## page was renamed from StoichiometricConversion ## 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''' : ../StoichiometricConversion || || '''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 one or more species are converted into another species or collection of species through a stoichiometric process. == 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 or collection of species to be converted 1. User specifies the species or collection of species that that results from the conversion 1. User specifies that there is a stoichiometric conversion process from source species to the products of the conversion 1. User optionally specifies the evidence for this relationship == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) The Kohn notation for this binding is the following: {{attachment:stoichiometricconversion1_061115_dwk.png}} If a conversion results in more than one product, then this is represented with the following notation: {{attachment:stoichiometricconversion2_061115_dwk.png}} Note that the angled lines here when representing multiple products from a stochiometric conversion are one of the few places where edges are not at right angles. The angle where the reaction splits to the competing products or sources, 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:stoichiometricconversion3_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") Could be modeled as a group, or perhaps more simply as a node and two edges. Not clear how the model would need to be adjusted if there are more than one input or product. Might require a new line type in Vizmapper. == 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"). Stochiometric conversion is fairly common on its own. In addition, the use cases of ../SpeciesDegradation and ../ShowTransport are in fact, special cases of Stochiometric conversion. == Variations == The following example illustrates a pair of common scenarios associated with this use case. First, is that a species (i.e. a catalyst), may be both an input and a product of the conversion. Second, the species that is the input into the conversion can be a complex. {{attachment:stoichiometricconversion4_061115_dwk.png}} There can be more than two products from a reaction. If that is the case, additional edges emanate from the vertex, but the outer angles should still be less than 90ºapart. {{attachment:stoichiometricconversion5_061115_dwk.png}} It is also possible to have more than one input into a stoichiometric conversion. The notation for this is the following: {{attachment:stoichiometricconversion6_061115_dwk.png}} An alternative to this notation for representing multiple inputs is to use ../StateCombination: {{attachment:stoichiometricconversion7_061115_dwk.png}} Enzymatic catalysis involves the stoichiometric conversion of the reagents to the products with regeneration of the enzyme. The example below shows the enzyme E catalyzing the addtion of a hydroxyl group OK onto protein S: {{attachment:stoichiometricconversion8_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 Biochemical Reaction object that has participants: A,A, and AA, left = A,A, and right=AA. AA = Conversion object (child of Interaction class), e.g. Conversion object with Participants=A,B, Left=A, Right=B, where A and B are physicalEntities. AJK: the figure below shows some examples built using the Hyperedge''''''Editor plugin for Cytoscape, prototype under development. ---- AllanKuchinsky - 2006-12-07 10:40:18   see {{attachment:stoichiometric_hyperedge.png}} for some examples built using the prototype HyperedgeEditor tool. ---- MiritAladjem - 2006-12-13 12:49:20   Thanks Ellen for your comment.  All the examples are correctly depicting the interactions in MIM language, but the example of catalyst as product requires an interction of the enzyme E with the substrate S, the product of which is being converted to E and P.  So the arrow from E to S should be a double-edged barbed arrow, which represents binding.  The product of the binding interactin should be converted to E and P.