Google Gene Project Comes into Question
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29 January 2006
BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms
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UniProtKB/Swiss-Prot entry Q01371 [WC1_NEUCR] White collar 1 protein
May function as a transcription factor involved in light regulation. Binds and affects blue light regulation of the AL-3 gene. WC1 and WC2 proteins interact via homologous PAS domains, bind to promoters of light regulated genes such as FRQ, and activate transcription.ooo[link]ooo ooo[bioinfo]ooo ooo[funny-gene]ooo
The LOV Domain Family: Photoresponsive Signaling Modules Coupled to Diverse Output Domains
Here, we review the properties of the light, oxygen, or voltage (LOV) family of blue-light photoreceptor domains, a subset of the Per-ARNT-Sim (PAS) superfamily. These flavin-binding domains, first identified in the higher-plant phototropins, are now shown to be present in plants, fungi, and bacteria. Notably, LOV domains are coupled to a wide array of other domains, including kinases, phosphodiesterases, F-box domains, STAS domains, and zinc fingers, which suggests that the absorption of blue light by LOV domains regulates the activity of these structurally and functionally diverse domains.
The LOV Domain Family: Photoresponsive Signaling Modules Coupled to Diverse Output Domainsooo[clip]ooo ooo[bioinfo]ooo ooo[funny-gene]ooo
I-95 New Haven Harbor Crossing Corridor Improvement Program
Traffic Cams of New Haven Areaooo[link]ooo ooo[general]ooo ooo[useful]ooo
Random Subspace Method for Linear Classifiers [clip]
Might be useful for dealing with feature subset statistics. (Suggested by Hongyu.)
http://citeseer.ist.psu.edu/skurichina02limited.html
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http://www.engadget.com/2005/11/07/macally-mtune-n-with-ipod-nano-dock [url]
Ipod on the head
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28 January 2006
Emergent behavior of growing knowledge about molecular interactions - Nature Biotechnology
Nat Biotechnol. 2005 Oct;23(10):1243-7.
Emergent behavior of growing knowledge about molecular interactions.
Cokol M, Iossifov I, Weinreb C, Rzhetsky A.
A billion nonredundant molecular interactions lie buried in the biomedical literature. A text-mining approach could help scientists better exploit this knowledge.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16211067&query_hl=4&itool=pubmed_docsumooo[clip]ooo ooo[bioinfo]ooo
http://liveplasma.com + Like This? You'll Hate That. (Not All Web Recommendations Are Welcome.) -- NY Times [url]
Thought this was a very neat way of showing web relationships.
http://liveplasma.com/index.php?data=51175&datatype=artis&ct=us&idmsg=2132
http://liveplasma.com/index.php?data=67314&datatype=artis&ct=us&idmsg=2133
http://www.nytimes.com/2006/01/23/technology/23recommend.html
Like This? You'll Hate That. (Not All Web Recommendations Are Welcome.)
By LAURIE J. FLYNN
Published: January 23, 2006
SAN FRANCISCO, Jan. 22 - On Amazon.com, a customer interested in buying the novel "The Life of Pi" is also shown "The Kite Runner" because other Amazon customers - presumably with similar tastes - also purchased that book. That's just one approach among many in the science of recommendation software.
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24 January 2006
Demystifying the eBay Selling Experience -- NY Times [clip]
Have you ever heard of iSoldIt and assisted eBay selling. This might be a good way to capitalize on my cleanup.
http://www.nytimes.com/2006/01/21/business/21shortcuts.html
http://www.i-soldit.com/index.asp
Demystifying the eBay Selling Experience
By ALINA TUGEND
Published: January 21, 2006
THE two collectible "Star Wars" light sabers - authentic sound effects! glowing
bright blue blade! - had been hanging around our garage for months. They were a
present from a well-meaning aunt to our 7-year-old son, who, unfortunately, had
outgrown his "Star Wars" phase a few years before.....Others, like iSold It -
the biggest eBay drop-off chain in the country, with about 500 branches - are individually owned franchises that complete the whole process internally. Typically, its commission is 30 percent of the first $500 and 20 percent of the remaining amount, which includes eBay listing fees.
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22 January 2006
The Battle of the Sexes - 92nd Street Y - New York, NY
Rather bizarre conclusion about Men and Women
The Battle of the Sexes
Harry Ostrer, MD
Recent research suggests that women are more complex than men because men have only 45 chromosomes while women have 46.
