I drew these Yeast protein interaction networks on a arc with the Javascript Protovis.js using the HTML5 canvas object as the pallet. Displayed are only a select number of edges though all the nodes of interest are listed. If you drill down on the baseline you can see the names of the ORFs. ORFs are clustered by gene, but otherwise there is little meaning in horizontal distance.

Ultimately, this should be an interactive tool for visual selection of biologically relevant interactions, resulting in tabular data retrieved from supporting databases.

(See also: protovis)

I watched, earlier this decade as Tamara Munzner’s H3Viewer came on the scene. Walrus is being developed by Young Hyun at CAIDA and builds on the idea. Although Walrus is based on research by Tamara Munzner, she is not connected with this effort in any way, nor does Walrus make use of any code from her H3Viewer.

The project appears to be dormant (since 2005) and claims it doesn’t run on modern Macintosh systems (no-longer the case). I’m looking for biological applications in non-directed graph visualization. Specifically, Yeast interaction networks.

(See also: walrus)

The Global edition of the New York Times has a nice tool on their site for tracking 2010 World Cup matches. Heat maps of field position, shot and possession timelines, updated every 15 seconds.

(See also: NYtimes: LIVE World Cup Match Tracker)

A tremendous image this morning. May your weather map appear less interesting.

(See also: www.wunderground.com)

Here is an early visualization I created of functional genomic interaction networks in yeast. I’m using Gephi 0.7 alpha3 to create the images and though this is a small subset of the greater hairball generated from 3531 nodes and 20,293 edges, it is perhaps the most beautiful.

Here is the same data rendered in Cytoscape v2.6.2, with labels turned on the nodes.

For my next trick, I will attempt to build a model of 4467 nodes and 8,394,136 edges. LGL appears to be built for large biological datasets like this.

(See also: DRYGIN: a database of quantitative genetic interactions of S. Cerevisiae)
(See also: gephi.org)
(See also: LGL is a compendium of applications for making the visualization of large networks and trees tractable.)
(See also: cytoscape.org)

(See also: YouTube.com: Lux Aurumque)

Do you know where that mouse has been? This is a visualization of where my mouse has been over the last 7.9 hours.IOGraph is an application that turns mouse movements into a modern art. The idea is that you just run it and do your usual day stuff at the computer. The image above is from 7.9 hours of work this afternoon. We’ll have to see what happens after a day or two of operation.

(See also: iographica.com)

$ traceroute 75.72.0.20
traceroute to 75.72.0.20 (75.72.0.20), 64 hops max, 40 byte packets
...
11  te-0-3-0-5-ar01.roseville.mn.minn.comcast.net (68.86.91.186)  38.256 ms  49.556 ms  49.310 ms
12  te-0-1-0-0-ar01.crosstown.mn.minn.comcast.net (68.87.174.218)  72.147 ms  66.879 ms  73.369 ms
13  te-8-1-ur02.pillsbury.mn.minn.comcast.net (68.86.232.86)  70.672 ms  73.403 ms  75.239 ms
14  ge-4-1-0-ten01.pillsbury.mn.minn.comcast.net (68.85.164.206)  78.400 ms  76.518 ms  72.266 ms
15  c-75-72-0-20.hsd1.mn.comcast.net (75.72.0.20)  75.868 ms  80.111 ms  86.035 ms

Is attempting to use an old Microsoft FrontPage remote administration tool exploit to cause a buffer overflow and gain access to my server. This is what it looks like in the Apache log file:

0\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\
x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x9
0\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90\x90" 414 546 "-" "-"
75.72.0.20 - - [29/Mar/2010:15:15:47 -0500] "GET / HTTP/1.0" 200 11988 "-" "-"
75.72.0.20 - - [29/Mar/2010:15:16:18 -0500] "POST /_vti_bin/_vti_aut/fp30reg.dll HTTP/1.1" 404 20680 "-" "-"

This is a known problem and it would be considerably more annoying if I were running FrontPage and/or IIS. All it does on my machine is dump my Apache processes and drive my systems loads through the roof.Effectively a DOS attack.

One of the canonical remedies simply redirects the requests to microsoft.com:

<IfModule mod_rewrite.c>
RedirectMatch permanent (.*)cmd.exe(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)root.exe(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)\/_vti_bin\/(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)\/scripts\/\.\.(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)\/_mem_bin\/(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)\/msadc\/(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)\/MSADC\/(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)\/c\/winnt\/(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)\/d\/winnt\/(.*)$ http://www.microsoft.com/
RedirectMatch permanent (.*)\/x90\/(.*)$ http://www.microsoft.com/
</IfModule>

There is humor in this, though the right thing to do would be a redirect to a local 404.html file. This should effectively stop the propagation of the exploit.

(See also: linuxquestions.com: security)

The multi-touch enabled display is a composite of 28 projectors with a total resolution of 7168 x 3072 pixels. It supports both physical and acoustic gestures to pan and zoom data sets of arbitrary size. It is driven by a 31-node ROCKs v4.x visualization cluster. Each node is a Dell Precision 370 workstations (Intel Pentium 4 EM64T at 3.2 GHz, 2 GB RAM, HyperThreading, NVIDIA Quadro FX 3400 with 256 MB VRAM on a PCI Express x16 bus).

Given the age of the ROCKs distro and the supporting compute hardware, this display must have been in place for a number of years.

(See also: Navigating 13.3 gigapixels on a 22 megapixel display wall)
(See also: YouTube: University of Tromsø wall Demonstration)
(See also: ROCKs Clusters)

This is not the latest from XKCD, but it is one of the best.

(See also: XKCD: Fields arranged by Purity)