31 December 2005

From the Earth to the Moon -- mini series [url]

This is an amazing portrayal of space race... really great!

From the Earth to the Moon
1998 mini series
[fun]ooo [url]ooo

Astronaut Bio: Buzz Aldrin

A PhD from MIT! Wow!
[fun]ooo [url]ooo

30 December 2005


Link below contains an interesting map showing locations in NJ (including Livingston), where the Sopranos were filmed.




[loc]ooo [fun]ooo

Raritan River Boat Club

Raritan River Boat Club

A location in Sopranos episode 11

29 December 2005

When Scholarship and Politics Collided at Yale -- New York Times [clip]

Hi, Thought this was an interesting article about another Associate Prof. at Yale ! Have you heard from him? -marK

When Scholarship and Politics Collided at Yale
Published: December 28, 2005

David Graeber pulled a green object shaped like a Champagne cork out of his pocket. The plastic bullet that was fired at Mr. Graeber in Quebec City in 2001....Battles with the police are a fact of life for Dr. Graeber, an associate professor of anthropology at Yale and a self-proclaimed anarchist. It was his battle with Yale that surprised him.... The university notified him in the spring of 2005 that it would not renew his contract next year. Yale gave no reason, and officials said they could not discuss the dismissal because personnel matters were confidential.....
[general]ooo [clip]ooo

http://web.media.mit.edu/~anmol/ [url]

Potentially, some interesting links in relation to getting social network data sets for analysis.

HBO: The Sopranos

[fun]ooo [url]ooo

27 December 2005

Albert-László Barabási

[link]ooo [bioinfo]ooo

Scientists Link a Prolific Gene Tree to the Manchu Conquerors of China - New York Times

[from-friend]ooo [sci]ooo

Science Friday: Making Science Radioactive

[podcast]ooo [link]ooo [sci]ooo

Spy Agency Mined Vast Data Trove, Officials Report - New York Times [clip]

Interesting article that mentioned "traffic analysis," which appears to be a bit different than traditional wire tapping. It suggests how an "anonymous cell-phone" can be identified by network analysis on his calling patterns. It's what we discussed over dinner!

Spy Agency Mined Vast Data Trove, Officials Report




WASHINGTON, Dec. 23 - The National Security Agency has traced and analyzed large volumes of telephone and Internet communications flowing into and out of the United States as part of the eavesdropping program that President Bush approved after the Sept. 11, 2001........What has not been publicly acknowledged is that N.S.A. technicians, besides actually eavesdropping on specific conversations, have combed through large volumes of phone and Internet traffic in search of patterns that might point to terrorism suspects. Some officials describe the program as a large data-mining operation.....Officials in the government and the telecommunications industry who have knowledge of parts of the program say the N.S.A. has sought to analyze communications patterns to glean clues from details like who is calling whom, how long a phone call lasts and what time of day it is made, and the origins and destinations of phone calls and e-mail messages. ..."If they get content, that's useful to them too, but the real plum is going to be the transaction data and the traffic analysis," he said.


[general]ooo [mining]ooo

What is Web 2.0? The Trend Spotter -- O'Reilly [clip]

Thought the combination of these two was very interesting. Some key points I liked:

* The importance of data and databases and the question of ownership;
* The utility of lightweight programming models (RSS and AJAX v. SOAP);
* Multi-device software (e.g. iTunes and also RFID to SPINE)

What is Web 2.0?



The Trend Spotter


[general]ooo [computers]ooo [bioinfo]ooo


26 December 2005

A Doctor for the Future -- New York Times [clip]

Another interesting article about medicine and genetics going forward.
Seems rare diseases have a use!

A Doctor for the Future
Published: November 6, 2005

Dr. D. Holmes Morton stood at the front of the red-and-white-striped
tent set up in a farm pasture in Lancaster County, Pa. Behind him were a
horse and a buggy - his host's main mode of transportation - and a
whitewashed barn and silo. To his left was a sunken barbecue pit, with
60 chickens cooking inside a homemade wire-mesh spit. Before him were
seven families, upward of 50 people. The women wore bonnets and aprons....



XML-Binary Optimized Packaging -- Dr Dobb's [clip]

thought this might be interesting in relation to formats for large-scale array data
Dr. Dobb's Journal December, 2005

XML-Binary Optimized Packaging

XML and nontext data can work together
By Andrey Butov
Andrey is a software developer in the Fixed Income division of Goldman Sachs & Company. He can be contacted at .....

For several years now, the development community has followed the emergence of XML-based solutions to common data-representation problems. As a metalanguage, XML is a success. A cursory search reveals several of the more popular custom languages utilizing XML as a metalanguage, including MathML for representing mathematical concepts [1], Scalable Vector Graphics (SVG) for representing two-dimensional vector and raster graphics [2], and Really Simple Syndication (RSS) [3] for distributing news headlines and other relatively frequently updated data such as weblog postings, for consumption by, among other things, RSS aggregators....

[clip]ooo [computer]ooo

http://refman.com/ [url]

More reference manager software
[url]ooo [link]ooo



Are Jews Smarter? -- New York Magazine [clip]

A rather controversial discussion of the intersection of psychology, behavior and genetics. Note that one of the scientists behind this is a NAS member.




Are Jews Smarter?

Did Jewish intelligence evolve in tandem with Jewish diseases as a result of discrimination in the ghettos of medieval Europe? That's the premise of a controversial new study that has some preening and others plotzing. What genetic science can tell us and what it can't.

