30 December 2006

Tennis Venues

Crosstown Tennis, 14 W. 31st St., New York
East River Tennis Club, 44-02 Vernon Blvd., Long Island City
Eastside Tennis Club, 220 E. 76th St., New York
Forest Hills Tennis Stadium, 69th Ave. And Burns Rd, Forest Hills
Hrc Tennis, South St., Piers 13 And 14, New York
Midtown Tennis Club, 341 Eighth Ave., New York
New York Health And Racquet Club - Village Tennis Courts, 110 University Place, New York
Prospect Park Tennis Center, 305 Coney Island Ave., Brooklyn
Randall's Island Indoor Tennis, Randall's Island Tennis Field House, New York
Tennis Club Grand Central, 15 Vanderbilt Ave., New York
Tower Tennis Courts, 1725 York Ave., New York
U.S.T.A. National Tennis Center, Flushing Meadows-Corona Park, Flushing
Van Cortlandt Park - Stadium Tennis Courts, W. 241st St. And Broadway, Bronx

29 December 2006

Lucrative store locations pinpointed by new model -- New Scientist

Interesting "geo" (realestate) mining

Lucrative store locations pinpointed by new model
07 October 2006
>From New Scientist Print Edition.
The old mantra about the three most important factors for a shop's success - location, location and location - has been borne out by a new mathematical model. It could help retailers pinpoint lucrative sites for their stores....

28 December 2006

A Letter in response to "Cyber-Neologoliferation" -- NY Times

Here's the letter I wrote in response to this article (which was never published):
I was struck by the recent article on the development of the third edition of the Oxford English Dictionary. I was impressed by the degree to which the curators of this dictionary are embracing modern, computerized search in addition to manual annotation. The parallels between making a lexicon of all the English words and the way scientists are annotating the genes in many genomes being sequenced are quite striking. In both cases, people are looking for where it (word or gene) first appeared and how it's varied in usage across many different contexts. One crucial difference, however, is in the gene annotation business, researchers are very interested in how often a gene is duplicated or how common it is. I feel that people should probably do the same in relation to the OED, tabulating words by their frequency of usage. In a rough fashion, this can simply be done by looking at some statistics, such as the number of "Google hits" for a given term.

Published: November 5, 2006
When I got to John Simpson and his band of lexicographers in Oxford earlier this
fall, they were working on the P's. Pletzel, plish, pod person, point-and-shoot,
polyamorous — these words were all new, one way or another. They had been
plowing through the P's for two years but were almost done (except that they'll
never be done), and the Q's will be "just a twinkle of an eye," Simpson said. He
prizes patience and the long view. A pale, soft-spoken man of middle height and
profound intellect, he is chief editor of the Oxford English Dictionary and sees
himself as a steward of tradition dating back a century and a half....

ooo[clip]ooo ooo[general]ooo ooo[L2E]ooo

26 December 2006

Oenology: Red wine procyanidins and vascular health -- Nature

Looks like I should shift from California Reds to those from département of Gers in the Midi-Pyrenees in southwest France and those from Nuoro province, Sardinia.

Nature 444, 566 (30 November 2006) | doi:10.1038/444566a; Received 29 August 2006; Accepted 9 November 2006; Published online 29 November 2006
Oenology: Red wine procyanidins and vascular health
R. Corder1, W. Mullen2, N. Q. Khan1, S. C. Marks2, E. G. Wood1, M. J. Carrier1 and A. Crozier1
Regular, moderate consumption of red wine is linked to a reduced risk of coronary heart disease and to lower overall mortality1, but the relative contribution of wine's alcohol and polyphenol components to these effects is unclear2. Here we identify procyanidins as the principal vasoactive polyphenols in red wine and show that they are present at higher concentrations in wines from areas of southwestern France and Sardinia, where traditional production methods ensure that these compounds are efficiently extracted during vinification. These regions also happen to be associated with increased longevity in the population....We used the 1999 census data to identify unusual patterns of ageing in France (see supplementary information) and found that there are relatively more men aged 75 or over in the département of Gers in the Midi-Pyrenees in southwest France.Wines from Nuoro and the Gers area have 2–4-fold more biological activity and OPC content than other wines (Fig. 1c, d). This difference remains (P < 0.001) when OPC measurements are extended to a wider selection of wines from the Gers area (2.9 0.1 mM, n = 58), from France (1.8 0.1 mM, n = 61) and from other parts of the world (1.5 0.04 mM, n = 227)....

American Culture’s French Connection -- NY Times

Why isn't there an AmericanCulture.org? The answer from France.

American Culture's French Connection
Published: December 26, 2006
In "Culture in America," Frédéric Martel challenges the view that (French) culture financed by the government is good and that (American) culture shaped by market forces is bad.... Reviewing the book in Le Monde, Michel Guerrin and Emmanuel de Roux also said its strength lay in its emphasis on investigation over opinion. And another article in Le Monde took the American cultural statistics collected by Mr. Martel and compared them with similar figures for France. Its unexpected conclusion was that measured per capita the cultural infrastructures in the two countries were roughly similar... The first half of "Culture in America" — the title echoes Tocqueville's own "Democracy in America" — is built around a question that puzzles some French: Why doesn't the United States have a Culture Ministry?...He seemed to be looking forward to a fight. "That's why my book is about France," he said, "while being about America."

Route to LGA over Queensboro

over queensboro bridge
* Northern Ave
* 51 St.
* 32 Ave.
* somehow get to 25 Ave.
* enter highway near 60T

"Everything before the but is a lie" -- anonymous quote

Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts -- PNAS

Interesting analysis of some yeast pseudogenes. However, omits reference to Harrison et al. (2002) JMB.

Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14144-9. Epub 2004 Sep 20.
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts.

25 December 2006

Literature mining for the biologist: from information retrieval to biological discovery -- Nat. Rev. Genetics

Good review... but doesn't mention pubnet!

Nat Rev Genet. 2006 Feb;7(2):119-29. 
Literature mining for the biologist: from information retrieval to biological discovery.Jensen LJ, Saric J, Bork P.

Co-evolution of transcriptional and post-translational cell-cycle regulation -- Nature

Regulatory network evolution

Co-evolution of transcriptional and post-translational cell-cycle regulation
Nature. 2006 Oct 5;443(7111):594-7. Epub 2006 Sep 27.


some bio textmining

Richard K. Belew
"Literature and its referents: Analyzing PubMed citations across PFAM", Richard K. Belew, Robert Finn, Alex Bateman, Poster at ISMB02

Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics -- J Mol. Biol.

Datamining the struc. genomics pipeline

Good Fats, Bad Fats, and Trans Fats -- sciencefriday.com

For the podcast listener: Thought this was a particularly good one. Nice discussion of different types of fats: good (monounsaturated and polyunsaturated, particularly from plants) and bad (saturated, trans-, from partially hydrogenated vegetable oil)

Restrictions on Trans Fats - SciFri Podcast - 2006110324
Good Fats, Bad Fats, and Trans Fats
A sizzling steak with a pat of butter on top. Tuna, trout, or herring. A pile of crispy french fries. A flaky biscuit or delicate pie crust. Sure, all have some fat in them - but which fats are good, which are bad, and which are somewhere in between?...

from http://en.wikipedia.org/wiki/Trans_fat
Trans fatty acids (commonly termed trans fats) are a type of unsaturated fat (and may be monounsaturated or polyunsaturated)...
Chemically, trans fats are made of the same building blocks as non-trans fats, but have a different shape. In trans fat molecules, the double bonds between carbon atoms (characteristic of all unsaturated fats) are in the trans rather than the cis configuration, resulting in a straighter, rather than a kinked shape. As a result, trans fats are less fluid and have a higher melting point than the equivalent cis fats.

Slow Is Beautiful -- NY Times

Turtles! living up to 250 years on a very sparse diet.

Slow Is Beautiful
Published: December 12, 2006
This was no euphemistic brushoff, no reptilian version of ''Sorry, I'll be busy that night washing my hair.'' Paddling around in a tropically appointed pool at the National Aquarium in Baltimore, the husky female Gibba turtle from South America made all too palpable her disdain for the petite male Gibba that pursued her....''The tale of the tortoise and the hare is the turtle's life story,'' said Mr. Cover, who calls himself a card-carrying member of the ''turtle nerds'' club. ''Slow and steady wins the race.'' With its miserly metabolism and tranquil temperament, its capacity to forgo food and drink for months at a time, its redwood burl of a body shield, so well engineered it can withstand the impact of a stampeding wildebeest, the turtle is one of the longest-lived creatures Earth has known. Individual turtles can survive for centuries, bearing silent witness to epic swaths of human swagger. Last March, a giant tortoise named Adwaita said to be as old as 250 years died in a Calcutta zoo, having been taken to India by British sailors, records suggest, during the reign of King George II....

The Man on the Table Devised the Surgery -- NY Times

Thought this was a great medical, human interest story....

The Man on the Table Devised the Surgery
Published: December 25, 2006
Dr. Michael DeBakey, one of the first surgeons to perform a coronary bypass operation, is its oldest survivor


Interesting niche data mining for sports.

Discounting NBA tickets like airline seats
An entrepreneur helps pro sports teams fill stadiums more efficiently, using new technology that tracks ticket sales.
FORTUNE Small Business Magazine
By Maggie Overfelt, FSB Magazine
December 11 2006: 10:06 AM EST
(FSB Magazine) -- As the NBA season gets underway, experts predict a tough slog for the Boston Celtics. Last year's team finished with 33 wins and 49 losses, and the roster this season is filled with younger players and few big names. The bottom line? Senior management has to rely on something else to help attract fans: StratBridge, a 15-person firm based in Cambridge, Mass.....

NIH in the Post-Doubling Era: Realities and Strategies -- Science magazine

Thought this was an interesting article on where NIH is going for the year.

Elias A. Zerhouni

Some notes from Data Mining 2006 (cs545)

Data mining lecture slides for courses based on reference text books

Ian Witten and Eibe Frank:

Margaret Dunham:

Pang-Ning Tan, Michael Steinbach, and Vipin Kumar:

Jiawei Han and Micheline Kamber:


Markov Blankets

Market Blankets (MB) are a promising, relatively new, set of datamining techniques for handling feature selection and related issues on Bayesian networks. Learn about MBs, read about different algorithms for implementing them , try them out for some typical problems (especially ones with many features), and write a short review paper.


Those Inflatable Santas: Eyepoppers to Eyesores -- NY Times

Seems to be an expensive new fad

Those Inflatable Santas: Eyepoppers to Eyesores
Published: December 22, 2006
Whatever else Christmas in America means, it now also includes inflatable outdoor decorations.... But the inflatables have brought the notion of Christmas self-expression to another plane. Now, the Macy's Thanksgiving Day Parade, that televised triumphal march that inaugurates the season, can live on in miniature for weeks at a time, swaying and bobble-heading across the front lawn of anyone willing to pay the electric bill — maybe a thousand dollars if you keep them inflated all the time, less if you leave the skins of your Christmas characters sprawled on the ground most of the day, their crumpled faces staring blankly at the sky or the sod, depending....The inflatables sell off the shelf for $69 to $300, and Gemmy Industries Corporation of Coppell, Tex., which claims to produce the majority of the large figures sighted this year on lawns, porches, terraces and roofs from Long Island to Los Angeles, is not shy about the product's corner-cutting appeal.

