AOI

Interesting acronym: AOI = achievements, objectives, issues

Triathlons I've done

2007 MADISON SPRINT TRIATHLON
Swim .5 miles/Bike 13 miles/Run 3 miles
Saturday Sept 8, 2007 | Surf Club - Madison, CT
Part of running route
http://www.madisonjc.com/trimaps.shtml
http://www.madisonjc.com/triathlon.shtml
Cache: C:\...\pers\misc\exercise\Sept07-triathlon\madtri07.txt + related

JONES BEACH TRIATHLON
SEPTEMBER 26, 2004
FINSIH LINE ROAD RACE TECHNICIANS - www.FLRRT.com
1/2 Mile Swim, 14 Mile Bike, 3.1 Mile Run
http://metrotri.com/document/45330
Cache: D:\...\y10.unzip\pers-pics\pers\clip\jones-beach-triathalon

VYTRA TOBAY TRIATHLON
TOWN OF OYSTER BAY, OYSTER BAY, NEW YORK
AUGUST 19, 2001
FINSIH LINE ROAD RACE TECHNICIANS, www.FLRRT.com
1K Swim - 15K Bike - 5K Run
http://bioinfo.mbb.yale.edu/~mbg/dom/fun3/tobay-triathalon
Cache: file:///D:/.../y6-021014-closed/y6/bikemaps/tobay-times/tri01m.txt

TRIATHLON IN MODESTO
Modesto, CA ; 13 October 1996
Pool swim, Bike, Run
Can't find any more details

let. to ed. re. "Mom's Genes or Dad's? Map Can Tell" -- Washington Post

Here's a letter to the Washington Post that was published:
Regarding the Sept. 4 front-page article "Mom's Genes or Dad's? Map Can Tell," about the unraveling of the Venter "diploid" genome: The article noted that sequencing an individual's DNA provides a wealth of information not only about that person but also about his or her relations. But it did not mention that sequencing also provides information about all of an individual's unborn descendants. Thus, when an individual's genome sequence is publicly released, consent implicitly is being given for these unborn descendants without their approval.
Fifty years from now, our understanding of genomic information will undoubtedly be more sophisticated than it is today. In the future, from a bit of sequence, it might be possible to glean a tremendous amount about such things as the diseases or behavioral anomalies that might befall someone. What might these unborn descendants have to say about the release of such highly personal information?
It is worth underscoring that when information is publicly released, it gets widely distributed (via the Internet and other means); any such decision made today will have far-reaching and irreversible consequences.

---

Citation of the Letter
http://www.washingtonpost.com/wp-dyn/content/article/2007/09/06/AR2007090602362.html
DNA Rights and Wrongs
Friday, September 7, 2007; A20
MARK GERSTEIN
New Haven, Conn.

Citation of Article Letter Responds to
http://www.washingtonpost.com/wp-dyn/content/article/2007/09/03/AR2007090301106.html
Mom's Genes or Dad's? Map Can Tell.
One Man's DNA Shows We're Less Alike Than We Thought
By Rick Weiss
Tuesday, September 4, 2007; Page A01
Scientists have for the first time determined the order of virtually every letter of DNA code in an individual, offering an unprecedented readout of the separate genetic contributions made by that person's mother and father....

Other Articles that this Letter Potentially Responds to
http://www.nytimes.com/2007/06/12/opinion/12tue4.html
June 12, 2007
Editorial
The Discoverer's DNA
When scientists talk about sequencing the human genome, they have been talking
so far about creating a composite picture drawn from the gene sequences of many
people. That has now changed for good. Recently, the director of the Human
Genome Sequencing Center at the Baylor College of Medicine gave James D. Watson
— who with Francis Crick discovered the structure of the DNA molecule — two DVDs
that contained the complete sequence of Mr. Watson's DNA.....

http://www.nytimes.com/2007/06/03/weekinreview/03harm.htm
June 3, 2007
6 Billion Bits of Data About Me, Me, Me!
By AMY HARMON
JAMES D. WATSON, who helped crack the DNA code half a century ago, last week
became the first person handed the full text of his own DNA on a small computer
disk. But he won't be the last.
Soon enough, scientists say, we will all be able to decipher our own genomes —
the six billion letters of genetic code containing the complete inventory of the
traits we inherited from our parents — for as little as $1,000.
Just what we will do with the essence of who we are once we bottle it, however,
is likely to be as much a social experiment as a scientific one....