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M.B.A. COM; Studying With Stanford-Columbia-Chicago* - Free Preview - The New York Times
Interesting article about distance learning.
"M.B.A. COM; Studying With Stanford-Columbia-Chicago*
April 25, 2004, Sunday
By SCOTT JASCHIK (NYT); Education Life Supplement
Late Edition - Final, Section 4A, Page 33, Column 3, 1008 words
DISPLAYING FIRST 50 OF 1008 WORDS -Last fall, I decided I should learn a little theory-of-business-strategy for a venture I was about to undertake, so I fired off e-mail inquiries to e-Cornell, Cardean University and the University of Phoenix. The first thing I noticed was the eagerness to sign me up for just one master's..."
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21 January 2006
Masters of the Semantic Web -- Bio-IT world [clip]
Thought this was an interesting article on the enthusiasm for semantic web. Liked the comparison to the subway map.
http://www.bio-itworld.com/issues/2005/oct/cover-story-semantic-web
http://www.bio-itworld.com/issues/2005/oct/cover-story-sidebar1
Masters of the Semantic Web
By Salvatore Salamone
Oct 17, 2005
“I see a huge amount of energy from people in the life sciences getting excited about the Semantic Web and what it can do to solve the big IT problems... But also the people involved in the Semantic Web pushing it along are also very excited about getting involved in the life sciences — it’s one of those areas that affect humankind, finding drugs, curing AIDS and cancer, etc. There seems to be a huge energy, and lots of practical technical reasons why this area is crying out to be one of the flagship areas that the Semantic Web really takes off...” — Sir Tim Berners-Lee, Bio•IT World Conference+Expo, May 2005
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The Scientist : Gene Association Studies Typically Wrong
Interesting Graphicooo[clip]ooo ooo[bioinfo]ooo
20 January 2006
Coding a Bridge Across the Data Divide -- The Scientist [clip]
Just read this year-old article. Thought the NAS colloquium was played up quite a bit!
http://www.the-scientist.com/article/display/15162
by Jane Salodof MacNeil
Coding a Bridge Across the Data Divide
Email: Jane Salodof MacNeil
The Scientist 2004, 18(24):25 -- Published 20 December 2004
If you want to know how biology will be practiced in the coming decades,
check out a recent National Academy of Sciences colloquium on frontiers
in bioinformatics. Assembling data is no longer the biggest challenge,
says meeting cochair Russ B. Altman, citing sophisticated presentations
on pseudogenes, RNA splicing, and molecular evolution. Instead, the
major hurdle these days is one of data integration....
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Bioinformatics on the Brink -- The Scientist [clip]
Just read this year-old article. Thought it was interesting in relation to bioinformatics business being driven by large hardware manufacturers.
http://www.the-scientist.com/article/display/15168
Bioinformatics on the Brink
Email: Kate Fodor - kfodor@the-scientist.com
The Scientist 2004, 18(24):34
Published 20 December 2004
When a working map of the human genome was announced in June 2000, it was immediately clear that it would open new avenues of study and transform the life sciences, both in academia and in industry. One of the many new opportunities was in bioinformatics: the use of computers to rapidly scan databases, analyze sequence data, and help predict protein structure based on DNA sequence. Companies and universities would be eager to purchase bioinformatics tools to help them manage the massive amounts of genomics and proteomics data they would be generating.
That has, indeed, turned out to be true. But for a number of reasons, the market opportunity for bioinformatics tools hasn't been as expansive as was thought, and many companies have suffered as a result.....
Despite the struggles that bioinformatics companies are experiencing, heavyweight, diversified IT companies such as IBM and Sun Microsystems show no signs of shying away from partnerships with the smaller companies or giving up on the bioinformatics market. "All the large IT vendors are getting very involved in life science," Zimmerman says. The big companies don't actually develop bioinformatics software, but they see opportunity in partnering with the software developers by providing hardware, service, and support for bioinformatics tools, and selling the complete package to firms involved in drug discovery.