By Jennifer Senior

Need Proteins? Just Do It in Canada -- Bio-IT World [clip]

an interesting article about Al Edwards and SG costs


[bioinfo]ooo [clip]ooo


Need Proteins?
Just Do It in Canada


By Mark D. Uehling
Nov 15, 2005 | TORONTO — Shorts, sandals, and a polo shirt. In autumn. Maybe that is what Aled Edwards always wears to work. Maybe his wardrobe was designed to challenge American preconceptions of Toronto winters that last 11 months of the year. Or maybe no one cares what you wear when you drive the cost of finding a sinewy, convoluted protein structure down to $125,000 — perhaps a quarter of the typical cost at less-efficient centers....


25 December 2005

The New Yorker: UP IN THE AIR

troops out and planes in
Where is the Iraq war headed next?
Issue of 2005-12-05
Posted 2005-11-28
In recent weeks, there has been widespread speculation that President George W. Bush, confronted by diminishing approval ratings and dissent within his own party, will begin pulling American troops out of Iraq next year. The Administration’s best-case scenario is that the parliamentary election scheduled for December....

The MySpace Generation - Business Week

[general]ooo [computers]ooo
DECEMBER 12, 2005
The MySpace Generation
They live online. They buy online. They play online. Their power is growing

The Toadies broke up. It was four years ago, when Amanda Adams was 16. ... She found it on Buzz-Oven.com, a social networking Web site for Dallas teens.

Googling For Gold - Business Week

[general]ooo [computers]ooo

DECEMBER 5, 2005

With the news that shares of online search giant Google Inc. (GOOG ) had crossed the lofty $400-per-share mark on Nov. 17, the world may have witnessed something akin to the birth of a new financial planetary system. Given its market cap of $120 billion, double that of its nearest competitor, Yahoo!, Google now has the gravitational pull to draw in a host of institutions and company matchmakers unable to resist the potential profit opportunities. Google stock, with a price-earnings ratio of 70, represents one of the richest dealmaking currencies anywhere....

The Agency That Could Be Big Brother - New York Times [clip]

An interesting article that highlights issues with data mining.


The Agency That Could Be Big Brother


Published: December 25, 2005

DEEP in a remote, fog-layered hollow near Sugar Grove, W.Va., hidden by fortress-like mountains, sits the country's largest eavesdropping bug. Located in a "radio quiet" zone, the station's large parabolic dishes secretly and silently sweep in millions of private telephone calls and e-mail messages an hour.....

22 December 2005

Andrew's conntea site

Andrew's conntea site

20 December 2005

NYTimes: Through His Webcam, a Boy Joins a Sordid Online World [clip-h]

Seems to be the polar opposite of the Nanny Cam!

Through His Webcam, a Boy Joins a Sordid Online World



Published: December 19, 2005

The 13-year-old boy sat in his California home, eyes fixed on a computer screen. He had never run with the popular crowd and long ago had turned to the Internet for the friends he craved. But on this day, Justin Berry's fascination with cyberspace would change his life....

[general]ooo [clip]ooo

19 December 2005

http://www.library.yale.edu/cite [url]

Reference manager software

18 December 2005

USA People Search


RiskMetrics Group

Featured in the Times!
The Boss Actually Said This: Pay Me Less
Published: December 18, 2005

BLIZZARDS swept through Wall Street last week - bonus blizzards, that is. Henry M. Paulson Jr., chief executive of Goldman Sachs, received $37 million in shares and options. Richard S. Fuld Jr. of Lehman Brothers got $15 million in...

Start With a Stock Index. Now Try to Turbocharge It. - New York Times


Start With a Stock Index. Now Try to Turbocharge It.
Published: December 18, 2005

A NEW kind of designer index fund has arrived on the scene. Instead of trying merely to match the performance of the stock market, as measured by some broad index like the Standard & Poor's 500, these new funds are aiming to outperform it....

http://freakonomics.com [clip-h]ooo

Here's column associated with the book... It show's interesting negative correlation.


The Economy of Desire

Published: December 11, 2005
Analyzing a Sex Survey
What is a price?

Unless you're an economist, you probably think of a price as simply the amount you pay for a given thing - the number of dollars you surrender for, let's say, Sunday brunch at your favorite neighborhood restaurant. But to an economist, price is a much broader concept. The 20 minutes you spend waiting for a table is part of the price. So, too, is any nutritional downside of the meal itself: a cheeseburger, as the economist Kevin Murphy has calculated, costs $2.50 more than a salad in long-term health implications. There are moral and social costs to tally as well - for instance, the look of scorn delivered by your vegan dining partner as you order the burger. While the restaurant's menu may list the price of the cheeseburger at $7.95, that is clearly just the beginning.

Bush Lets U.S. Spy on Callers Without Courts - New York Times

[general]ooo [swim]ooo
December 16, 2005
Bush Lets U.S. Spy on Callers Without Courts

WASHINGTON, Dec. 15 - Months after the Sept. 11 attacks, President Bush secretly authorized the National Security Agency to eavesdrop on Americans and others inside the United States to search for evidence of terrorist activity without the court-approved warrants ordinarily required for domestic spying, according to government officials.

Under a presidential order signed in 2002, the intelligence agency has monitored the international telephone calls and international e-mail messages of hundreds, perhaps thousands, of people inside the United States without warrants over the past three years in an effort to track possible 'dirty numbers' linked to Al Qaeda, the officials said. ....