http://www.nytimes.com/2007/06/01/science/01gene.html
June 1, 2007
Genome of DNA Discoverer Is Deciphered
By NICHOLAS WADE
The full genome of James D. Watson, who jointly discovered the structure of DNA
in 1953, has been deciphered, marking what some scientists believe is the
gateway to an impending era of personalized genomic medicine.
A copy of his genome, recorded on two DVDs, was presented to Dr. Watson
yesterday in a ceremony in Houston by Richard A. Gibbs, director of the Human
Genome Sequencing Center at the Baylor College of Medicine, and by Jonathan M.
Rothberg, founder of the company 454 Life Sciences.
"I am thrilled to see my genome," Dr. Watson said....

let. to ed. re. "Logged In and Sharing Gossip, er, Intelligence" -- NY Times

To the Editor:

I was very impressed by the recent article in the week in review about
how the intelligence community could use collective knowledge in the
form of wikis and blogs to help combat potential threats. While I
think this idea is great, I was surprised that the article did not
mention the public episode a few years ago where it was suggested that
the Defense Advanced Research Projects Agency (DARPA) establish a
Policy Analysis Market to help predict terrorist threats. In the
framework of the article, the DARPA proposal appears to be quite
prescient. Given the clear incentive of profit, efficient markets are
an even better idea for harnessing collective intelligence than wikis
and blogs. However, this proposal was strongly criticized in the
press, which led to the resignation of DARPA head John Poindexter.

Mark Gerstein

---

Above is an unpublished letter in response to:
September 2, 2007
Logged In and Sharing Gossip, er, Intelligence
By SCOTT SHANE
http://www.nytimes.com/2007/09/02/weekinreview/02shane.html
Week in Review

AMERICA’S spies, like America’s teenagers, are secretive, talk in code and get
in trouble if they’re not watched closely. It’s hard to imagine spies logging on
and exchanging “whuddups” with strangers, though. They’re just not wired that
way. If networking is lifeblood to the teenager, it’s viewed with deep suspicion
by the spy.....

Cycling along the Hudson

BikeNyack
Cycling through Palisades Park to Nyack, with a long lunch at famous Runcible Spoon.
Route taken on Google Maps
(kmz colored by elevation, note tough climb at end of park when one joins highway)
Associated useful links.
Summary: ~51.2 miles cycling (7.3 beyond that shown in KML)

BikeStormKing
Walking in StormKing sculpture park then cycling from there through Newburgh, over Hudson on I84 bridge, and into Beacon and then back.
Route taken on Google Maps
(kmz colored by speed)
Associated useful links.
Summary: ~23.1 miles cycling and 3 miles walking

BikeCroton
Cycling along Old Croton Aqueduct Trail, which is dirt. Trip aborted by rain in northern portion.
Route taken on Google Maps
Associated useful links.
Summary: ~18.5 miles

Cycling in the Bronx (BikeBx)

Into Bronx over Broadway Bridge and then to City Island
Route taken on Google Maps (kmz Color Ramped)
Associated useful links.
Summary: apx 10:30 AM-4PM, 26 miles

Jogging in Cambridge, UK (CamUK4Jogs)

Here are four slow jogs projected onto Google Maps in Cambridge radiating outwards from Trinity in four directions (in chronological order): CamWest (53:57 - 5.1km), CamNorth (34:30 - 3.8km), CamSouth (59:32 - 6.2km), CamShort (33:35 - 3.7km)

Cycling in Queens (BikeQueens)

Into Queens over Queensboro, then Roosevelt Island and Triboro to Randall's Island
Route taken on Google Maps (kml)
Summary: apx 11AM-5:30PM, 31 miles

Total Time (h:m:s)	6:40:21	12:53 pace
Moving Time (h:m:s)	4:06:06	7:55 pace
Distance (mi )	31.07
Moving Speed (mph)	7.6 avg.	231.3 max.
Temperature (°F)	53.6°F avg.	55.4°F high
Wind Speed ( mph)	SSE 3.8 avg.	SSE 6.9 max.

let. to ed. re. "Sowing Seeds Of Cures" -- C&EN

Here's a letter that wasn't published:
I read with great interest the recent article on venture philanthropy. I think
this is an interesting trend allowing philanthropic contributions to energize
the commercial process towards a good end. However, an important aspect was not
emphasized is the significant potential for conflicts of interest to arise.
Non-profits, such as medical charities, are given special status in the United
States by the tax code. However, in the scenario described in the article where
a philanthropist contributes money to making a biotech investment opportunity
more favorable for venture capital fund, he is essentially using charitable,
untaxed money towards a profitable end. This raises obvious conflicts: One could
imagine a person contributing money sheltered from taxes to a charity and then
having the charity redirect the funds to a commercial endeavor from which he
would directly benefit. Clearly, safeguards need to be developed to prevent this.

