Diff for "EditingBiochemicalReactions"

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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

Here

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.

attachment:krebs_cycle.png