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War of the Worlds [clip]
Liked this movie but wonder why they didn't use nukes?
ooo[movie]ooo ooo[fun]ooo
18 January 2006
New Improved Brooklyn -- New York Magazine [clip]
Thought this was interesting in relation moving to DUMBO!
http://newyorkmetro.com/nymetro/realestate/urbandev/features/n_10288/
http://www.newyorkmetro.com/realestate/articles/04/brooklyn/
New Improved Brooklyn
By Alexandra Lange
A glittering skyline, waterfront condos, new jobs, Frank Gehry buildings galore:
Brooklyn is on the verge of a makeover even more extreme than you thought,
re-creating itself in Manhattan’s image. What’s wrong with this picture?
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Nailing Your New York Number -- New York Magazine [clip]
What's your number? These numbers seem so high!
http://newyorkmetro.com/nymetro/news/bizfinance/finance/features/14865
Nailing Your New York Number
Here’s what it will take for you to stop working and never run out of money. A formula for the good life.
By Lee Eisenberg
How large a nest egg do you need to fund a secure, satisfied post-career life in New York and be confident that your assets will outlast your pulse? What is your New York Number? It’s an annoying question, fraught with the things you don’t want to think about: destitution, deterioration, death. It’s therefore a question that’s usually asked at night, almost always silently. How you frame the question depends on your age and temperament......
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Lowering Expectations at Science's Frontier -- nytimes.com [clip]
Contrast between textbook and frontier science is why I disfavor "traditional" Journal Clubs.
http://www.nytimes.com/2006/01/15/weekinreview/15wade.html
Crumpled Papers
Lowering Expectations at Science's Frontier
Jeon Kyung Woo/Newsis via Reuters
By NICHOLAS WADE
Published: January 15, 2006
THERE is considerable disorder in heaven when stem-cell scientists are chided by the Roman Catholic Church for the folly of pursuing "miracle cures." But such are the paradoxes generated by the implosion of a South Korean researcher's widely believed claims to have created human embryonic stem cells from patients.....The contrast between the fallibility of Dr. Hwang's claims and the general solidity of scientific knowledge arises from the existence of two kinds of science - a distinction that is often blurred when new advances are reported first by scientific journals and then by the news media. There is textbook science and frontier science, and the two types carry quite different expiration dates.
Textbook science is material that has stood the test of time and can be largely relied upon. It may include findings made just a few years ago, but which have been reasonably well confirmed by other laboratories. Science from the frontiers of knowledge, on the other hand, is wild, untamed and often either wrong or irrelevant to future research. A few years after they are published, most scientific papers are never cited again. Scientific journals try to impose order on the turbulent flow of new claims by having expert reviewers assess their merit. But even at the best journals, reviewers provide only a rough screen. Many papers slip through that later turn out to be innocently wrong. A few, like Dr. Hwang's, are found to be fraudulent....
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Mashups mix data into global service -- Nature [clip]
Interesting to think about this in relation to data-sharing, interoperability and a bio. information architecture.
http://www.nature.com/nature/journal/v439/n7072/full/439006a.html
Nature 439, 6-7 (5 January 2006) | doi:10.1038/439006a
Mashups mix data into global service
Declan Butler
Is this the future for scientific analysis?
Will 2006 be the year of the mashup? Originally used to describe the mixing together of musical tracks, the term now refers to websites that weave data from different sources into a new service. They are becoming increasingly popular, especially for plotting data on maps, covering anything from cafés offering wireless Internet access to traffic conditions. And advocates say they could fundamentally change many areas of science — if researchers can be persuaded to share their data.....
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Nature Podcast!
other ones from NEJM, NASA & http://www.sciencefriday.com/audio
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A robust approach : Nature
Comparisons of planes and people in relation to robustness.
Nature 439, 19-20 (5 January 2006) doi:10.1038/439019a
A robust approach
Eörs Szathmáry
The functional overlap between different components protects biological systems.
BOOK REVIEWED - Robustness and Evolvability in Living Systems
by Andreas Wagner
When sitting on an aeroplane, we obviously hope that it won't crash. A tacit assumption behind this wish is that our biological system isn't about to crash either. It so happens that these systems share several features. Both have specific parts that serve certain functions. The plane was designed by engineers, who were in turn designed by evolution through natural selection. Both systems seem robust and yet fragile, but how can we reconcile these two seemingly opposing features? One answer is that they are robust and fragile to different perturbations, being particularly robust to perturbations that are common in their 'niche'. Another answer is that robustness can be in a trade-off with other features, such as price and reproduction rate...