---

Letter in response to:
http://pubs.acs.org/cen/coverstory/85/8519cover.html
May 7, 2007
Volume 85, Number 19
pp. 19-26
Sowing Seeds Of Cures
As venture capitalists' priorities shift, venture philanthropists fill the gap
in funding of drug discovery by biotechs
Chemical & Engineering News (C&EN)
Lisa M. Jarvis
IN 1989, when scientists found the defective gene that causes cystic fibrosis,
it seemed that a cure, or at least an array of better treatment options, was
just around the corner. Research efforts, largely funded by the Cystic Fibrosis
Foundation (CFF), gained momentum, and by the mid-1990s, scientists had pieced
together much of the complex biology behind this debilitating and eventually
deadly disease.....

let. to ed. re. "Biology's Big Bang" -- Economist

Here's a letter to the Economist that wasn't published:
I read, with great interest the recent cover article describing biology's big
bang. I agree wholeheartedly agree with the thrust of this piece. The article
makes the point that there is a revolution in biology akin to that in early
20th-century physics. It also compares the genome to a computer operating
system. One can take these comparisons even further. The revolution in biology
is fundamentally about how a discipline once preoccupied with descriptions of
anatomy and taxonomy is now increasingly concerned with digital information
processing. We are, in fact, witnessing the fusion of parts of biology and
computer science. The new roles found for RNA are so important because of its
central place in cellular information processing.

---

Letter in response to:
http://www.economist.com/opinion/displaystory.cfm?story_id=9339752
The RNA revolution
Biology's Big Bang
Jun 14th 2007
>From The Economist print edition
What physics was to the 20th century, biology will be to the 21st—and RNA will
be a vital part of it.
NATURE is full of surprises. When atoms were first proved to exist (and that was
a mere century ago), they were thought to be made only of electrons and protons.
That explained a lot, but it did not quite square with other observations. Then,
in 1932, James Chadwick discovered the neutron. Suddenly everything made
sense—so much sense that it took only another 13 years to build an atomic bomb....

let. to ed. re. "A Challenge to Gene Theory, a Tougher Look at Biotech" -- NY Times

Here's a letter to the Times (in response to their one mention of ENCODE) that wasn't published:
As a participating scientist in the consortium cited in the July 1st Sunday
edition, I was excited that the Times covered some of the findings of our
project (ENCODE). The article discussed how the consortium's work is changing
the definition of a gene, and it was fascinating to see how scientific findings
ripple over into commercial and legal contexts. One of the interesting things
about genes is how plastic their definition has been over time. The current
definition, which is being recast by the ENCODE project's findings, derives from
the cracking of the genetic code in the 1960s. However, before that, a gene had
a more abstract definition as a unit of heredity, divorced from the physical
molecules actually encoding it. One of the amazing things about successive
redefinitions of a gene is that they have all been "backwards compatible" in a
scientific sense, still allowing old findings to apply to the current
definitions, with a bit of mental gymnastics. However, maybe we will find that
this backwards compatibility only applies in a scientific sphere and that a
redefinition of the gene will require substantial changes outside of it, in our
notions of commercially viable entities.
(Also, you might note that this subject is quite related to some recent publications, viz:
http://papers.gersteinlab.org/papers/grgenerev/
http://papers.gersteinlab.org/papers/whatisgene )

---

Letter in response to:
http://www.nytimes.com/2007/07/01/business/yourmoney/01frame.html
A Challenge to Gene Theory, a Tougher Look at Biotech - New York Times
July 1, 2007
Re:framing
A Challenge to Gene Theory, a Tougher Look at Biotech
By DENISE CARUSO
THE $73.5 billion global biotech business may soon have to grapple with a
discovery that calls into question the scientific principles on which it was
founded. Last month, a consortium of scientists published findings that
challenge the traditional view of how genes function. The exhaustive four-year
effort was organized by the United States National Human Genome Research
Institute and carried out by 35 groups from 80 organizations around the world.
To their surprise, researchers found that the human genome might not be a "tidy
collection of independent genes" after all, with each sequence of DNA linked to
a single function, such as a predisposition to diabetes or heart disease.
Instead, genes appear to operate in a complex network, and interact and overlap
with one another and with other components in ways not yet fully understood.
According to the institute, these findings will challenge scientists "to rethink
some long-held views about what genes are and what they do."...

