wjrl

4 ms·

1.
by wjrl 12y ago
You're welcome, and thanks! Anybody who wants to can play with different layouts, which are just linear orderings of nodes and edges, which you specify using node and edge attribute files. Features like that are discussed in the blog p
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by wjrl 12y ago
Of course, YMMV, but the Stanford web network ( http://www.biofabric.org/gallery/index.html#Stanford ) has 2.3 million edges but you can glean structure from it. You can visually estimate things like the network radius a
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by wjrl 12y ago
Not sure what you mean in first sentence? I have found the node lines to be useful for navigation, and the edge lines (drawn darker and in front) create "edge wedges" that make nodes with similar neighborhoods stand out. Without l
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by wjrl 12y ago
If you have a complicated system, the best way to deal with the complexity is to organize it in some fashion. BioFabric provides a way to do that, since it allows the network to be arranged in a linear fashion. Kinda like the advantages of
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by wjrl 12y ago
Sorry, newbie at commenting, so my replies are actually in separate comments below. Summary: you can create a layout that orders nodes, and edges, to fit what you are trying to look at.
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by wjrl 12y ago
I think the protein-protein interaction network on the BioFabric home page (www.BioFabric.org) shows how one can recognize nodes with similar neighborhoods at the global level. Being able to spot these patterns is unique. Can also do networ
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by wjrl 12y ago
Placing infected individuals in the top rows, ranking uninfected individuals by probability of infection, lay out the network. Overall shape of network might give clues to network structure? I find that with contact networks, dynamic networ
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by wjrl 12y ago
BioFabric should be able to handle that OK. Import as tab-delimited sif file. Default layout is breadth-first search, in order of decreasing degree, starting from highest degree node. If that is not what you want, can specify node order. Se
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by wjrl 12y ago
Note that since the nodes-as-lines approach gives you a new degree of freedom to work with, you can organize edges into semantically useful groups by placing similar links next to each other. E.g. think about link communities instead of nod
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by wjrl 12y ago
BioFabric layouts are just a linear ordering of the nodes and edges, and you can specify those with input files. For example, you can break out clusters and show intra- and inter- cluster links separately. See http://www.biofabri