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| If you look closely at these two figures, you will see some small squares at the intersections of the edges. In Cytoscape, we refer to this small square as a ''connector'' node. We also refer to the collection of edges and ''connector'' node as a ''hyperedge''. | If you look closely at these two figures, you will see some small squares at the intersections of the edges. In Cytoscape, we refer to this small square as a ''connector'' node. We also refer to the collection of edges and ''connector'' node as a Hyper''''''Edge. |
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| ''''' /!\ Here ''''' |
The following two figures show examples of Biochemical''''''Reactions that you can build up using Cytoscape's editor. The first figure below illustrates glycolysis. attachment:glycolosis.png |
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To connect two nodes with an edge, drag and drop an arrow shape onto a node on the canvas. This node becomes the source node of the edge. Move the cursor and a rubber-banded line follows the cursor. As the cursor passes over another node, that node is highlighted and the rubber-banded line will snap to a connection point on that second node. Click the mouse while over this node and the connection is established. attachment:glycolosis.pmg You can abort the drawing of the edge by clicking on an empty spot on the palette. Note that if you change the Visual Style, the palette used by the current network view will also change to be consistent with the mappings in the new Visual Style. There is also an __Edit → Connect Selected Nodes__ menu item that, when chosen, creates a clique amongst the selected nodes. The editor provides accelerators for adding nodes and edges. Control-clicking at a position on the canvas creates a node at that position. The NODE_TYPE attribute of the node will be the same as the NODE_TYPE of the node most recently added, defaulting to "DefaultNode" type. In this manner, you can use control-clicking as a kind of "stamp" to add multiple nodes of the same type to the network. Control-clicking on a node on the canvas starts an edge with source at that node. Move the cursor and a rubber-banded line follows the cursor. As the cursor passes over another node, that node is highlighted and the rubber-banded line will snap to a connection point on that second node. Control-click the mouse again and the connection is established. The EDGE_TYPE attribute of the edge will be the same as the EDGE_TYPE of the edge most recently added, defaulting to "DefaultEdge" type. You can abort the drawing of the edge by control-clicking on an empty spot on the palette. You can delete nodes and edges by selecting a number of nodes and edges, then selecting the __Edit → Delete Selected Nodes and Edges__ menu item. You can recover any nodes and edges deleted from a network by selecting the __Edit → Undo__ menu item. Note that this will restore '''all''' nodes and edges that were previously deleted from the network, not just those deleted by the most recent delete operation. |
The second example below uses a Circle Graph Layout to illustrate the Krebs Cycle. |
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| === A Closer Look === | === A Closer Look === |
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| As was stated earlier, a ''Biochemical''''''Reaction'' is composed of a set of ''substrates'', ''products'', and ''mediators'', and a ''hyperedge'' that connects them. Here are some basic definitions, plus some rules and constraints for working with ''hyperedges''. | As was stated earlier, a ''Biochemical''''''Reaction'' is composed of a set of ''substrates'', ''products'', and ''mediators'', and a Hyper''''''Edge that connects them. Here are some basic definitions, plus some rules and constraints for working with Hyper''''''Edges: |
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This page is Under Construction. Please do not modify.
A Cytoscape Edge typically connects two Nodes, which we commonly refer to as Source and Target Nodes. While this is sufficient for most cases, there are cases where you may want to have Edges that connect more than two Nodes. One example of this is a Biochemical Reaction, where an Edge represents a reaction that may have multiple substrates, products, and mediators. An example of this is shown in the figure below,
attachment:biochemcial_reaction_eg.png
where L-glutamine and 2-oxoglutarate are substrates for the reaction, the catalyst glutamate substrate is a mediator for the reaction, 2 L-glutamate is a product of the reaction, the co-factor NADPH is a substrate for the reaction, and the co-factor NADP is a product of the reaction.
There may also be cases in which you may want to connect one edge with another edge, for example to represent the activity of a molecular species that modulates the action of a catalyst. This is illustrated in the figure below
attachment:edge_connect_edge.png
where molecular species S_643 inhibits the action of catalyst M_643.
If you look closely at these two figures, you will see some small squares at the intersections of the edges. In Cytoscape, we refer to this small square as a connector node. We also refer to the collection of edges and connector node as a HyperEdge.
Using Cytoscape's Editor and the BioChemicalReaction visual style, you can build and modify reactions by dragging and dropping shapes from the editor palette onto the main network view window. You can add products, substrates, and mediators, to a reaction.
The figure below shows the Editor palette for the BioChemicalReaction visual style and the result of dragging/dropping the AddReaction shape from the palette onto the canvas.
attachment:hyperEdgeEditor.png
The AddReaction palette shape serves as a template that enables you to add a connected set of nodes and edges to a network. You can change the names of the substrates, products, and mediators by editing them in Cytoscape's Attribute Browser.
You can connect additional products, substrates, and products to a reaction by dragging their associated shapes from the palette and dropping them on the reaction's connector node. An example of a reaction with two products is shown in the figure below.
attachment:hyperedge_two_products.png
An example of a reaction with two products and two substrates is shown in the figure below.
attachment:hyperedge_two_products_two_substrates.png
You can connect a conventional Cytoscape node to a reaction by creating an edge from the conventional Cytoscape node to a connector node (via drag/dropping an edge from the editor palette onto the node). Conversely, you can connect a reaction to a conventional Cytoscape node by creating an edge from the connector node to the conventional Cytoscape node (via drag/dropping an edge from the editor palette onto the connector node).
The following two figures show examples of BiochemicalReactions that you can build up using Cytoscape's editor. The first figure below illustrates glycolysis.
attachment:glycolosis.png
The second example below uses a Circle Graph Layout to illustrate the Krebs Cycle.
attachment:krebs_cycle.png
A Closer Look
As was stated earlier, a BiochemicalReaction is composed of a set of substrates, products, and mediators, and a HyperEdge that connects them. Here are some basic definitions, plus some rules and constraints for working with HyperEdges:
A HyperEdge is an Edge that connects two or more Nodes. A HyperEdge consists of a set of Edges and a special Node referred to as a ConnectorNode. The ConnectorNode is a generated Node that serves as one endpoint for all Edges contained by a HyperEdge.
Some assumptions about HyperEdges are:
HyperEdges are mutable. They can be modified.
A HyperEdge may have more than one Node with the same Edge interaction type.
A HyperEdge may have more than one Edge to the same Node.
A HyperEdge has exactly one ConnectorNode.
A HyperEdge ConnectorNode may be used as a regular Node within another HyperEdge.
A HyperEdge is associated with one or more CyNetworks.
The only shared Edges in a HyperEdge are those connecting two ConnectorNodes (HyperEdges) that must exist in the same CyNetwork.
A regular Cytoscape Edge may directly connect to a HyperEdge ConnectorNode, but it will not be considered part of the HyperEdge.
HyperEdges are shared, in that any change to a HyperEdge existing in more than one CyNetwork is reflected in all CyNetworks to which the HyperEdge belongs.