Cycling in Brooklyn (Aborted5boro07 + BikeBeltPkwy)

Aborted 5 Boro, following course route to Brooklyn Bridge and then improvising to Verrazano after a long lunch
Route taken on Google Maps (kml)
Summary: apx 6:30AM-5PM, 46 miles

Total Time (h:m:s)	10:08:40	13:07 pace
Moving Time (h:m:s)	6:39:03	8:35 pace
Distance (mi )	46.4
Moving Speed (mph)	7.0 avg.	67.8 max.
Temperature (°F)	55.6°F avg.	62.6°F high
Wind Speed ( mph)	NE 8.5 avg.	NE 11.5 max.

Central Park to Prospect Park and then onto Belt Parkway Bikeway
Route taken on Google Maps (kml)
Summary: apx 8:30AM-5PM, 49 miles, with stops, including lunch

Total Time (h:m:s)	9:47:41	12:05 pace
Moving Time (h:m:s)	6:29:44	8:01 pace
Distance (mi )	48.55
Moving Speed (mph)	7.5 avg.	51.0 max.
Temperature (°F)	67.3°F avg.	71.6°F high
Wind Speed ( mph)	SE 5.3 avg.	SE 12.6 max.

Cycling on Northern Part of Farmington Valley Greenway (BikingCTGreenwayN)

Actuals
Route taken on Google Maps (kml)
Summary Data (apx. 11:30AM-6:30PM, with stops, 46 miles)

Total Time (h:m:s)	7:05:31	9:19 pace
Moving Time (h:m:s)	5:08:33	6:45 pace
Distance (mi )	45.67
Moving Speed (mph)	8.9 avg.	59.8 max.
Temperature (°F)	82.1°F avg.	84.2°F high
Wind Speed ( mph)	W 9.2 avg.	W 11.5 max.

Planning
Useful links: http://del.icio.us/mbgmbg/FunBikingCTGreenwayN

Great quote: “I’m an editor. I’m paid to make choices. My work still has meaning—but does it have value?”

The Rise of Craigslist and How It's Killing Your Newspaper -- New York Magazine

let. to ed. re. "A Smarter Web" -- Tech Review

Here's a letter to Technology Review that was published:
We read with interest John ­Borland's piece on the Semantic Web ("A Smarter Web," March/April 2007). We agree that this is an exciting time in the Semantic Web's development, yet we want to point out that its great degree of structure has drawbacks. As the article noted, Semantic Web users must learn complex ontology languages and structure their information and data using them. This difficulty inhibits the growth of the Semantic Web. It is thus arguable whether the Semantic Web can approach the scale of the standard Web, where anyone can easily create and publish content.
Ideally, we should combine the strengths of the Semantic Web and the normal Web. Search would be a good place to start. Today, global free-text search is the primary means of querying the whole Web, but it provides only coarse-grained access to documents. In contrast, the Semantic Web allows much more precise queries across multiple information sources (say, querying for a particular attribute, such as "street address"). However, it is on a much smaller scale, involving far fewer documents. We could imagine combining normal and Semantic Web queries--for instance, to search the free text of all real-estate Web pages written by women in Boston during the last week for the word "Jacuzzi." Taking this further, the few structured relationships currently in the Semantic Web could be used to refine the results of mainstream search engines.
Finally, as so much activity in the life sciences is focused on large-scale interoperation on the Web (as found in drug discovery), we feel that biological research could serve as a useful guide and driving force for the development of Web 3.0.

---

Citation of Letter
http://www.technologyreview.com/Infotech/18851/page2/
The Semantic Web
July/August Issue of Technology Review
Mark Gerstein and Andrew Smith
Computational Biology and Bioinformatics Program
Yale University
New Haven, CT

Letter in response to:
http://www.technologyreview.com/Infotech/18395/
Monday, March 19, 2007
Part I: A Smarter Web
New technologies will make online search more intelligent--and may even lead to a "Web 3.0."
By John Borland
Last year, Eric Miller, an MIT-affiliated computer scientist, stood on a beach in southern France, watching the sun set, studying a document he'd printed earlier that afternoon. A March rain had begun to fall, and the ink was beginning to smear....

