavidKane ||

## EXAMPLE: 
## Use Case Name: Representation of Protein Complex
## For Feature: Grouping Function
## Editors: Mr. Knowitall

<<TableOfContents([2])>>

== Summary ==
## Provide a one paragraph description of the use case
A user wants specify that a species is an enzyme that stimulates a reaction

== 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 the enzymatic stimulator
 1. User specifies a reaction to be stimulated
 1. User specifies that there is a stimulation relationship
 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 Kohn notation for enzymatic stimulation is the following:

{{attachment:enzymaticstimulation1_061115_dwk.png}}
 
An example using this notation follows:

{{attachment:enzymaticstimulation2_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")

Assuming that this can use the same approach that is used for ../ShowInhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation), node2: A, node3: B 

View: Use case for hyperedge view 


== 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 high importance, because it is very common in the maps.

== Variations ==

When an enzyme stimulates two or more reactions, the enzyme reaction line branches and leads to enzyme reaction symbols at each target reaction.

TBD (Add a graphical example of this)

== 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 

This is a special case of a ../ProcessStimulation.  The enzyme binds to the complex as part of the reaction, and is unmodified after the reaction.

This could be modeled in BioPAX as a Catalysis object (e.g. Catalysis object with participants = a physicalInteraction object and a enzyme A, Controlled = the physicalInteraction object, Controller=A, Control-Type = Activation, and Direction = IRREVERSIBLE-LEFT-TO-RIGHT)

----
AllanKuchinsky - 2007-01-19 03:44:41

At the model level, this would be represented by ActivatingMediator nodes in HyperEdges.