Dosage sensitivity and the evolution of gene families in yeast -- Nature

Interesting in relation to copy number. (Also, other papers by Hurst.)

Nature. 2003 Jul 10;424(6945):194-7.Click here to read  Links
Dosage sensitivity and the evolution of gene families in yeast.
Papp B,Pal C, Hurst LD.

Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations -- J Comput Biol.

structure and covariation angle looks interesting

J Comput Biol. 2006 May;13(4):929-45.
Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.
Gunewardena S, Jeavons P, Zhang Z.

24 December 2006

A particular only bacterial fold

A particular only bacterial fold -- beta-lactamases and D-Ala carboxypeptidases.
These enzymes perform functions associated with the unique structure of the bacterial cell wall (i.e. antibiotic resistance and cleavage of D-Ala peptides).

23 December 2006

A Scientist's Nightmare: Software Problem Leads to Five Retractions -- Science

Computer bugs mess up membrane protein structures... Could this have been seen ahead of time? (Also note use of Google scholar by Science to find citations.)

Until recently, Geoffrey Chang's career was on a trajectory most young scientists only dream about. ...His lab generated a stream of high-profile papers detailing the molecular structures of important proteins embedded in cell membranes....Then the dream turned into a nightmare. In September, Swiss researchers published a paper in Nature that cast serious doubt on a protein structure Chang's group had described in a 2001 Science paper. When he investigated, Chang was horrified to discover that a homemade data-analysis program had flipped two columns of data, inverting the electron-density map from which his team had derived the final protein structure. Unfortunately, his group had used the program to analyze data for other proteins. As a result, on page 1875, Chang and his colleagues retract three Science papers and report that two papers in other journals also contain erroneous structures....Chang's MsbA structure was the first molecular portrait of an entire ABC transporter, and many researchers saw it as a major contribution toward figuring out how these crucial proteins do their jobs. That paper alone has been cited by 364 publications, according to Google Scholar.

A impressionists view of Connecticut

"Road to the Land of Nod" 1910 by Frederick Childe Hassam
was painted in the Weir farm in CT
The image -- http://mylifestream.net/photostream/2006/12/c-hassam-road-to-land-of-nod-20dec06.html]

http://metnet.vrac.iastate.edu/browser -- pubmed assistant

Perhaps worth a download...


17 December 2006

Some random but interesting quotes and tidbits

Some random but interesting quotes and tidbits I've been accumulating.... might find them interesting.

"This will be a better world when the power of love replaces the love of power."

"Ontology = Specification of a conceptualization"

"REST = random episodic silent thought"

"The 'four M's', measurement, mining, modeling and manipulation" -- D Lauffenburger.

"When easter is: 1st Sunday after 1st full moon after Vernal equinox"
(difficult to place because involves joining solar & lunar calendars)

"The more choices we are presented with, the more likely it is we'll become a "maximizer" and cease being a "sufficer", (to use the terminology psychologist Barry Schwartz uses in The Paradox of Choice), meaning we're more likely to be unsatisfied with anything less than perfection. "
(from http://www.popmatters.com/pm/columns/article/6668/freedom-from-choice)

13 December 2006

12 December 2006

‘Sonic Hedgehog’ Sounded Funny, at First -- NY Times

Interesting article on gene names in the same spirit as "What's in a name?"

'Sonic Hedgehog' Sounded Funny, at First
Published: November 12, 2006
"Lunatic fringe," "head case" and "one-eyed pinhead" might sound like insults from the schoolyard or talk radio. But these are actually examples of the kind of oddball names that scientists give to genes they discover....

Listing of Statistical Software, besides R

Made up this listing of Statistical Software, besides R -- thought it might be useful

Splus -- http://www.mathsoft.com/webstore
SAS -- http://www.sas.com/software/products.html
statview -- www.statview.com (mac only?)
statistica ??
sigma plot -- www.spss.com
sigma stat --
SPSS -- www.spss.com
MatLab statistics -- http://www.mathworks.com/
NAG excel add ins -- http://www.nag.com/
atlantis -- http://sigmasoftc.com/atlantis/
Good listing of software at


Perhaps (!) a promising biotech startup, as featured in the 16 Nov. WSJ


11 December 2006

The Artist and the Mathematician -- Science Friday

"Chris" lives!

Science Friday > Archives > 2006 > November > November 17, 2006, Hour Two:
The Family that Couldn't Sleep / The Artist and the Mathematician
Starting in the 1930s, Nicolas Bourbaki published dozens of papers, becoming a famous mathematician. There was just one problem: he didn't exist. Join Ira in this hour on Science Friday for a conversation with Amir Aczel about the genius mathematician who never existed.

KT event

According to Wikipedia, mice and men diverged 75 million years ago and then we had the major KT event 10 million years later.


Cycling Around NYC

Top of Manhattan

Route on Google maps

Summary Data
Total Time (h:m:s) 3:41:08 10:46 pace
Moving Time (h:m:s) 2:33:33 7:28 pace
Distance (mi ) 20.53
Moving Speed (mph) 8.0 avg. 24.5 max.
Elevation Gain (ft) +7,875 / -8,006

Avg. Heart Rate 74 bpm Zone 0.8

Temperature (°F) 50.4°F avg. 51.8°F high
Wind Speed ( mph) S 3.7 avg. S 5.8 max.

