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)

Sarah and I are enjoying exploring ManyBooks.net. In addition to finding old classics we want to revisit we have found some new publications that are quite entertaining. (Everyone in Silico, by Jim Munroe) Collections of poetry, science fiction from Wells and Verne, and Shakespeare‘s plays and sonnets.

The texts are available in nearly every imaginable format. The ePub files are easily imported to iBooks, include cover art, and read on the iPad and iPod Touch. ePub readers are available from Adobe (Digital Editions and others) and run on nearly all modern computing hardware.

Here are the most popular 21,657,732 copies of 27,788 titles have been downloaded since 1/1/2008:

• 113,942 – The Art of War by Sun Tzu
  
• 89,659 – The Kama Sutra of Vatsayayana by Richard Burton
  
• 78,449 – The Adventures of Sherlock Holmes by Arthur Conan Doyle
  
• 51,364 – Pride and Prejudice by Jane Austen
  
• 51,062 – The Art of Public Speaking by Dale Carnegie
  
• 45,809 – Fanny Hill by John Cleland
  
• 45,217 – The Grammar of English Grammars by Goold Brown
  
• 44,093 – Alice in Wonderland by Lewis Carroll
  
• 41,852 – 20,000 Leagues Under the Sea by Jules Verne
  
• 37,906 – The Call of Cthulhu by H. P. Lovecraft
  
• 37,313 – Adventures of Huckleberry Finn by Mark Twain
  
• 37,176 – The Curious Case of Benjamin Button by F. Scott Fitzgerald
  
• 36,513 – The Count of Monte Cristo by Alexandre Dumas, père
  
• 34,914 – The Arabian Nights by Andrew Lang
  
• 31,283 – Adventures of Tom Sawyer by Mark Twain
  
• 27,868 – Wuthering Heights by Emily Brontë
  
• 26,923 – The Communist Manifesto by Karl Marx and Friedrich Engels
  
• 26,504 – The Complete Works of William Shakespeare by William Shakespeare
  
• 24,742 – Ulysses by James Joyce
  
• 24,624 – The Age of Reason by Thomas Paine
  

I have no doubt you will find something of interest here.

(See also: manybooks.net/recent_additions.php)
(See also: Adobe ePub Reader – Digital Editions)
(See also: ebook readers)

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)

Maybe this hits too close to home.

I did like the part about burning all the Service Desk tickets, “It’s the quickest and most efficient way to deal with service requests in a timely manner… this way we can address all of them at once.”

The smoke is a nice touch.

It’s all fun and games until the Halon fire suppression system dumps.

(See also: fnal.gov: April Fools 2010)

$ 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)