BubbleRouterRFC

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About this document

This is an official Request for Comment (RFC) for feedback and critique of the new Bubble Router plugin.

For details on RFCs in general, check out the Wikipedia Entry: Request for Comments (RFCs)

Biological Questions / Use Cases

You have a network or list of genes from an array study or literature search and you want to organize and layout the nodes in a biologically meaningful way. Instead of using the current layout algorithms that rely on network-based parameters, the Bubble Router plugin provides an interactive layout experience. You can draw rectangular regions anywhere on the canvas and then route nodes to the region by selecting an attribute and value from the available node attributes. You can also load and reference species-specific cellular component attributes that we've prepared and will distribute with the plugin, allowing layouts based on a compact set of cell compartments such as Nucleus, Cytoplasm, Extracellular, Plasma Membrane, etc.

Instructions

Bubble Router Manual

Comments

AllanKuchinsky - 2007-01-19 15:41:37

The BubbleRouter is also a test vehicle for two additional constructs we are experimenting with for Cytoscape: multi-layered canvas and arbitrary graphical annotations. The multi-layered canvas extends the current notion of a network view to also support FOREGROUND and BACKGROUND layers, which can be used to place annotations, background figures, etc. Arbitrary graphical annotations are graphical elements -- such as brackets, freestanding text, and arbitary lines and shapes -- that are not tied to Cytoscape Nodes and Edges.

GaryBader - 2007-02-01 10:23:50

Cool! Could the edge crossing be implemented to work for all components at once? (global minimization?) I think there is some edge crossing reduction code in Rob Sheridan's hierarchical layout code (implementing Sugiyama)