Central Park to Prospect Park

Route on Google maps
http://www.onnyturf.com/subway and http://monkeyhomes.com/map/nycsubway.php have matching subway maps giving connections back.

Summary Data
Total Time (h:m:s) 5:09:31 11:24 pace
Moving Time (h:m:s) 4:02:56 8:57 pace
Distance (mi ) 27.14
Moving Speed (mph) 6.7 avg. 49.2 max.
Elevation Gain (ft) +2,803 / -2,833

Avg. Heart Rate 84 bpm Zone 0.9

Temperature (°F) 63°F avg. 64.4°F high
Wind Speed ( mph) SSE 6.2 avg. SSE 8.1 max.

Up West Side to NJ

Route on Google maps

Summary Data
Total Time (h:m:s) 3:12:13 16:19 pace
Moving Time (h:m:s) 1:38:16 8:20 pace
Distance (mi ) 11.78
Moving Speed (mph) 7.2 avg. 17.6 max.
Elevation Gain (ft) +4,407 / -4,375

Avg. Heart Rate 83 bpm Zone 0.9

Temperature (°F) 45.8°F avg. 46.4°F high
Wind Speed ( mph) N 1.9 avg. N 5.8 max.

10 December 2006

Metcalfe's Law is Wrong -- IEEE Spectrum

Thought this social networking analogy gave some nice intuition about the power-law network structures.

Metcalfe's Law is Wrong
By Bob Briscoe, Andrew Odlyzko, and Benjamin Tilly
Communications networks increase in value as they add members—but by how much? The devil is in the details

Of all the popular ideas of the Internet boom, one of the most dangerously influential was Metcalfe's Law. Simply put, it says that the value of a communications network is proportional to the square of the number of its users....The foundation of his eponymous law is the observation that in a communications network with n members, each can make (n–1) connections with other participants. If all those connections are equally valuable—and this is the big "if" as far as we are concerned—the total value of the network is proportional to n(n–1), that is, roughly, n^2.... We propose, instead, that the value of a network of size n  grows in proportion to n log(n)....To understand how Zipf's Law leads to our n log(n) law, consider the relative value of a network near and dear to you—the members of your e-mail list. Obeying, as they usually do, Zipf's Law, the members of such networks can be ranked in the same sort of way that Zipf ranked words—by the number of e-mail messages that are in your in-box. Each person's e-mails will contribute 1/k to the total "value" of your in-box, where k is the person's rank. The person ranked No. 1 in volume of correspondence with you thus has a value arbitrarily set to 1/1, or 1. (This person corresponds to the word "the" in the linguistic example.) The person ranked No. 2 will be assumed to contribute half as much, or 1/2. And the person ranked kth will, by Zipf's Law, add about 1/k to the total value you assign to this network of correspondents. That total value to you will be the sum of the decreasing 1/k values of all the other members of the network. So if your network has n members, this value will be proportional to 1 + 1/2 + 1/3 +… + 1/(n–1), which approaches log(n). More precisely, it will almost equal the sum of log(n) plus a constant value. Of course, there are n-1 other members who derive similar value from the network, so the value to all n of you increases as n log(n). Zipf's Law can also describe in quantitative terms a currently popular thesis called The Long Tail.....

To Probe Further
David P. Reed argues for his law in "The Sneaky Exponential" on his Web site at http://www.reed.com/Papers/GFN/reedslaw.html.
Several additional quantitative arguments are made for the n log(n) value for Metcalfe's Law on the authors' Web sites at http://www.cs.ucl.ac.uk/staff/B.Briscoe and http://www.dtc.umn.edu/~odlyzko.
Chris Anderson's article "The Long Tail" was featured in the October 2004 issue of Wired. Anderson now has an entire Web site devoted to the topic at http://www.thelongtail.com.
An article in the December 2003 issue of IEEE Spectrum, "5 Commandments," which can be found at http://www.spectrum.ieee.org/dec03/5com, discusses Moore's and Metcalfe's laws, as well as three others: Rock's Law ("the cost of semiconductor tools doubles every four years"); Machrone's Law ("the PC you want to buy will always be $5000"); and Wirth's Law ("software is slowing faster than hardware is accelerating").

03 December 2006

cycling fast loops in Central Park

4 fast (for me) loops in Central Park. Some stats and images below.

route on Google Maps
Total Time (h:m:s) 2:08:16 5:08 pace
Moving Time (h:m:s) 1:55:04 4:36 pace
Distance (mi ) 24.96
Moving Speed (mph) 13.0 avg. 30.9 max.
Avg. Heart Rate 133 bpm
Temperature (°F) 53.6°F avg. 53.6°F high
Wind Speed ( mph) WNW 8.0 avg. WNW 12.6 max.

Cycling Around New Haven

Route on Google Maps [static cached image]
Elevation Profile

Total Time (h:m:s)7:36:5110:54 pace
Moving Time (h:m:s)4:52:576:59 pace
Distance (mi )41.91
Moving Speed (mph)8.6 avg.20.0 max.
Elevation Gain (ft) +3,583 / -3,586

Avg. Heart Rate88 bpm Zone 1.0

Temperature (°F)48°F avg.57.2°F high
Wind Speed ( mph)SSE 5.1 avg.SSE 8.1 max.

