Also Sprach Zarathustra

OK, before we get started with this post, you first have to view this video clip to set the appropriate mood:

And with that memorable introduction, I present the BioFabric version of Brendan Griffen's Graph of Influential Thinkers, with 7239 nodes and 14560 edges:

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And what's that got to do with the opening credits of 2001: A Space Odyssey? Well, that memorable piece of music, Einleitung, oder Sonnenaufgang (Introduction, or Sunrise), is the famous opening section of Richard Strauss's tone poem Also Sprach Zarathustra. And who was the author of the book Also sprach Zarathustra: Ein Buch für Alle und Keinen that inspired Strauss? Friedrich Nietzsche, who happens to hold the premier, top-left, row #1 position in the BioFabric version of the network:

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The graph was built using the "influenced" and "influenced by" links that appear in the sidebar of many Wikipedia articles about historical and current figures. Go and visit Dr. Griffen's blog post to learn about the creation of his network, and to see his beautiful Gephi-based renderings!

I'll be spending the next couple blog posts discussing this network, which will give me a chance to discuss BioFabric's "similar connectivity" algorithm, since it was used to layout the network instead of the default method. But to get started in this post, I've just included some screen shots of BioFabric showing some of the same thinkers as were depicted in the original blog post. First some artists, with Pablo Picasso as the most visible node:

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Some authors, where Stephen King and H.P. Lovecraft are prominent:

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The comedians include George Carlin and Richard Pryor:

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More philosophers, who are placed a little further over than Nietzsche:

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And some more writers, with Beat poets and other Beat Generation writers showing prominently on the left:

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Of course, the best way to explore the network is to view it in BioFabric. Head on over to the BioFabric Gallery to pick up the .bif file (in a compressed gzip archive file) and have fun! Thanks to Brendan Griffen for providing the data, and keep an eye out for my next blog posts on the network.

I Was Lost, But Now I'm Found...

In my last posting, I showed a variety of node ordering schemes that could be applied to the combined glucose/oleate network. Of course, the only way to actually do these different layouts is to create a .noa node attribute file that specifies a node ordering and then install it using the Layout->Layout Using Node Attributes... feature. To make that whole process more understandable, I've posted the code for the little standalone Java program I used to create the files up at my BioFabric Github repository at:

https://github.com/wjrl/BioFabric/blob/master/src/org/systemsbiology/biofabric/layouts/GluOleNodeOrder.java

It's a quick-and-dirty implementation that is totally hardwired to this specific example, but taking a look at that code can give you an idea of how to extend it to your particular situation.