10 December 2005

The Day the Sea Came - Free Preview - The New York Times

The Day the Sea Came - Free Preview - The New York Times: "FREE PREVIEW Sign In to E-Mail This
The Day the Sea Came
*Please Note: Archive articles do not include photos, charts or graphics. More information.
November 27, 2005, Sunday
Late Edition - Final, Section 6, Page 47, Column 1, 18641 words

DISPLAYING FIRST 50 OF 18641 WORDS -For the earth, it was just a twinge. Last Dec. 26, at 7:59 a.m., one part of the planet's undersea crust made an abrupt shift beneath another along a 750-mile seam near the island of Sumatra. The tectonic plates had been grating against each other for millenniums, and now..."

THE WAY WE LIVE NOW:11-27-05: IDEA LAB; Revolting High Rises - Free Preview - The New York Times

THE WAY WE LIVE NOW:11-27-05: IDEA LAB; Revolting High Rises - Free Preview - The New York Times: "THE WAY WE LIVE NOW:11-27-05: IDEA LAB; Revolting High Rises
*Please Note: Archive articles do not include photos, charts or graphics. More information.
November 27, 2005, Sunday
Late Edition - Final, Section 6, Page 28, Column 3, 1076 words

DISPLAYING FIRST 50 OF 1076 WORDS -There is a somewhat comic lining around the cloud of France's suburban riots. Suddenly the word banlieue has been embraced by people not known for peppering their conversation with French words -- callers to right-wing talk shows, for instance. Obviously, they want to stress how different those suburbs (burning..."

Coach Leach Goes Deep, Very Deep - New York Times

[fun]ooo [inpool]ooo
Coach Leach Goes Deep, Very Deep
Published: December 4, 2005

7:02 . . . 7:01 . . . 7:00 . . .

It was still ordinary time. The seconds ticked off the digital clock on the locker-room wall. A smell: the acrid odor of vomit. They were still ordinary college football players, and a few of them had lost their pregame meals to a war of nerves. Side by side at their lockers the players sat, silently, almost penitently, stomachs churning, waiting for their coach to show up and to make the place a lot less ordinary.....

06 December 2005

Science Projects in Genetic Data and Physics Win Scholarships - New York Times

Science Projects in Genetic Data and Physics Win Scholarships - New York Times: "Science Projects in Genetic Data and Physics Win Scholarships

Published: December 6, 2005

As summer interns working at a laboratory in Phoenix, Anne Lee and Albert Shieh, two high school students, came across a problem reading computerized information on the human genome"....

05 December 2005

Bioinformatics: Detection of DNA copy number alterations using penalized least squares regression [clip]

looks interesting in relationship to CGH

T. Huang, B. Wu, P. Lizardi, H. Zhao (2005)
Detection of DNA copy number alterations using penalized least squares regression
Bioinformatics (in press)

"I thought if I married a hub, I'd get an edge."

A quote at ORFeome 2005



NYTimes: Wheels and Deals in Silicon Valley [clip-h]

Appears that all that cycling up Page Mill in the early '90s was the beginning of a building trend....

Wheels and Deals in Silicon Valley






Published: December 4, 2005

NY Times


RANDY KOMISAR, a Silicon Valley venture capitalist, used to consider his cycling habits extreme even by the standards of the fanatically fit Bay Area. An energetic 51, Mr. Komisar says he rides 70 miles a day on the weekends and more than 10,000 miles a year on his custom-built titanium Serotta road bike. In Silicon Valley even sweat is quantifiable, so each week he is careful to log at least 10,000 vertical feet, climbing the golden hills of the Santa Cruz Mountains....

04 December 2005

NYTimes - Rewriting History: Snared in the Web of a Wikipedia Liar [clip-h]

thought this was interesting in relation to traceability of internet info. and also defamatory websites...



NYTimes - Rewriting History: Snared in the Web of a Wikipedia Liar



FALSE WITNESS How true are "facts" online?



Published: December 4, 2005


ACCORDING to Wikipedia, the online encyclopedia, John Seigenthaler Sr. is 78 years old and the former editor of The Tennessean in Nashville. But is that information, or anything else in Mr. Seigenthaler's biography, true?


The question arises because Mr. Seigenthaler recently read about himself on Wikipedia and was shocked to learn that he "was thought to have been directly involved in the Kennedy assassinations of both John and his brother Bobby."....

The Gamer as Artiste - New York Times

Pixel Canvas
The Gamer as Artiste
Published: December 4, 2005

LAST week, I spent several days living - and dying - inside the new Xbox 360 console, with four popular games pegged as particularly cinematic. I entered as a curious novice, less concerned with breaking the games than with exploring the worlds they opened, and the worlds you die in.....
I died as a princess in a green miniskirt, as a space warrior, a World War II soldier named Vasili and a humorless F.B.I. agent tracking a sadistic killer. My deaths, rendered in state-of-the-art detail, were not illustrious or mourned.

01 December 2005

http://www.cfar.umd.edu/~fer/optical [url]ooo

Liked the optical illusions on :
http://www.cfar.umd.edu/~fer/optical ,

Do people study how they can trick mice with illusions?

28 November 2005

http://monod.molsci.org [url]ooo

Thought this might be interesting in relation to future SPINE stuff.
Monod is a web-based environment supporting collaborative work by scientists
studying complex biological systems.

27 November 2005

NY Times: Sex and Chess. Is She a Queen or a Pawn? [clip-h]

the way to win in chess ---- distract your opponent!
Sex and Chess. Is She a Queen or a Pawn?
Thomas Lohnes/Agence France-Presse--Getty Images
Published: November 27, 2005

VANESS REID, a 16-year-old student from Sydney, Australia, runs cross-country,
plays touch football, enjoys in-line skating, swims and goes bodyboarding. She
also has a cerebral side: she plays competitive chess. ... But Ms. Reid, who has
auburn hair, light-blue eyes and a winning smile, is arguably the top player in
the world based on a more subjective criterion: her looks. A Web site called
World Chess Beauty Contest (www.1wcbc.com) ranks her as the world's most
beautiful woman in the game....