25 November 2006

Marshall's IT Plan for Janelia Farm -- Bio IT World

Might be useful to think about in terms of future high-performance computing purchases. See extracted snippets below.

Oct. 2006 
Marshall's IT Plan for Janelia Farm
By  Kevin Davies
Oct. 16, 2006 |  Driving north from Washington Dulles Airport towards the Potomac River, it's easy to miss Janelia Farm. The only road sign faces the opposite direction, belatedly guiding lost taxi drivers retracing their route in search of the campus. Outside a makeshift hut in the middle of a construction site, the security guard waves a visitor's taxi down a long, winding dirt road appropriately named Helix Drive. Around a corner, however, the scene changes dramatically.....
The data center is completely fiber and boasts a multi 10-Gb network. "That's a constant question," says Peterson. "Am I going to get the data to my desktop fast? If I can't, then I'm going to start having people buying their own supercomputers and sliding it under their desk. I don't want that - it's not cost effective, and you can't manage it." He adds: "We're going to have very high-resolution graphics, and people are going to see it very fast. Just one set of microscopes will be generating 500 GB data/day. 24x7x365."....
With some 1,200 64-bit Intel Xeon processors in all, cooling was a major concern. Peterson explains: "We ended up going with Dell and Xeons, which are hot, but we did a calculation: given the price we got with them and given the increased power requirements, it still came in price effective. Having said that, we're very interested in the new generation of Intels and obviously AMD." ...
Everything in the data center is designed to be ripped out and replaced if needed. "The idea is to design infrastructure that is cost effective and easy to replace. We try to be open source - everything is Linux-based, low stress. It helps hugely with the maintenance."....
Peterson selected three tiers and 150 TB of spinning disk storage from EMC. "We started small... seriously!" Peterson smiles. Tier 1 is 30 TB of SAN. Tier 2 is 70 TB of NAS. Tier 3 - the archive - consists of more NAS on disk plus tape. Peterson wants to expand tier 3. "We have capability of over 1 PB of tape," says Peterson. "I can grow to multi petabytes without adding another cabinet." He opens one of a long row of EMC cabinets to show rows of vacant racks....

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements -- Nature Biotech

Might be good to use as benchmark to judge tiling arrays and protein chips

Nat Biotechnol. 2006 Sep;24(9):1151-61.
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Great Example of Spring Minimization


original URL

How to get on the Farmington Canal Heritage Trail in Hamden

How to get on the Farmington Canal Heritage Trail in Hamden

Official Info.

Hamden – Farmington Canal Heritage Trail
Cheshire – Farmington Canal HeritageTrail

Useful maps
Looking at map on
Looks like approximate entry point is at:

Some Distances
Farmington Canal Greenway:
Simsbury-Avon section; 8 mi
Avon-Farmington section; 2.3 mi
Hamden-Cheshire section; 8 mi

24 November 2006

Global variation in copy number in the human genome -- Nature

Assume everyone has seen this. Might be nice to start using this data.

Nature 444, 444-454 (23 November 2006)
Global variation in copy number in the human genome
Richard Redon1, Shumpei Ishikawa2,3, Karen R. Fitch4, Lars Feuk5,6, George H. Perry7, T. Daniel Andrews1, Heike Fiegler1, Michael H. Shapero4, Andrew R. Carson5,6, Wenwei Chen4, Eun Kyung Cho7, Stephanie Dallaire7, Jennifer L. Freeman7, Juan R. González8, Mònica Gratacòs8, Jing Huang4, Dimitrios Kalaitzopoulos1, Daisuke Komura3, Jeffrey R. MacDonald5, Christian R. Marshall5,6, Rui Mei4, Lyndal Montgomery1, Kunihiro Nishimura2, Kohji Okamura5,6, Fan Shen4, Martin J. Somerville9, Joelle Tchinda7, Armand Valsesia1, Cara Woodwark1, Fengtang Yang1, Junjun Zhang5, Tatiana Zerjal1, Jane Zhang4, Lluis Armengol8, Donald F. Conrad10, Xavier Estivill8,11, Chris Tyler-Smith1, Nigel P. Carter1, Hiroyuki Aburatani2,12, Charles Lee7,13, Keith W. Jones4, Stephen W. Scherer5,6 and Matthew E. Hurles

13 November 2006

Machine Over Man: Stock Pickers' Woes -- WSJ

Appears indexing maybe back in fashion....

Machine Over Man: Stock Pickers' Woes
November 6, 2006; Page R1
Stock pickers' recently healed egos are about to be battered anew....

ooo[clip]ooo ooo[general]ooo ooo[finance]ooo

The Word on Warranties: Don’t Bother -- NY Times

What I always thought...

After the Sale
The Word on Warranties: Don’t Bother
Published: November 1, 2006
IT may be tempting to buy extended warranties with all those high-tech gadgets on your holiday list, but the experts say they are almost always a waste of money.

ooo[clip]ooo ooo[computers]ooo ooo[purchases]ooo

07 November 2006

Gaming the Search Engine, in a Political Season -- NY Times

Interesting article pointing to the future of misinformation

Gaming the Search Engine, in a Political Season
Published: November 6, 2006
A GOOGLE bomb — which some Web gurus have suggested is perhaps better called a link bomb, in that it affects most search engines — has typically been thought of as something between a prank and a form of protest. The idea is to select a certain search term or phrase (“borrowed time,” for example), and then try to force a certain Web site (say, the Pentagon’s official Donald H. Rumsfeld profile) to appear at or near the top of a search engine’s results whenever that term is queried.....