[publink]ooo[bioinfo]ooo
17 January 2006
http://www.keyfitz.org/nathan/memoir/17.html [url]
Contains a family tree that includes me!
ooo[url]ooo ooo[fun]ooo
Alone in the Dark -- New Yorker [clip]
Check out picture! There is such a contrast between North and South Korea. It's also interesting how quickly the lights go off after you cross the border.
http://azurehat.com/scrapbook/2003/09/lead-photo-from-new-yorker-on-north.html
http://www.newyorker.com/fact/content/articles/030908fa_fact4
ALONE IN THE DARK
Kim Jong Il plays a canny game with South Korea and the U.S.
by PHILIP GOUREVITCH
Issue of 2003-09-08
In 1866, the S.S. General Sherman, an ironclad schooner recommissioned for use in the China trade after service for the Union as a blockade runner in the Civil War, came sailing across the Yellow Sea and entered the mouth of the Taedong River on the west coast of the Korean peninsula. What the ship’s commander, a Captain Preston, was after—trade or spying or pillage, or all three—remains a matter of speculation. Korea, a feudal kingdom ruled according to a strictly paternalistic Confucian code, was notoriously hostile to foreigners, and with reason......
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15 January 2006
yalealumnimagazine.com : Yale's $8 billion man [clip]
What do you think of this? Appears that endowment monies are very well invested. I'd rather put my savings into this than into a bank!
Yale's $8 billion man
http://www.yalealumnimagazine.com/issues/2005_07/swensen.html
by Marc Gunther '73
Last spring, Yale president Richard C. Levin '74PhD held a cocktail reception for David F. Swensen '80PhD, who was celebrating his 20th year as Yale's chief investment officer. Inside the president's official residence, posters and news clippings mounted on easels tracked the growth of Yale's endowment from $1.3 billion to $14 billion under Swensen's stewardship. The display culminated in a bar chart titled "Value of Key Contributors to Yale University."...Towering above them was a bar bearing Swensen's name and an astonishing number: $7.8 billion....
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The Next Big One - BusinessWeek
The Next Big One: "The Next Big One
Where America is most vulnerable and how the nation can better manage the risks ahead.
Dr. Irwin E. Redlener is in Baton Rouge, La., setting up mobile medical units. He has been in Louisiana and Mississippi for many long days helping people deal with the horror of Hurricane Katrina, and his voice is full of anger and despair. 'The country is really just not prepared for a major catastrophic event,' says the director of the National Center for Disaster Preparedness at Columbia University's Mailman School of Public Health. 'Whatever it is -- the Big One in San Francisco, a terrorist attack -- it doesn't matter. The unfortunate truth is our ability to imagine and plan for catastrophic disasters is woefully inadequate.....
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Questions for Allegra Goodman -- nytimes.com [clip]
Appears that this is famous (!) college classmate of mine from college who's writing about scientists.
I think she's married to another classmate, David Karger.
http://classes.harvard.edu/college/1989/cn9507.html
http://theory.csail.mit.edu/~karger/
+
http://www.nytimes.com/2006/01/15/magazine/15wwlnq4.html
Questions for Allegra Goodman
Interview by DEBORAH SOLOMON
Your new novel "Intuition" revolves around a scandal in which a research biologist in Cambridge, Mass., deliberately falsifies his data in order to get credit for a cancer breakthrough. Is it based on a true story?...
No. I had the idea of writing about a couple. One of them suspects the other one is cheating. But not cheating in the usual way. I've always found tales of adultery rather dull...
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Galileos Daughter [clip]
Just finished reading this book. It mentions that Galileo's famous and heretical dialogue was published by Elsevier! Perhaps Elsevier is not such an evil empire.
Galileos Daughter by Dava Sobel
(done15-Jan-06)
http://en.wikipedia.org/wiki/Lowys_Elzevir
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http://bip.weizmann.ac.il/sqfbin/bestPrimers [url]
Might be useful to investigate. Perhaps integration with FoldIndex?
ooo[url]ooo ooo[bioinfo]ooo
14 January 2006
Derek Isaacowitz Emotion Laboratory at Brandeis University
A catchy name for a lab.
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nytimes.com: When the Market Values Hope Over Experience by a Factor
Thought this was an interesting comparison of stock prices, illustrating Google's popularity and how's it's still a little less than Yahoo's was.
