The CBRI purchased a Sun Microsystems x4100 with four cores and 8GB of RAM to serve as an assembler, what the vendor calls a ‘DataRig’, to process data from a Genome Sequencer 20™ System, developed by 454 Life Sciences, an ultra-high-throughput automated DNA sequencing system capable of resolving hundreds of thousands of DNA sequences in one run.

While the minimum suggested requirements for the DataRig were not impressive the x4100 device is:

The Opteron processors are rated to provide a significant boost over similar Xeon systems. We plan to run a 64-bit openSUSE LINUX environment and integrate the system in to the LENTI/NIS domain. The campus SAN project has not answered the question about compatible HBAs. We anticipate the successful deployment of this device may require the purchase of others for use as pipeline processors. In this case it might be best to mount the /san partition from an existing Tier II server via NFS over GB network connection. This architecture allows for an arbitrary number of processing hosts, limited by the number of ports on the supporting GB switch and not SAN HBAs.

When the system is in production I will post relevant benchmark data.

“Piled Higher and Deeper” (PhD) is the comic strip about life (or the lack thereof) in academia. I’ve explained it to others as ‘Dilbert for grad students’. Sometimes I wonder if Jorge Cham (the author) works in our lab.

September 27, 2006 I’ll be speaking to the Bioinformatics Journal Club about Nature Publishing Group‘s social bookmarking system ‘Connotea‘. The following links are a good start:

The site: http://www.connotea.org/

The source: http://sourceforge.net/projects/connotea

The paper: http://www.dlib.org/dlib/april05/lund/04lund.html

Connotea is a free online reference management and social
bookmarking service for scientists created by Nature Publishing
Group. While somewhat experimental in nature, Connotea already
has a large and growing number of users, and is a real, fully
functioning service. The label ‘experimental’ is not meant to
imply that the service is any way ephemeral or esoteric, rather
that the concept of social bookmarking itself and the application
of that concept to reference management are both recent
developments. Connotea is under active development, and we are
still in the process of discovering how people will use it. In
addition to Connotea being a free and public service, the core code
is freely available under an open source license

Background: http://www.dlib.org/dlib/april05/hammond/04hammond.html

Context: http://www.shirky.com/writings/ontology_overrated.html

(Note: PDF Slides available.)

(Larger version available here.)

The Access Grid tools don’t seem to have changed substantially since the MBONE days. Compatibility reasons meant I had to launch rat and vic from the command-line without use of the Venue Client management interface. Fine with me, but this wouldn’t fly in some locations where the mere sight of command-line inflicts paralysis.

Seen but not heard. Something to do with audio encoding and compatibility problems. So I resorted to napkins inscribed in sharpie with ‘Yes”, “No”, and “Maybe”. This made for a somewhat limited technical presentation on my part.

With all the fits and starts, the effect is compelling. I was able to see and hear a large number of people, over widely distributed locations. Ideas were discussed and plans made. We accomplished something useful.

The National Science Foundation posted the list of winners from the 2006 Science and Engineering Visualization Challenge. My favorite category is ‘Informational Graphics’ and the winner looks like a graphic pulled from a recent issue of National Geographic.

First Place

Hawaii, the Highest Mountain on Earth
Credit: Nils Sparwasser, Thorsten Andresen, Stephan Reiniger; Robert Meisner, German Aerospace Center (DLR)

Mount Everest is the highest mountain on Earth above sea level, but it’s not the world’s tallest mountain. That honor goes to the Hawaiian volcano Mauna Kea. When measured from its base on the Pacific Ocean floor, it os about 1,000 meters taller then Mount Everest. Mauna Kea is part of a 5,600-kilometer-long string of volcanoes stretching westward from the main Hawaiian island. Geographer Nils Sparwarrer and his colleagues at the German Aerospace Center in Oberpfaffenhofen introduce us to the Hawaiian volcanoes with this panoramic view across the Pacific Ocean.

Second Place

The Mona Lisa: A Montage of Scientific Images
Credit: Louis Borgeat, François Blais, John Taylor, Luc Cournoyer, Michel Picard, Angelo Beraldin, Guy Godin, Marc Rioux, Guillaume Poirier, National Research Council of Canada; Christian Lahanier, Centre de Recherche et de Restauration des musées de France

It may not be the prettiest Mona Lisa image you have seen, but it is most certain to be the most informative. This “montage”, jointly produced by the National Research Council Canada and the Center for Research and Restoration of the Museums of France, depicts the information obtained by analyzing Leonardo da Vinci’s painting using the latest scientific imaging technologies, such as a high-resolution 3Dscanner and a polychromatic 13-band multispectral camera. Such analyses help museum curators and conservation experts study the condition and authenticity of old paintings as well as revel techniques used by the artists.

Honorable Mention

Materials Informatics: Visualization of High Dimensional Combinatorial Data
Credit: Matt Heying, Changwon Suh, Krishna Rajan, James Oliver, Iowa State University; Simone Seig, Wilhelm Maier, Universität des Saarlandes

Chemists are forever hunting for newer and more efficient catalysts. The task can require sifting through enormous amounts of data on the chemistry of potential candidates. Here materials scientist Krishna Rajan and colleagues have made the job easier with this visually captivating yet comprehensive informational graphic.

The rest of the winners can be viewed here. The full story is here.