ooo[clip]ooo ooo[computers]ooo ooo[search]ooo

01 November 2006

A loss-of-function RNA interference screen for molecular targets in cancer -- Nature

Interesting datasets related to cancer and phenotypes

Nature. 2006 May 4;441(7089):106-10. Epub 2006 Mar 29.
A loss-of-function RNA interference screen for molecular targets in cancer.
Ngo VN, Davis RE, Lamy L, Yu X, Zhao H, Lenz G, Lam LT, Dave S, Yang L, Powell J, Staudt LM.

ooo[clip]ooo ooo[bioinfo]ooo ooo[phenotypes]ooo

The Connectivity Map: using gene-expression signatures to connect

Interesting dataset related to cancer and phenotypes

Science. 2006 Sep 29;313(5795):1929-35.
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP,
Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ,
Clemons PA, Wei R, Carr SA, Lander ES, Golub TR.

ooo[clip]ooo ooo[bioinfo]ooo ooo[phenotypes]ooo

Letter ("Programming Pedigrees") responding to "The Semicolon Wars" -- American Scientist

Resurrected one of my favorite letters, which might be good to follow up on. Viz: :
I read with great interest Brian Hayes's recent column "The Semicolon Wars" on the genealogy of computer languages (Computing Science, July-August). I was struck by the first figure that shows how many well-known languages are related to each other in a tree-like structure. Mr. Hayes carefully compared the development of computer languages to that of spoken languages. This is, of course, quite appropriate. However, another illuminating comparison is to the development and evolution of genomes in biology.
The genome has often been compared to an organism's operating system, and in this sense, its underlying genetic coding is the ultimate computer language. The triplet codons in the literal genetic code have not changed much over time. However, the specific features they encode in different genomes have changed dramatically since life first appeared.
One of the nice things about biology, moreover, is that the main mechanisms underlying this evolution can be studied experimentally. It is believed that the genome evolves through a variety of processes duplicating and copying chunks of DNA, and then further variation happens to these copies. One also sees, most often in bacteria, whole genetic elements horizontally transferred from one organism to another.
The parallels to computer languages in the operation of these mechanisms are quite strong: In a specific lineage of languages (such as that for Algol60, C and Java) one sees the duplication and variation of basic control structures for such items as loops and subroutines, and horizontal transfer of new structures (such as the object-oriented constructions from Simula67).

Citation of Letter:
Programming Pedigrees
Volume 94, Number 6 (November-December 2006)
Mark Gerstein
Yale University
New Haven, CT

Article Commented on:
The Semicolon Wars
Every programmer knows there is one true programming language.
A new one every week
Brian Hayes
American Scientist, July-August 2006
If you want to be a thorough-going world traveler, you need to learn 6,912 ways to say "Where is the toilet, please?" That's the number of languages known to be spoken by the peoples of planet Earth, according to Ethnologue.com. If you want to be the complete polyglot programmer, you also have quite a challenge ahead of you, learning all the ways to say: printf("hello, world\n") ;.....

30 October 2006

The Thin Pill -- Wired

Interesting article on how medicines are labelled and targeted

Issue 14.10 - October 2006
WIRED magazine
The Thin Pill
FOR PATIENTS, disease puts a name to an affliction. It answers that question we all face at one time or another: What's the matter with me? If there is a clear and precise explanation for what's wrong, then surely there is an equally clear way to get better.....

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21 October 2006

A limited universe of membrane protein families and folds -- Prot Sci

Yang Liu et al. part II

Protein Sci. 2006 Jul;15(7):1723-34. 
A limited universe of membrane protein families and folds.
Oberai A, Ihm Y, Kim S, Bowie JU.

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20 October 2006

Cyberface: New Technology That Captures the Soul -- NY Times

Thought this was an interesting fusion of science and art -- biophysicists go to Hollywood.  Got to check out the video.

Cyberface: New Technology That Captures the Soul
Published: October 15, 2006
THERE’S nothing particularly remarkable about the near-empty offices of Image Metrics in downtown Santa Monica, loft-style cubicles with a dartboard at the end of the hallway. A few polite British executives tiptoe about, quietly demonstrating the company’s new technology....

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18 October 2006

Structural biology: proteins flex to function -- Nature

Nice cartoon of protein motions, related to order-disorder transitions. Might be useful in expanding classification.

Nature. 2005 Nov 3;438(7064):36-7.
Structural biology: proteins flex to function.

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17 October 2006


Zoho might be nice in a similar way to Google Spreadsheet.

12 October 2006

A Letter in response to "Inspired by the Cell, With Mitochondrial

Here's the letter I wrote in response to this article (which was never published):
I read with great interest the recent article in Science Times about the new biomedical research center in China with architecture inspired by the cell. It's a great thing having man-made creations inspired by fundamental molecular and cellular architecture. It's ironic that this hasn't happened to a greater degree. Many of the shapes in scientific structures are particularly interesting. Good examples would be the famous double helix of DNA and lipid bilayer of the cell membrane. Moreover, a key aspect of post-modern architecture is referring to and playing with evocative shapes and forms borrowed from non-architectural contexts. Thus, the irony in why famous pieces of post-modern architecture -- such as the AT&T building in New York, which makes reference to a grandfather clock or a Chippendale highboy -- seem to ignore the fundamental designs of nature.

FINDINGS; Inspired by the Cell, With Mitochondrial Pools
Article Tools Sponsored By
Published: September 12, 2006
The blob is coming to Chengdu. A biomedical research institute in Chengdu,
China, is planning to show true commitment to scientific principles by erecting
an innovative building inspired by cells. Bulges on the surface are meeting
rooms and are intended to represent the proteins embedded in a cell membrane.
The interior pools, shaped like mitochondria, border on the surreal....