When the Market Values Hope Over Experience by a Factor of 18
By FLOYD NORRIS
http://www.nytimes.com/2006/01/14/business/14charts.html
http://azurehat.com/scrapbook/2006/01/interestesting-analysis-of-market.html
Published: January 14, 2006
THREE companies with household names are worth about the same amount now - at least in the opinion of investors. Google, I.B.M. and Berkshire Hathaway all have market capitalizations in the vicinity of $135 billion...
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Disclosure Won't Tame C.E.O. Pay - New York Times
A bit extreme...
Disclosure Won't Tame C.E.O. Pay
By JOSEPH NOCERA
Published: January 14, 2006
THIS Tuesday, the Securities and Exchange Commission plans to unveil its first overhaul of executive compensation disclosure rules in 14 years. The new rules, which were leaked to the news media this week, are intended to give investors a fuller picture of the staggering amounts of money going to America's chief executives and other top corporate officers.
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13 January 2006
12 January 2006
http://walkjogrun.net [url]
Great way of saving running routes around the City!
http://walkjogrun.net/index.cfm?rid=431F9974-FFDA-3479-C257FB212BA55234
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Genetics: Copy correction and concerted evolution in the conservation of yeast genes [clip]
Might be useful in relation to proteomics project.
Genetics. 2005 Aug;170(4):1501-13. Epub 2005 May 23.
Copy correction and concerted evolution in the conservation of yeast genes.
Pyne S, Skiena S, Futcher B.
The yeast Saccharomyces cerevisiae and other members of the genus Saccharomyces are descendants of an ancient whole-genome duplication event. Although most of the duplicate genes have since been deleted, many remain, and so there are many pairs of related genes. We have found that poorly expressed genes diverge rapidly from their paralog, while highly expressed genes diverge little, if at all. This lack of divergence of highly expressed paralogous gene pairs seems to involve gene correction: one member of the pair "corrects" the sequence of its twin, and so the gene pair evolves as a unit. This correction presumably involves gene conversion and could occur via a reverse-transcribed cDNA intermediate. Such correction events may also occur in other organisms. These results support the idea that copies of poorly expressed genes are preserved when they diverge to take on new functions, while copies of highly expressed genes are preserved when they are needed to provide additional gene product for the original function.
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http://www.cellreception.com/towers [url]
Might be useful in relation to realestate!
http://www.cellreception.com/towers/towers.php?city=new%20haven&state_abr=ct&page=1
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Reviews on Systems Biology and Molecular Networks [clip]
* Some Yale reviews on data integration and molecular networks
http://papers.gersteinlab.org/papers/tongperspec/
http://papers.gersteinlab.org/papers/netrev/
* Reviews by Kitano on systems biology
Computational systems biology
Nature 420, 206-210 (14 November 2002)
Hiroaki Kitano
http://www.nature.com/nature/journal/v420/n6912/full/nature01254.html
Systems biology: a brief overview.
Science. 2002 Mar 1;295(5560):1662-4.
Kitano H.
http://omni.isr.ist.utl.pt/~sm3/biomedica/systems-biology/Systems.pdf
* Reviews by Vidal on systems biology and data integration
Ge H, Walhout AJ, Vidal M.
Integrating 'omic' information: a bridge between genomics and systems biology.
Trends Genet. 2003 Oct;19(10):551-60. Review.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&dopt=Citation&list_uids=14550629
A Biological Atlas of Functional Maps
Marc Vidal
Cell. 2001 Feb 9;104(3):333-9.
http://cmbi.bjmu.edu.cn/cmbidata/proteome/reviews/05.pdf
ooo[bioinfo]ooo[clip]ooo[nets]ooo
09 January 2006
http://hardtoremember.org/lifegraph/ [url]
A new view of romance and development...
http://hardtoremember.org/lifegraph/
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Lunar Module, SpaceCraft Assembly & Test, Grumman Bethpage NY
The lunar module -- the single most innovative aspect of Apollo -- was built on Long Island.
[fun]ooo [url]ooo
times.com: The Prodigy Puzzle [clip]
Here's an article about prodigies in the Times. Might be interesting. Thought the discussion of the "Termites" was good.
