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Cytoscape 3.0 Use Cases

Please write the use cases in terms of Cytoscape, meaning talk about node, edges, and attributes rather than talking about proteins and interactions. Instead, use specific biological discussions to illustrate instances of particular use cases. Try to be as general as possible. Try to see how your use case might match another use case that already exists.

Use Case: Biochemical Reactions (HyperEdges)

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 a user 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 a user 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. We refer to this small square as a ConnectorNode. We also refer to the collection of edges and ConnectorNode as a HyperEdge.

The following two figures show examples of biochemical reactions -- Krebs Cycle and Glycolysis Reaction.

The first figure below illustrates Glycolosis Reaction. Note the use of shared edges and multiple connections to the same Node within a HyperEdge.

attachment:glycolosis.png

The second example below uses a Circle Graph Layout to illustrate the Krebs Cycle.

attachment:krebs_cycle.png

A detailed discussion of HyperEdge design issues can be found on the wiki page at Cytoscape_3.0/HyperEdges.

Use Case: Scientific Illustration

Cytoscape is used by researchers who need to publish and present their work. Often a user will want to include figures of Cytoscape networks in their publications and/or presentations. This requires presenting the Cytoscape network in a way that is intuitive to biologists. But Cytoscape networks are designed for computation, not presentation. The figure below shows a segment of a Cytoscape network for Apoptosis, imported originally from BioPAX.

attachment:apoptosis_biopax.png

Contrast this with a manually illustrate Apoptosis pathway, as shown in the figure below, derived from Wikipathways (http://www.wikipathways.org).

attachment:apoptosis_wikipathway.png