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10 October 2006

Connecting the Dots -- Am. Sci.

Nice social network analogies. In particular, discussion of Granovetter paper relates nicely to ‘socio-affinity’ index in Gavin et al. (2006) [http://www.nature.com/nature/journal/v440/n7084/abs/nature04532.html]

September-October 2006
Connecting the Dots
Can the tools of graph theory and social-network studies unravel the next big plot?
Brian Hayes
In the five years since that wrenching Tuesday morning when hijacked aircraft sliced into the World Trade Center and the Pentagon, Americans have been living with a new undercurrent of worry and mistrust. Naturally, there's fear of further attacks. But there's also concern that measures taken to forestall such attacks could erode traditional rights and liberties. In recent months, controversy has erupted over reports that government agencies are monitoring Internet and telephone communications as well as financial transactions. Some of the surveillance programs are said to be sifting through gigantic data sets, scanning for patterns that might reveal criminal intent or activity....
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09 October 2006


A baby named for a nucleic acid -- http://adenine.org/
Based on http://en.wikipedia.org/wiki/Adenine , there are many potential
derivative names here: AMP, Deoxyadenosine, &c.

04 October 2006

Scenic Routes Bike Routes -- NY Magazine

Thought this was interesting... includes bike trip to Bear Mountain and a route through DUMBO.

Brooklyn Waterfront
Approximately 24 miles
1. Start at City Hall. Head across Park Row onto the bridge.
2. Take first right off the bridge onto Tillary Street.
3. Left on Cadman Plaza West, quick right on Clark Street. Left on Henry Street, down about a mile.
4. Right on Sackett Street, three blocks.
5. Left on Van Brunt Street, down to the end.
6. Walk bike at Beard Street Warehouse.
7. Go back up Van Brunt Street a block, then left on Van Dyke Street to the end.
8. Take sidewalk to avoid cobblestones.
9. Walk bike down Valentino Pier. Exit on Coffey Street, two blocks.
10. Left on Van Brunt Street.
11. Right on Union Street, quick left on Columbia Street.
12. Right on Congress Street, two blocks.
13. Left on Hicks Street, parallel to highway.
14. Left on Montague Street, to the Promenade.
15. Right on Promenade, walk bike to end.
16. Left on Columbia Heights, down the hill to Fulton Landing.
17. First left on Water Street, two blocks against traffic.
18. Left on Washington Street, quick right on Plymouth Street.
19. Enter park on left for a block, under the Manhattan Bridge.
20. Left back onto Plymouth Street.
21. Right on Hudson Avenue, then merge onto Navy Street for a block.
22. Right on Sands Street, down toward Manhattan Bridge.
23. Follow signs to the bridge entrance across the street on the left.
24. Coast down to the Manhattan exit, cross onto Canal Street.
25. Take Canal Street down to the Broadway subway station.

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03 October 2006

Which Was Painted by a Child? -- NY Times

Stumbled on this old article... the pictures are very evocative. It really does call into question what is art.

Which Was Painted by a Child?
Published: October 3, 2004
A 4-YEAR-OLD in Binghamton, N.Y., whose splattery paintings have been selling for $6,000, is the latest child to raise the question: What is art?
The painter is Marla Olmstead. Her preferred medium is acrylic on canvas. She gives titles like "Dinosaur" to cheerful smears of blue and red with dark squiggles on top. Her break came at 3 when a family friend hung her art in a local coffee shop. Now collectors are lapping it up....

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And if You Liked the Movie, a Netflix Contest May Reward You Handsomely -- NY Times

Might be nice to download this huge dataset for comparison in some mining applications.

And if You Liked the Movie, a Netflix Contest May Reward You Handsomely
Published: October 2, 2006
Netflix, the popular online movie rental service, is planning to award $1 million to the first person who can improve the accuracy of movie recommendations based on personal preferences. To win the prize, which is to be announced today, a contestant will have to devise a system that is more accurate than the company’s current recommendation system by at least 10 percent. And to improve the quality of research, Netflix is making available to the public 100 million of its customers’ movie ratings, a database the company says is the largest of its kind ever released....

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27 September 2006

26 September 2006

Meet the Life Hackers -- NY Times

Thought this interesting in relation to computer UI design...

Meet the Life Hackers
Published: October 16, 2005
In 2000, Gloria Mark was hired as a professor at the University of California at Irvine. Until then, she was working as a researcher, living a life of comparative peace. She would spend her days in her lab, enjoying the sense of serene focus that comes from immersing yourself for hours at a time in a single project. But when her faculty job began, that all ended. Mark would arrive at her desk in the morning, full of energy and ready to tackle her to-do list - only to suffer an endless stream of interruptions. No sooner had she started one task than a colleague would e-mail her with an urgent request; when she went to work on that, the phone would ring. At the end of the day, she had been so constantly distracted that she would have accomplished only a fraction of what she set out to do. "Madness," she thought. "I'm trying to do 30 things at once."...Lots of people complain that office multitasking drives them nuts. But Mark is a scientist of "human-computer interactions" who studies how high-tech devices affect our behavior, so she was able to do more than complain: she set out to measure precisely how nuts we've all become.
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Hungry Workers, Tied to Desks, Clicking to Get Culinary Delights -- the New York Times

web food

Hungry Workers, Tied to Desks, Clicking to Get Culinary Delights
Published: September 17, 2006
EVERY weekday, when they are hungry, thousands of the most highly paid workers in New York City will log on to the same Web site. Finding food while they work requires just a few clicks of the mouse, and fits neatly into their multitasking, desk-bound work lives. Few of those employees will ever see the bill or pay a tip when their food is delivered. Instead, their orders are processed, and billed to their employers, through a single company: SeamlessWeb.....