The Prodigy Puzzle
November 20, 2005, Sunday
By ANN HULBERT (NYT); Magazine
http://select.nytimes.com/search/restricted/article?res=F10617FF3B5A0C738EDDA80994DD404482
'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. Michigan had distinguished itself, Levin had been informed: the state boasted two Davidson Fellows, and he had clearly been told these teenagers came trailing brainy superlatives. ''Genius loves company,'' announced the September press release about the students who had won scholarships awarded annually since 2001 by the Davidson Institute for Talent Development, a foundation that supports ''profoundly intelligent'' youths, a more recent term for off-the-charts children. ''Seventeen prodigies,'' the press release went on, were ''to be honored at the Library of Congress for contributions to society'' in the fields of science, math, technology, music and literature....
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Yale University Bulldogs, Official Athletic Site
Location of course schedules during winter 2006
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[url]ooo [fun]ooo
06 January 2006
Some groups interested in Computational Geometry in Relation to Proteins
Duke
http://www.cs.duke.edu/~edelshttp://kinemage.biochem.duke.edu
Stanford
http://csb.stanford.edu (M Levitt)http://geometry.stanford.edu/member/guibas
Scripps
http://www.scripps.edu/mb/olsonYale
http://geometry.molmovdb.orghttp://papers.gersteinlab.org/papers/subject/volumes ... and, in particular,
http://papers.gersteinlab.org/papers/geom-inttab
ETH
http://www.mol.biol.ethz.ch/groups/richmondSmith
http://maven.smith.edu/~streinu/Research/interests.htmlUIC
http://cast.engr.uic.edu/casthttp://tigger.uic.edu/~jliang
http://gila.bioengr.uic.edu/lab
TAG[url]ooo TAG[bioinfo]ooo
05 January 2006
04 January 2006
stuff at live.com
Might want to convert your hotmail to this....
mail.live.com
Check out some of the views of Manhattan
at local.live.com -- e.g.
http://local.live.com/?v=2&sp=adr.1760%202nd%20Ave%2C%20New%20York%2C%20NY%2010128
(click on the bird's eye icon!)
TAG[url]ooo TAG[computer]ooo
NYTimes: Credit Cards With Rewards Are Worth a Look [clip]
A useful article... I have Citibank Dividend Mastercard. Looks like one can get a better deal.
By DAMON DARLIN
Published: December 31, 2005
If it seems like you are getting a lot of credit card solicitations, you are. Credit card companies sent out about six billion letters in the last year. But if you opened any, you may have noticed a dwindling number of zero-percent balance-transfer offers and more pitches for cash-back reward cards. Half of them are for reward cards....
TAG[General]ooo TAG[clip]ooo03 January 2006
WSJ: Computer Makers Cater to Big Business, Slight the Rest of Us
Goes a long way to explaining why we had such a hard time with Dell vs. Apple. If you went to work this morning and sat down at your desk in front of a personal computer, your experience probably took one of two routes.
http://ptech.wsj.com/archive/ptech-20051229.html
December 29, 2005
Computer Makers Cater to Big Business, Slight the Rest of Us
By WALTER S. MOSSBERG
Lots of you found yourself logging in, probably multiple times, using passwords you could barely remember because you are forced to change them so often. Then, you entered a world of computing where much of the power and variety of the technology was closed off to you in the name of security or conformity by an information-technology department in your large corporation or organization. Various Web sites were off-limits, as were tools like instant messaging, even though they might have legitimate business purposes.....
TIG: Microeconomic principles explain an optimal genome size in bacteria [clip]
Thought this was interesting in relation to soc. sci. vs. genome and network organization.
Trends Genet. 2005 Jan;21(1):21-5.
Microeconomic principles explain an optimal genome size in bacteria.
Ranea JA, Grant A, Thornton JM, Orengo CA
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15680509&query_hl=4&itool=pubmed_docsum
Bacteria can clearly enhance their survival by expanding their genetic
repertoire. However, the tight packing of the bacterial genome and the fact that
the most evolved species do not necessarily have the biggest genomes suggest
there are other evolutionary factors limiting their genome expansion. To clarify
these restrictions on size, we studied those protein families contributing most
significantly to bacterial-genome complexity. We found that all bacteria apply
the same basic and ancestral 'molecular technology' to optimize their
reproductive efficiency. The same microeconomics principles that define the
optimum size in a factory can also explain the existence of a statistical
optimum in bacterial genome size. This optimum is reached when the bacterial
genome obtains the maximum metabolic complexity (revenue )
for minimal regulatory genes (logistic cost).
