Diff for "EditingBiochemicalReactions"

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Allan, here are some suggestions and missing info:

1. Once the HyperEdgeEditor plugin is loaded, you can perform File->Import->HyperEdge Sample Networks to play with two sample networks--Krebs Cycle and Glycolysis Reaction.

2. The popup menu presented when right-clicking on a ConnectorNode will bring up an additional HyperEdgeEditor submenu that allows selection and deletion of HyperEdges. Selection selects the connector node and all edges. Deletion allows deletion from just the existing Network, or from all Networks, if the HyperEdge is shared.

3. HyperEdges can be create by first dropping an edge palette item onto a Node (source) and then

   • dropping again (with the rubberband edge) on another Edge (target). This leads to a few different cases:

   • If the source node is a regular node and the target is a regular edge--the target edge is removed and a HyperEdge is created that connects source node, target edge's source and target edge's target (obviously need example). For example, if we have:

     • A--->B C--->D

     • If we drop an edge palette item onto C (source) and then onto the

       edge in between A & B (target), then this creates:

       • A---.-->B

         • ^ | C
   • If the source node is a regular node and the target is a hyperedge edge--

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:

1. HyperEdges are mutable. They can be modified.

2. A HyperEdge may have more than one Node with the same Edge interaction type.

3. A HyperEdge may have more than one Edge to the same Node.

4. A HyperEdge has exactly one ConnectorNode.

5. A HyperEdge ConnectorNode may be used as a conventional Node within another HyperEdge.

6. A HyperEdge is associated with one or more Cytoscape Networks.

7. The only shared Edges in a HyperEdge are those connecting two ConnectorNodes (HyperEdges) that must exist in the same Cytoscape Network.

8. A regular Cytoscape Edge may directly connect to a HyperEdge ConnectorNode, but it will not be considered part of the HyperEdge.

9. HyperEdges are shared, in that any change to a HyperEdge existing in more than one !Cytoscape Network is reflected in all Cytoscape Networks to which the HyperEdge belongs.