Google Local - from: New Rochelle Rd and Labelle Rd., New Rochelle, NY 10804 to: I-95., New Rochelle, NY

A potential interconnect between the beginning of the Hutch and I-95.



Distance: 2.2 mi (about 5 mins)

Start address: New Rochelle Rd & Labelle Rd, Bronxville, NY 10708
End address: New England Thwy, New Rochelle, NY
1. Head east from New Rochelle Rd - go 0.3 mi
2. Bear right at Pelhamdale Ave - go 0.1 mi
3. Turn left at Eastchester Rd - go 0.8 mi
4. Bear right and head toward North Ave - go 0.0 mi
5. Bear right at North Ave - go 1.0 mi

New York Area Roads, Crossings and Exits

Interesting histories of Bronx River and Hutchison River Parkways.


A Big Debate on Little People: Ancient Species or Modern Dwarfs? - Free Preview - The New York Times


A Big Debate on Little People: Ancient Species or Modern Dwarfs?
October 12, 2005, Wednesday
Late Edition - Final, Section A, Page 11, Column 1, 983 words
DISPLAYING FIRST 50 OF 983 WORDS -New discoveries in a cave on the Indonesian island of Flores, notably another jawbone, appear to give additional support to the idea that a separate species of little people new to science and now extinct lived there as recently as 12,000 years ago. But a vigorous minority of skeptical..."

25 November 2005

Web Based DNS Lookup (NSLookup) (ZoneEdit.com)

Nice web based NS lookup


Google Local - Bergen St & Nostrand Ave, Brooklyn, NY 11216

A pretty bad neighborhood as evident in the "the Interpreter". Location of the B133 busline in Crown Heights.


http://www.flagshipventures.com/news/06152005p.html [url]


John Mendlein's location after AFNM


21 November 2005

NYTimes: $100 Billion in the Hands of a Computer [clip-h]

Thought this was interesting article about quantitative analysis. I think this
guy uses Data mining!
November 19, 2005
$100 Billion in the Hands of a Computer

PEOPLE ask me all the time: What's your secret?" James Simons said.

We were sitting in an office in Manhattan that Mr. Simons uses when he's not at
the Long Island offices of Renaissance Technologies, the money management firm
he founded in 1982. He was wearing an elegant shirt and tie, and loafers with no
socks. He took a drag from a cigarette, the second of three he would smoke in
the course of a long interview....


Yale Alumni Strike Back at Tailgating Limits - New York Times

Yale Alumni Strike Back at Tailgating Limits
Published: November 19, 2005

When Yale University distributed new rules last month to curb binge drinking and public drunkenness at football games, the reaction was swift. But the loudest outcry came not from students but from alumni who have returned here for decades to watch the Yale Bulldogs and to fraternize at often-elegant tailgate parties.....

NYTimes: 1955 Vision of an 2005 City: Times Square Dies but 2nd Ave. Has a Subway [clip-h]

Thought this was a fascinating glimpse of the past and where we thought we would
be. This is quite interesting from both a real-estate and demographic perspective.


+ attached gif

1955 Vision of an 2005 City: Times Square Dies but 2nd Ave. Has a Subway
Published: November 21, 2005

TV antennas were beginning to sprout on rooftops like spindly metallic weeds,
the alternate-side parking minuet was just being choreographed and air raid
sirens still rumbled daily at noon in 1955 when New Yorkers paused briefly to
contemplate a city "strained almost to bursting" after the "tensest quarter
century" in its history.
Titled "Our Changing City," a 20-part series of articles in The New York Times
painted a largely optimistic panorama of the century's second half.....


See OLD 1955 PDFs at:

Our Changing City
In 1955, The New York Times ran a series that ran predictions about the future
of New York....

20 November 2005

2can Genomes - Bacteria Genomes

useful listing of pathogen genomes


The Prodigy Puzzle - New York Times

The Prodigy Puzzle
Published: November 20, 2005
'So you're the geniuses," Senator Carl Levin said, looking pleased as he peered over his glasses. He was addressing the flaxen-haired Heidi Kaloustian, a 17-year-old freshman at the University of Michigan, and John Zhou, a superfriendly 17-year-old senior at Detroit Country Day School, unusual visitors to Room 269 of the Russell Office Building on Capitol Hill....

18 November 2005

Science: Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer [clip]

Article includes Mark Rubin....

1: Science. 2005 Oct 28;310(5748):644-8.

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate

Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S,
Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA,
Chinnaiyan AM.

Recurrent chromosomal rearrangements have not been well characterized in common
carcinomas. We used a bioinformatics approach to discover candidate oncogenic
chromosomal aberrations on the basis of outlier gene expression. Two ETS
transcription factors, ERG and ETV1, were identified as outliers in prostate
cancer. We identified recurrent gene fusions of the 5' untranslated region of
TMPRSS2 to ERG or ETV1 in prostate cancer tissues with outlier expression....


USATODAY.com - Findings identify likely origins of prostate cancer

USA Today article on Mark Rubin's finding gene alterations linked to prostate cancer

Posted 10/27/2005 10:06 PM

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Findings identify likely origins of prostate cancer
By Liz Szabo, USA TODAY
Researchers have found a set of genes that may play a key role in prostate cancer — a discovery that doctors are hailing as a major breakthrough that changes the way they think about the genetic roots of the disease.