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[clip]ooo [bioinfo]ooo
More sopranos locations in NJ
More sopranos locations in NJ
http://gonyc.about.com/od/photogalleries/l/bl_soprano01.htm
==
[fun]ooo [loc]ooo [url]ooo
01 January 2006
31 December 2005
From the Earth to the Moon -- mini series [url]
This is an amazing portrayal of space race... really great!
http://www.imdb.com/title/tt0120570
From the Earth to the Moon
1998 mini series
==
[fun]ooo [url]ooo
30 December 2005
http://www.nj.com/sopranos/index.ssf?/sopranos/map.html
Link below contains an interesting map showing locations in NJ (including Livingston), where the Sopranos were filmed.
http://www.nj.com/sopranos/index.ssf?/sopranos/map.html
http://www.nj.com/sopranos/
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[loc]ooo [fun]ooo
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
http://www.nytimes.com/2005/12/28/nyregion/28anarchist.html
By KAREN W. ARENSON
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.....
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[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.
http://web.media.mit.edu/~anmol/
http://www.media.mit.edu/~anmol/GroupMedia_for_Mobisys.ppt
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[url]ooo [nets]ooo
27 December 2005
Scientists Link a Prolific Gene Tree to the Manchu Conquerors of China - New York Times
[from-friend]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
http://www.nytimes.com/2005/12/24/politics/24spy.html
By ERIC LICHTBLAU and JAMES RISEN
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.
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[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?
http://www.oreillynet.com/lpt/a/6228
http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html
The Trend Spotter
http://www.wired.com/wired/archive/13.10/oreilly.html
[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
http://www.nytimes.com/2005/11/06/magazine/06amish.html
By LISA BELKIN
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....
TAG[general]ooo
TAG[clip]ooo
XML-Binary Optimized Packaging -- Dr Dobb's [clip]
thought this might be interesting in relation to formats for large-scale array data
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http://www.ddj.com/documents/s=9914/ddj0512g/0512g.html?temp=-eroQeDikW
Dr. Dobb's Journal December, 2005
XML-Binary Optimized Packaging
XML and nontext data can work togetherBy 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
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.
[general]ooo
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http://newyorkmetro.com/nymetro/news/culture/features/1478
Are Jews Smarter?
Need Proteins? Just Do It in Canada -- Bio-IT World [clip]
an interesting article about Al Edwards and SG costs
[bioinfo]ooo [clip]ooo
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http://www.bio-itworld.com/issues/2005/nov/sci-canada/
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
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[general]ooo
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UP IN THE AIR
Where is the Iraq war headed next?
by SEYMOUR M. HERSH
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
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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
http://www.businessweek.com/magazine/content/05_49/b3962004.htm
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.
[general]ooo
http://www.nytimes.com/2005/12/25/weekinreview/25bamford.html
The Agency That Could Be Big Brother
By JAMES BAMFORD
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
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
http://www.nytimes.com/2005/12/19/national/19kids.ready.html
By KURT EICHENWALD
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
18 December 2005
RiskMetrics Group
Featured in the Times!
[general]ooo
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http://www.nytimes.com/packages/pdf/business/17gret.pdf
http://select.nytimes.com/2005/12/18/business/yourmoney/18gret.html
The Boss Actually Said This: Pay Me Less
By GRETCHEN MORGENSON
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
[general]ooo
Start With a Stock Index. Now Try to Turbocharge It.
By JACK EGAN
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.
[fun]ooo
http://www.nytimes.com/2005/12/11/magazine/11wwln_freak.html
Freakonomics
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
scary??
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December 16, 2005
Bush Lets U.S. Spy on Callers Without Courts
By JAMES RISEN and ERIC LICHTBLAU
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. ....
16 December 2005
11 December 2005
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
By BARRY BEARAK (NYT); Magazine
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
By CHRISTOPHER CALDWELL (NYT); Magazine
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
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Coach Leach Goes Deep, Very Deep
By MICHAEL LEWIS
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
By SUSAN SAULNY
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
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[clip]ooo
T. Huang, B. Wu, P. Lizardi, H. Zhao (2005)
Detection of DNA copy number alterations using penalized least squares regression
Bioinformatics (in press)
http://bioinformatics.med.yale.edu/PDF/29_THuang2005.pdf
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
http://www.nytimes.com/2005/12/04/fashion/sundaystyles/04SILICON.html
[clip-h]ooo
By ALEX WILLIAMS
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....
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