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| || '''RFC Name''' : Bubble Router Plugin || '''Editor(s)''': Alex Pico, Allan Kuchinsky, Kristina Hanspers, Nathan Salomonis || | || '''RFC Name''' : Bubble Router Plugin || '''Editor(s)''': Alex Pico, Allan Kuchinsky, Kristina Hanspers, Nathan Salomonis || '''Status''': Closed|| |
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== Status == ##Put the date and the status. Status can be e.g. "Not yet completely written", "Open for public comment", "Closed for public comment". There could be some explanation of the status Under Construction == How to Comment == To view/add comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Here is an example to get things started: ["/Comment"]. ##The sections below may be useful when creating an RFC, delete the ones that are not |
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== Demo == View [http://chianti.ucsd.edu/~mes/BubbleRouterTest.mov this demo video] to see how it work! ~-(Can you name that voice?)-~ |
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| Coming soon... | [http://conklinwolf.ucsf.edu/BubbleRouter/manual.htm Bubble Router Manual] |
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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. |
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. |
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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) |
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) |
RFC Name : Bubble Router Plugin |
Editor(s): Alex Pico, Allan Kuchinsky, Kristina Hanspers, Nathan Salomonis |
Status: Closed |
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 [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments 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
[http://conklinwolf.ucsf.edu/BubbleRouter/manual.htm 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)