If further research confirms these findings, published Friday in the journal Science, the discovery eventually might lead to better tests for prostate cancer as well as targeted therapies, says one of the study's authors, Mark Rubin, chief of urologic pathology at Brigham and Women's Hospital in Boston.....

USATODAY.com - Findings identify likely origins of prostate cancer

14 November 2005

Phys-Rev-E: Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. [clip]

Fig. 3 of this paper looks a lot like the "C-runs" artifact on Affy chips.
Other Naef & Magnasco and Magnasco lab papers are also quite interesting in
relation to Affy analysis -- see http://asterion.rockefeller.edu/felix/CV .



Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jul;68(1 Pt 1):011906. Epub 2003
Jul 16.
Solving the riddle of the bright mismatches: labeling and effective binding
in oligonucleotide arrays.

Naef F, Magnasco MO.



RNA binding to high-density oligonucleotide arrays has shown tantalizing
differences with solution experiments. We analyze here its sequence specificity,
fitting binding affinities to sequence composition in large datasets. Our
results suggest that the fluorescent labels interfere with binding.....

13 November 2005

Home Page for Gonçalo Abecasis

An interesting overview of the Hapmap project at Renal Week.

Rafael Irizarry's Web Page

Interesting work on Affy analysis described at a recent talk in NY.

O'Reilly Network: What Is Web 2.0

06 November 2005

Routine Changes, or 'Bait and Switch'? - New York Times

Routine Changes, or 'Bait and Switch'?

Published: November 6, 2005

When the Atlantic Yards project in Brooklyn was unveiled in 2003, pamphlets given out at a news conference said it would feature "iconic" new buildings while balancing "the needs of the existing communities and those of the people who would live, work in or visit the new complex."

23 October 2005

Web of the Free - New York Times


Op-Ed Contributors
Web of the Free

Published: October 23, 2005

New Haven

THERE is a move afoot at the United Nations and in the European Union to get the United States to give up control of the Internet - a medium that America created and on which it now critically relies.

22 October 2005

A Lifetime in Recovery From the Cultural Revolution - New York Times

A profile of Xu Tian, Yale Genetics.
The Saturday Profile
A Lifetime in Recovery From the Cultural Revolution

Published: October 22, 2005

SOMETIMES a single life can tell more about a country's experience than a shelfful of history books. Many Chinese people of a certain age have such lives - rich in struggle, in suffering, in the consequences of man's folly, but often enough, too, in a measure of redemption....

17 October 2005

'Postwar': Picking Up the Pieces - New York Times

Starts with a great quote (below).
Published: October 16, 2005

An old Soviet-era joke, retold by Tony Judt on the next-to-last page of his enormous book 'Postwar,' is about a phone-in on 'Armenian Radio.' Is it possible, an eager caller asks, to foretell the future? 'Yes,' comes the weary answer. 'No problem. We know exactly what the future will be. Our problem is with the past: that keeps changing.'


Asthma Medication: Learn more about asthma & asthma treatment


nytimes.com: The Way We Drive Now : Motoring Toward A Post-Gasoline Age; The High-Performance Hybrids [clip-h]

These are the articles I alluded to about hybrids....
Style: The Way We Drive Now : Motoring Toward A Post-Gasoline Age; The
High-Performance Hybrids
September 25, 2005, Sunday
Late Edition - Final, Section 6, Page 77, Column 1, 3893 words

DISPLAYING FIRST 50 OF 3893 WORDS -''Hold on to your hat!'' Jim Burns shouted as
he slammed the accelerator to the floor. With a high-pitched whine, the electric
motor behind my seat burst into action, and ''the Enigma'' -- an experimental
red sports car in which I was riding shotgun -- bolted forward, pressing me...

Style: The Way We Drive Now: Motoring Toward A Post-Gasoline Age; Pimp My Prius
September 25, 2005, Sunday
Late Edition - Final, Section 6, Page 94, Column 1, 816 words

DISPLAYING FIRST 50 OF 816 WORDS -Driving a hybrid can satisfy more than your
conscience. With a little help from the flourishing car-customization business,
it's an easy matter to add a bit of style -- some blue racing stripes, beige
leather interior -- to an otherwise anonymous Prius. Or fully surrender to your
id, and...

WSJ: Wi-Fi Camera Offers Email, Quality Photos, But Still Needs Work [clip]


Might be the best solution to the office camera.

Wi-Fi Camera Offers Email, Quality Photos, But Still Needs Work
September 29, 2005; Page B1

If a wireless device like a cellphone can have a built-in camera, why can't
a camera have built-in wireless capability?

That's the question Kodak seeks to answer this week as it ships an unusual
digital camera that's able to wirelessly email the photos it takes, and
upload them to a Web site, all by itself -- without the need for a computer
or a cellphone.

Besttaxi in New Haven


Wired 13.10: The Elements Get Some Style

interesting graphic

The New York Times > Exxon Mobil is back on top, and for the first time is worth more than $400 billion.\


Exxon Mobil Back at No. 1 in Market Value, Even as It Shrinks Shares
Published: September 24, 2005

Exxon Mobil is back on top, and for the first time is worth more than $400 billion."

The Short of It - New York Times


Meet the Life Hackers - New York Times


Chasing Ground - New York Times


15 October 2005

To Build Arena in Brooklyn, Developer First Builds Bridges - New York Times [clip-h]

Ratner seems to be quite organized

To Build Arena in Brooklyn, Developer First Builds Bridges

Published: October 14, 2005

In the two years since he announced his ambitious Atlantic Yards development
in downtown Brooklyn, Bruce Ratner has lined up an impressive roster of
supporters, including Gov. George E. Pataki, Mayor Michael R. Bloomberg, the
Rev. Al Sharpton, and even the rap artist Jay-Z.

