Microsoft researcher, sailor, and father of database transactions, Jim Gray, 63, is reported lost at sea in clear weather and moderate four to five foot seas. He embarked alone on a day sailing trip aboard his 40-foot C&C yacht Tenacious from San Francisco Bay to the Farallon Islands to scatter his mother’s ashes. He called a family member at 10:30AM Sunday to say he was sailing out of cell phone range. He was not heard from again. Authorities were first notified when his wife called the Coast Guard around 8:30PM Sunday.

By all counts, the weather in the Bay area has been glorious since Sunday Morning. But local sailors consider this a tricky time of year to sail to the Farallons, as distant storms can cause large swells in the shallow waters between the Golden Gate and the islands.

NBC11.com posted 10 minute raw video interview with Coast Guard spokeswoman Lt. Amy Marrs (from KNTV, NBC 11 San Jose). The interview explains the status of the Coast Guard’s search efforts as of yesterday 1/30/2007.

Other news accounts include:

New York Times (article link)
C|Net (article link)
Information Week (article link)
KTVU.COM (article link)
NBC11.COM (article link)

(Update: The Coast Guard called off its search Thursday 2/1/2007, ending a four-day hunt.)

Word swept through the high-technology community, dozens of Dr. Gray’s colleagues, friends and former students began working together on Monday to supplement the Coast Guard’s efforts with computer technology.

The activity, which began Tuesday, escalated over the course of the week. A Who’s Who of computer scientists from Google, Amazon, Microsoft, NASA and universities across the country wrote ad hoc software, created a blog and reconfigured satellite images so that dozens of volunteers could search for a speck of red hull among the digitized images.

Hopes remain high.

New York Times (Silicon Valley’s High-Tech Hunt for Colleague)
Community BLOG: (http://www.openphi.net/tenacious)
Microsoft site: (http://research.microsoft.com/displayArticle.aspx?id=1621)

Help find him by searching High Resolution Satellite Imagery

A call came across the HPCwire news list this morning:

Over the past weekend many of Jim Gray’s friends worked to obtain
satellite and aerial imagery, hoping to find him and his 40-foot
sailboat. A team of engineers and scientists from Google, Amazon,
Microsoft and NASA, along with the public, have been invited to scan
thousands of the satellite photographs of the search area. Two
approaches are being used: human and computer analysis. The human
analysis is taking place via Amazon’s Mechanical Turk site
(http://www.mturk.com/mturk/preview?groupId=J0XZ58STDWJZ5QY4F9M0), and
this has involved some 6,000 volunteers looking through nearly 100,000
images since Friday evening. Once these volunteers flag an image as
containing an object of interest, these are passed to another group of
experts who look through all of the flagged images, also using
Mechanical Turk. The group is still looking for volunteers to search the
satellite photos and experts to analyze the flagged images.

Amazon mechanical turk site: (link)
An overview of the process: (link)

His family is in our thoughts and prayers.

The World Question Center asks one question a year and several of the best minds in science have responded to this year’s question: “What are you optimistic about?”. According to the publishers, over 160 responses thus far span topics such as string theory, intelligence, population growth, cancer, and climate change. Contributers include:

MARVIN MINSKY
Computer Scientist; 1st Generation Artificial Intelligence Pioneer, MIT; Author, The Emotion Machine: Commonsense Thinking, Artificial Intelligence, and the Future of the Human Mind.

BRIAN GREENE
Physicist, String Theorist, Columbia University; Author, The Fabric of the Cosmos

RAY KURZWEIL
Inventor and Technologist; Author, The Singularity Is Near: When Humans Transcend Biology

HOWARD RHEINGOLD
Communications Expert; Author, Smart Mobs

On the Open Culture blog, there is an entry regarding Digital MBA: America’s Best Business Schools on Your iPod. They cite the following links:

Wharton at The University of Pennsylvania (iTunes – Feed – Web Site)

Harvard (iTunes – Feed)

Duke’s Fuqua School of Business (iTunes – Web Site)

University of Chicago Graduate School of Business (iTunes – Feed – Web Site)

Certainly worth checking. I’ve subscribed and look forward to discussing new ideas on this forum. From a recent Harvard Business Review podcast:

A leader who does not produce other leaders, is not a leader.

Always think from the outside in.

New leaders will find new ways to harness the abilities of others without the use of power.

Santiago Calatrava: The Poetics of Movement, by Alexander Tzonis is an unusual art book. The text is as rich and vivid as the photographs of Calatrava’s soaring structures.

The inclusion of sketch studies provide insight into his training and design process. I especially appreciated Calatrava’s sketches of Notre-Dame du Haut, Ronchamp, by Le Corbusier. I have similar sketches (though only from photographs) and was pleased to learn what he chose to highlight in his drawings.

Calatrava: Public Buildings, by Stanislaus von Moos, Anthony Tischhauser, and Quim Nolla. From the forward, by Santiago Calatrava:

In my Ph.D. thesis ‘On the Foldability of Structures‘, I was guided by the motto “Natura mater et magistra” – nature is both, mother and teacher. This motto has guided all my work. There are many lessons one can draw from nature, real guiding rules and metaphors from observing plants and animals. To me, there are two overriding principles to be found in nature which are most appropriate for building: one is the optimal use of material; the other is the capacity of organisms to change shape, to grow, and to move. Movement in particular has been a source of real inspiration to me.

I’m interested in the biological themes behind his designs. Moving structures with bone-like joints. The Planetarium of the Valencia Science Center, Valencia, Spain, 1991 is an eye with a moving eye-lid.

His work reminds me of Pier Luigi Nervi‘s work during the 1970′s, but Calatrava benefits from the availability of lighter and stronger materials. Others liken his work in Valencia to Antoni Gaudi’s work in Barcelona. I prefer Calatrava.

The focus of biomedical text-mining has been on automatic data retrieval, rather than including the user in the discovery process. The web is an inherently user-centered information discovery resource. Interactive literature exploration can take advantage of the inherent links between biomedical publications. In the biomedical field, genes are a common denominator. Genes and proteins serve as basic unit of information.

Biomedical knowledge can be seen as networks of concurrent genes and proteins that include relationships ranging from direct physical interaction to less direct associations with phenotypic observations and pathologies.

iHOPerator is a GreaseMonkey user-script that operates over the iHOP (information Hyper-linked Over Proteins) website. It enhances the gene-centered pages on iHOP by providing a compact, configurable visualization of defining information for each gene. Enabling additional data, such as biochemical pathway diagrams collected from third party resources (KEGG) and displaying it all together in the same browsing context.

It is little better than screen-scraping. Content in HTML was not designed for this and is difficult for GreaseMonkey scripts to parse consistently. HTML may change and require changes in your parser. This could make the scripts brittle and unreliable.
A Semantic representation of this data would mediate this problem.

We need new tools to explore and combine data in meaningful ways. The Semantic Web puts data into a machine-readable format so computers can aggregate data and make inferences about relationships.

(Presentation: 2007 Spring BIOINF JC.pdf 13.6MB)