## page was renamed from ProcessStimulation
## 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''' : ../ProcessStimulation ||
|| '''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 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 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 process stimulation is the following:

{{attachment:processstimulation1_061115_dwk.png}}
 
An example using this notation follows:
 
{{attachment:processstimulation2_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: process 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.  Stimulation of biological process by molecules that do not directly participate in the process is very common in biology.  In some cases a process is contingent upon another reaction – in this case the relationship is defined as a ../ShowNecessity.  Other special casees include ../EnzymaticStimulation and ../EnzymaticStimulationInTrans, which have their own symbols. 

== Variations ==

The stimulator does not necessarily have to be a molecular species; it can be a modified species or a process.  In the example below, the phosphorylation of a molecule A enhances its ability to bind another molecule B:

{{attachment:processstimulation3_061115_dwk.png}}

This example illustrates the concept of cooperative binding using the ../ProcessStimulation relationship.

{{attachment:processstimulation4_061117_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 

This could be modeled in BioPAX as either a Control (for catalysts) or a Biochemical Reaction.
----
AllanKuchinsky - 2006-11-26 04:25:13
should be handled in the same way as for ShowInhibition