Lipitor or Generic? Billion-Dollar Battle Looms - New York Times [clip-gen]

Forms from Yale University | Postdoctoral Office

includes a sample appointment letter...

14 October 2005

10 October 2005

LJ: At the Forge - Rails and Databases [clip]

A bit of discussion of the way to interface programming languange objects with
standard relational tables.

04 October 2005

http://sleepycat.com/products/xml.shtml [url]

Might be of use:

Berkeley DB XML is the native XML database engine for your product. Berkeley DB
XML provides XQuery access into a database of document containers. XML documents
are stored and indexed in their native format using Berkeley DB as the
transactional database engine. Berkeley DB XML is not a client/server database
management system; it is a C++ library linked into your application.....

Nat Gen: Clustering of housekeeping genes provides a unified model [clip]

might be useful in relation to ongoing work....
Nat Genet. 2002 Jun;31(2):180-3. Epub 2002 May 6.
Clustering of housekeeping genes provides a unified model of gene order in the
human genome.
Lercher MJ, Urrutia AO, Hurst LD.


It is often supposed that, except for tandem duplicates, genes are randomly
distributed throughout the human genome. However, recent analyses suggest that
when all the genes expressed in a given tissue (notably placenta and skeletal
muscle) are examined, these genes do not map to random locations but instead
resolve to clusters. We have asked three questions: (i) is this clustering true
for most tissues, or are these the exceptions; (ii) is any clustering simply the
result of the expression of tandem duplicates and (iii) how, if at all, does
this relate to the observed clustering of genes with high expression rates? We
provide a unified model of gene clustering that explains the previous
observations. We examined Serial Analysis of Gene Expression (SAGE) data for 14
tissues and found significant clustering, in each tissue, that persists even
after the removal of tandem duplicates. We confirmed clustering by analysis of
independent expressed-sequence tag (EST) data. We then tested the possibility
that the human genome is organized into subregions, each specializing in genes
needed in a given tissue. By comparing genes expressed in different tissues, we
show that this is not the case: those genes that seem to be tissue-specific in
their expression do not, as a rule, cluster. We report that genes that are
expressed in most tissues (housekeeping genes) show strong clustering. In
addition, we show that the apparent clustering of genes with high expression
rates is a consequence of the clustering of housekeeping genes.

Rick Weissman's FunWithWine.com [fun]

3 Share Nobel for Work on Behavior and Use of Light - New York Times

2005 Physics Nobel !

Slashdot | Bioinformatics in the Post-Genomic Era

03 October 2005

02 October 2005

Bioinformatics: Mining ChIP-chip data for transcription factor and

Looks interesting...

Bioinformatics. 2005 Jun 1;21 Suppl 1:i403-i412.
Mining ChIP-chip data for transcription factor and cofactor binding sites.
Smith AD, Sumazin P, Das D, Zhang MQ.

MOTIVATION: Identification of single motifs and motif pairs that can be
used to predict transcription factor localization in ChIP-chip data, and gene
expression in tissue-specific microarray data. RESULTS: We describe methodology
to identify de novo individual and interacting pairs of binding site motifs from
ChIP-chip data, using an algorithm that integrates localization data directly
into the motif discovery process. We combine matrix-enumeration based motif
discovery with multivariate regression to evaluate candidate motifs and identify
motif interactions. When applied to the HNF localization data in liver and
pancreatic islets, our methods produce motifs that are either novel or improved
known motifs. All motif pairs identified to predict localization are further
evaluated according to how well they predict expression in liver and islets and
according to how conserved are the relative positions of their occurrences. We
find that interaction models of HNF1 and CDP motifs provide excellent prediction
of both HNF1 localization and gene expression in liver. Our results demonstrate
that ChIP-chip data can be used to identify interacting binding site motifs.
AVAILABILITY: Motif discovery programs and analysis tools are available on
request from the authors. CONTACT: asmith@cshl.edu.

Just a Really Bad Stretch? - New York Times

A really good "network graphic"

30 September 2005

http://www.chem.ufl.edu/~richards/loew2005/ [url]

NY area meeting, very easy to go to for some....

25 September 2005

If You Can Make It in Silicon Valley, You Can Make It . . . in Silicon Valley Again - New York Times [clip-h]

Amazing examples of wealth creation !


June 5, 2005
If You Can Make It in Silicon Valley, You Can Make It . . . in Silicon
Valley Again

One evening this spring, Marc Andreessen, the first outsize icon of the
Internet era, caught a glimpse of his former life while mingling at the San
Francisco launch party for Current, Al Gore's new 24-hour cable station. In
1994, when Andreessen was only 22, he and a high-tech veteran named Jim
Clark created the Internet-browser company Netscape Communications. Two
years later, there he was on the cover of Time, sitting barefoot on a golden
throne, dressed in jeans and a rumpled black polo. The magazine cast him as
the king of the ''golden geeks,'' a group that popularized the formerly
novel notion of surfing the Web and, not incidentally, helped create a
vision of Silicon Valley as a glittering gold field where the young, bright
and vigorous could stake a claim and make themselves unimaginably wealthy
before they even had the time to put up posters in their barely furnished

The Quantitative, Data-Based, Risk-Massaging Road to Riches - New York Times [clip-h]

Thought this was an interesting in relation to Yale, Goldman Sachs, and
Quantitative modeling. Looks like the Yale finance people -- in particular,
David Swensen -- are pretty good at this!