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Metal Mouth: What You Should Know About the Mercury in Dental Fillings -- WSJ

I have Hg fillings and have worried about this hidden diet additive as well...

Metal Mouth: What You Should Know About the Mercury in Dental Fillings
Wall Street Journal
September 12, 2006
Whether you have a mouthful of silver teeth or just a few cavities, new questions about the safety of mercury fillings have made many of us nervous about our dental work. Last week, an expert panel for the Food and Drug Administration rejected an agency report that had concluded mercury dental fillings are safe. In a 13-7 vote....

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25 September 2006

Where Do Rivals Draw the Line? - New York Times

New Haven appears to be near the border of Red Sox country...
What is a person who wears a Yankees cap and a Red Sox shirt!

Where Do Rivals Draw the Line? - New York Times
New Britain, Connecticut is where Yankees country ends and Red Sox nation begins...
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Reimagined Math -- NY Times

Thought these were quite pretty from a mathematical perspective

It's hard to imagine that these plaster forms, so starkly beautiful, were originally used to teach advanced students trigonometry. ...Last year, the Japanese photographer Hiroshi Sugimoto shot each object, the tallest of which is less than a foot high, from below at close range so that they appear monumental. His series of photographs, ''Mathematical Forms,'' reimagine these scientific models as things of wonder. ...
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22 September 2006


Really liked the photos in the Industrial Landscape book by Brian Hayes. Kind of similar in spirit to those in those in my photostream.

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20 September 2006

Maureen Hillenmeyer

Interesting image morph


10 September 2006

e-mail bankruptcy -- Wired

Perhaps email bankruptcy would be good for me as well....

Call It the Dead E-Mail Office
By Michael Fitzgerald|
02:00 AM Jun, 07, 2004
If you've been waiting for internet legal visionary Lawrence Lessig to reply to your e-mail, forget about it.
In a script-driven note sent out last week, Lessig wrote: "Dear person who sent me a yet-unanswered e-mail, I apologize, but I am declaring e-mail bankruptcy.".....

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08 September 2006

A Letter in response to "Homo Conexus" -- Tech Review

A letter of mine commenting on trust in technology was just published in TR. Thought it was interesting how it was edited.

Published Version of the Letter:
Friday, September 08, 2006 (Sept./Oct. '06 issue)
"Homo Conexus"
I read with interest James Fallows's piece on the new wave of Web-based
applications sometimes called Web 2.0 ("Homo Conexus," July/August 2006). In
using these new programs, he sometimes found that while a new online service was
impressive, he was just too old to enjoy it. Unfortunately, I often feel quite
the same way. I enjoy reading about exciting technological innovations,
but--nose pressed to glass--cannot really participate.

I also liked Fallows's observation that trust, in general, is important to Web
2.0, but would like to add that Web 2.0 demands a specific kind of trust between
a given application's makers and users. Desktop software, such as Microsoft Word
and the Thunderbird e-mail ­client, is the same day-to-day. Not so with Web 2.0.
One can log on to Gmail or Yahoo Mail and find that the interface has radically
changed and that the arrangement and filtering of one's e-mail has been altered.
Mark Gerstein
New Haven, CT

The Original Version of My Letter (which I submitted):
I read with great interest James Fallow's article on Web 2.0. I
empathize with his initial statement about "Dodgeball truth" --
realizing that while a new computational service was impressive, he
had outgrown its potential utility. Unfortunately, I often feel this
way with regards towards many technological innovations. I enjoy
reading about them but -- eyes pressed to glass -- can not really
participate. I also liked Mr. Fallow's emphasis on trust as being
important to Web 2.0. However, I felt he could have elaborated on this
further, discussing the degree to which Web 2.0 requires an explicit
element of trust between users and providers. If one is using a
standard piece of desktop software, such as Microsoft Word or the
Thunderbird email client, one correctly assumes that it is going to be
the same day to day and that the structure of one's creations will
also remain static (unless, of course, we opt to upgrade). Likewise,
when one builds a website in the old Web 1.0 paradigm we can assume
that it will look the same going into the future. This is not the
case with Web 2.0 content. One can suddenly log on to Gmail or Yahoo
Mail and find that the interface has radically changed and that the
arrangement and filtering of one's email has been altered. Likewise,
when one posts content into an online review services, such as Amazon,
one is trusting that the presentation of an opinion will remain the
same going into the future. Of course, the Amazon can easily change
the way its reviews are presented without anyone's consent. Thus,
there really is an additional element of trust in Web 2.0.

Article Commented on:

Tuesday, July 25, 2006
Homo Conexus
A veteran technology commentator attempts to live entirely on Web 2.0 for two weeks.
By James Fallows
Sooner or later, we all face the Dodgeball truth. This comes at the moment when you realize that one of life's possibilities -- a product, an adventure, an offer, an idea -- is really meant for people younger than you. This bitter revelation is named for the relatively new Web-based service Dodgeball.com. This is a social networking site, and it represents most of what is supposed to be advanced and exciting about the current wave of "Web 2.0" offerings. Dodgeball's goal is to help you figure out, at any moment of the day or night, whether your friends or people who might be friendly are nearby... Dodgeball is light, mobile, interactive. And for the life of me, I can't imagine when I would use it....
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