June 5, 2005
The Quantitative, Data-Based, Risk-Massaging Road to Riches

Clifford Asness is probably going to be annoyed when he sees that this
article begins with a discussion about how much money he makes, but there's
no way around it. Asness is a very successful hedge-fund manager, and very
successful hedge-fund managers make stupendous amounts of money, even by
Wall Street's extravagant standards. And in the public mind, their
staggering compensation tends to overshadow pretty much everything else.
''Filthy Stinking Rich'' was New York magazine's unambiguous take on the
hedge-fund phenomenon some months ago. Last month, in its survey of the
best-paid hedge-fund managers, Institutional Investor's Alpha magazine
reported that the average pay for the top 25 hedge-fund managers was an
astounding $251 million in 2004. Asness himself has written, in one of his
better lines, that hedge funds ''are generally run for rich people in
Geneva, Switzerland, by rich people in Greenwich, Conn.'' .....

12 September 2005

11 September 2005

MTV.com - Lifehouse

You and Me (2005) -- nice song.

FEBS-let: Functional essentiality from topology features in metabolic

Interesting in relation to ongoing work on essentiality and lethality.
FEBS Lett. 2005 Aug 29;579(21):4642-4646.

Functional essentiality from topology features in metabolic networks: A
case study in yeast.

Palumbo MC, Colosimo A, Giuliani A, Farina L.

The relation between the position of mutations in Saccharomyces cerevisiae
metabolic network and their lethality is the subject of this work. We represent
the topology of the network by a directed graph: nodes are metabolites and arcs
represent the reactions; a mutation corresponds to the removal of all the arcs
referring to the deleted enzyme. Using publicly available knock-out data, we
show that lethality corresponds to the lack of alternative paths in the
perturbed network linking the nodes affected by the enzyme deletion. Such
feature is at the basis of the recently recognized importance of 'marginal' arcs
of metabolic networks.



postdoctoral fellowship deadlines (uk applicant) [url]

Hi, I've added to the list and posted to my bookmarks. -cheers, marK


- Helen Hay Whitney Foundation (http://www.hhwf.org): July 15

- Life Sciences Research Foundation (www.lsrf.org): October 1st

- GWIS Grants and Fellowships (http://www.gwis.org/grants/Gerry.htm)
Is this only for graduates?: December 1st

- Jane Coffin Childs Memorial Fund (www.jccfund.org): February 1st

- Damon Runyon Cancer Research Foundation (www.drcrf.org): March 15th

- 1851 Royal Commission (www.royalcommission1851.org.uk): Feb 1st

The New York Times > Real Estate > Interactive Feature > Dodging a Downturn

06 September 2005

Quote on introverts [quote]

Introverts recharge by being by themselves, whereas extroverts energize through being with others.

05 September 2005

Bioinformatics: A statistical framework for genomic data fusion + Other papers by Noble et al. on Kernel methods [clip]

Papers of interest:

In some recent work, Noble and colleagues describe the way they
develop kernel methods that generalize their (and other's) earlier
work on SVMs. Kernel methods allow one to express the similarity
between a pair of objects with respect to various different types of
data (e.g. expression correlations or similarity in hydrophobicity) in
a uniform framework, and then to combine all these methods of
similarity in an optimized fashion. Lanckreit et al describe an
overall formalism for using these kernel methods in the framework of
bioinformatics. Ben-Hur & Noble describe how these kernel methods can
be specifically adapted to protein-protein interactions where one is
computing the similarity between pairs of proteins rather than
individuals. Tsuda & Noble describe a particular method of kernel


Tsuda K, Noble WS. Learning kernels from biological networks by
maximizing entropy. Bioinformatics. 2004 Aug 4;20 Suppl 1:I326-I333.

Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein
interactions. Bioinformatics. 2005 Jun 1;21 Suppl 1:i38-i46.

Lanckriet GR, De Bie T, Cristianini N, Jordan MI, Noble WS. A
statistical framework for genomic data fusion. Bioinformatics. 2004
Nov 1;20(16):2626-35. Epub 2004 May 6.

PNAS: Protein ranking: from local to global structure in the protein similarity network [clip]

A paper of interest:

In Weston et al., Noble and colleagues develop an algorithm for
comparing protein sequences that has inspired from this similarity
measures used by the Google search engine. They use a diffusion
distance type of approach that takes into account the overall
connectivity of similarity relationships. This paper represents a
great synthesis of the way a computer scientist can apply general
methods developed outside of biology into the biological context.

Weston J, Elisseeff A, Zhou D, Leslie CS, Noble WS. Protein ranking:
from local to global structure in the protein similarity network.
Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6559-63. Epub 2004 Apr

04 September 2005

Yale University's Interdisciplinary Bioethics Project -- yale.edu/bioethics [url]

Phys Rev E: Information-theoretic approach to network modularity [clip]

Uses diffusion distance in relationship to modularity

Ann Rev Soc: The New Science of Networks by Duncan Watts [clip]

Looks interesting and simultaneous in relation to our review

kleinbottle.com [fun]

Got something from them!

~ { : DNAstuff : } ~ what stuff life is made of...+ [fun]

Some interesting things to buy, shaped like DNA.

Listen & Live Audio: Ear-Catching Audiobooks [fun]

A slightly useful audiobooks list

HarperCollins Publishers -- Audiobooks [url]

A listing of audiobooks, not that useful.

03 September 2005

In Chimpanzee DNA, Signs of Y Chromosome's Evolution - New York Times [clip]

Does the Nature paper discuss the inactivation in terms of pseudogenes?


In Chimpanzee DNA, Signs of Y Chromosome's Evolution

Scientists have decoded the chimp genome and compared it with that of
humans, a major step toward defining what makes people human and developing
a deep insight into the evolution of human sexual behavior.

The comparison pinpoints the genetic differences that have arisen in the two
species since they split from a common ancestor some six million years

A Baby Step Toward Wi-Fi Photos - New York Times [clip-h]

Useful to think about in relation to taking photos of the board.



David Pogue
A Baby Step Toward Wi-Fi Photos

Published: September 1, 2005

EVERY now and then, someone combines two technologies into a single new
product, and the result is a triumphant new category that changes the
industry. Clock + radio. Cellphone + camera. Music player + hard drive.

the new Nikon P1, due in stores on Sept. 15. It's an iPod-size,
eight-megapixel camera dressed in brushed-metal black, with a list price of
$550. (A sister model, the P2, is a silver, 5.1-megapixel version that lists
for $400. Online prices will be much lower once the cameras actually arrive
in stores.)


But the best Shoot & Transfer feature of all is a true parlor trick. At a
party, conference or any other social gathering, you can start up a slide
show on your Mac or PC, complete with music. You can then walk around the
room, snapping pictures of the guests or attendees. These photos join the
slide show already in progress, automatically, in real time.

30 August 2005

'The Man Behind the Microchip': The Next Small Thing - New York Times [clip]


'The Man Behind the Microchip': The Next Small Thing - New York Times: "THE MAN BEHIND THE MICROCHIP
Robert Noyce and the Invention of Silicon Valley.
By Leslie Berlin.
402 pp. Oxford University Press. $30."

Noyce & Fairchild vs. TI, who's the inventor?

29 August 2005

Columbus Avenue Business Improvement District - columbusavenuebid.org [ref]

Contains a useful map.

Manhattan Kayak Company - Home Page [fun]

Potentially interesting but maybe a little dirty!

http://cyclelogicaltours.com [fun]

A cycle touring organization

Genome Biology | Full text | Statistical tests for differential expression in cDNA microarray experiments

Nice discussion of instability of the denominator of the t-test.

Phys Rev E : Software systems as complex networks: structure, function, and evolvability of software collaboration graphs. [clip]


Take a Chance: Science News Online, Dec. 4, 2004

Points out the problem of the seed and the difficulty in generating random numbers.
Science News Online

Week of Dec. 4, 2004; Vol. 166, No. 23
Take a Chance
Scientists put randomness to work

Erica Klarreich

Since the dawn of written history, people have exploited the randomness of a roll of a die to inject their games with the thrill of the unpredictable. Today, randomness is finding myriad other uses, such as encrypting credit card numbers in Internet transactions, deciding how to allocate treatments in drug trials, choosing precincts to call in national polls, running online gambling sites, and helping physicists simulate phenomena ranging from the weather to traffic patterns.........

A Few Words About Sudoku, Which Has None - New York Times


Notes of a Wayfarer: Preface

Notes of a Wayfarer: Preface

Interesting recollections....

Notes of a Wayfarer: Page 17

Notes of a Wayfarer: Page 17

Do You MySpace? - New York Times

Do You MySpace? - New York Times

Google Anything, so Long as It's Not Google - New York Times

Google Anything, so Long as It's Not Google - New York Times

with associated stuff:

Google balances privacy, reach | CNET News.com

Eric Schmidt's Home Page

Does Lighter Equal Deadlier? - New York Times

Does Lighter Equal Deadlier? - New York Times

28 August 2005

Times: If the Law Is an Ass, the Law Professor Is a Donkey [clip]

Thought this was an interesting article about the academic outlook.

August 28, 2005
If the Law Is an Ass, the Law Professor Is a Donkey

PROFESSORS at the best law schools are generally assumed to be overwhelmingly
liberal, and now a new study lends proof. But whether the ideological imbalance
matters - to the academic environment students encounter, to the kinds of
lawyers the schools produce and to the stock of ideas the professors generate -
depends on whom you ask.

The study, to be published this fall in The Georgetown Law Journal, analyzes 11
years of records reflecting federal campaign contributions by professors at the
top 21 law schools as ranked by U.S. News & World Report. Almost a third of
these law professors contribute to campaigns, but of them, the study finds, 81
percent who contributed $200 or more gave wholly or mostly to Democrats; 15
percent gave wholly or mostly to Republicans.


Coach Carter Movie Info - Yahoo! Movies

A good movie!

The Breaking Point - New York Times

An interesting article potentially pointing out the importance of energy conservation.

26 August 2005

this-is-not-spam header

thought this guy had a interesting way of avoiding losing mail due to spam filters

http://www.morphases.com/ [url]

Thought this was fun!

A face from Morphases by

This e-mail was sent from www.morphases.com by your friend .

Hi! Check the picture of me :)

Generation ID (GID) of this face is 47877:CD84D57A
View this face at http://www.morphases.com/editor/viewer.php?GID=47877:CD84D57A

Some useful exercises



Sit up with arms in front (abdominal crunch)
Dumbell shoulder Shrug
Bicep curls
Tricep pressdowns

hamstring stretch
thigh pull
Hip flexor stretch
butterfly stretch for inner thighs
free weight lat pull down machine
seated row

Nice directory of exercises

best ab exercises - lower abdominal exercises, free ab workouts, thigh pictures hip stomach leg knee inner outer butt waist back

Nice directory of exercises