Original Letter Text (before edit by magazine)
We read with great interest John Borland's March/April 2007 article "A Smarter
Web." We agree that this is an exciting time in the development of the semantic
web (or Web 3.0), and that it is on the cusp of more widespread acceptance and
use. A problem with the semantic web, however, is that it is not as flexible as
the free-text publishing supported by the standard web. As the article noted,
users must learn the semantic web's ontology languages and structure their
information and data using them. This presents a learning curve to users, acting
to inhibit the growth and spread of semantic web data. It is thus arguable
whether the semantic web can approach the huge size of the standard web where
almost anyone can easily create and publish web pages. The standard web will
likely still be the primary web most users see and use for the foreseeable
future, while the semantic web could remain a niche.

We thus feel that a practical direction is to investigate ways that the semantic
web and standard web can work together and leverage each other in a kind of
symbiosis. Keyword-based web search ala Google is the primary way of mining the
web for information today, but it only provides coarse-grained topical access to
documents and there are many kinds of information requests it cannot handle. For
example, queries that combine general relational information (such as provided
by the semantic web) about pages with keyword based searches are not supported.
Furthermore, one wants to be able to develop ways of leveraging small amounts of
highly structured information (as in the semantic web) as "training sets" to
better enable querying and clustering of the large bodies of unstructured, free
text information on the web; i.e. the small amount of highly structured
information could be used to bootstrap the automated organization, in support of
better querying, of the much larger unstructured information through data
mining. Since searching is widely perceived to be a crucial web application, the
semantic web's ability to improve it could be of high practical value and an
important driving force to help more fully realize the vision of the semantic
web. An important part of Web 3.0 should thus be to enumerate the kinds of
information requests that could be fruitfully made, and the kinds of information
infrastructure and data mining techniques needed to fulfill them. Finally, there
is much activity and excitement within biological research towards the goal of
truly large-scale integration and interoperation of its vast data, e.g. to aid
in more efficient drug discovery. The life sciences could thus be a useful
guide, test case, and driving force for Web 3.0.

Cycling in Southern Westchester (BikeSW)

Actuals
Riverdale into Southern Westchester, following Bronx River trailway after Bronxville
Route taken on Google Maps (kml) (Streetview works for part of the route, showing some of the Bronx River Parkway Trailway.)
With elevation information, which is too big for Google Maps but works with Earth (kml, kmz)
Summary Data: 23.7 miles, most of the day with stops

Planning
Rough google map route of lower (aborted) part of trip.
Nearby places on this route created with Google's My Maps: early and late.
Some useful links.

Cycling in Northern Westchester (BikeNW)

Actuals
Route taken on Google Maps (kml, kmz)
Bottom Southern and Northern Westchester Trails to Yorktown Heights and back with detour through Tarrytown (on old aqueduct trail)
Summary Data (apx. 9:30AM-6:10PM, with stops, 56 miles, uncorrected)

Planning
Links collections relevant to planning the trip: http://del.icio.us/mbgmbg/FunBikingNW

Hamptons Cycling (BikeHamptonsBM)

Actuals
Route taken on Google Maps (kml)
Bridgehampton to Montauk and back.
Summary Data (apx. 8AM-4PM, with stops, 53 miles)

Total Time (h:m:s)	8:11:17	9:09 pace
Moving Time (h:m:s)	5:22:45	6:01 pace
Distance (mi )	53.56
Moving Speed (mph)	10.0 avg.	23.2 max.
Temperature (°F)	69.1°F avg.	69.8°F high
Wind Speed ( mph)	SSW 12.4 avg.	SSW 13.8 max.

(51 miles without correction)

Planning
A useful reference map from ResortMaps.com
A suggested route plan and some places to stop (from Google Map's My Map)

tennis courts near CU & GWB

For reference:
For tennis courts near GWB, there appears to be only nearby bridges over tracks, with the best entry point at 165th & Riverside.
For tennis courts near CU, best entry point is near 120th and Riverside.

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http://maps.google.com/maps?f=q&hl=en&q=W+165th+St+%26+Riverside+Dr,+New+York,+NY+10032&ie=UTF8&om=1&z=19&ll=40.847148,-73.945726&spn=0.001781,0.004227&t=h
http://maps.google.com/maps?f=q&hl=en&q=W+120th+Street+%26+Riverside+Dr,+New+York,+NY&ie=UTF8&z=18&ll=40.81132,-73.96394&spn=0.003557,0.00685&t=h&om=1

ooo[link]ooo

ooo[maps]ooo

ooo[fun]ooo

The Drive for the $1000 Genome -- BioITWorld

Interesting overview the high-throughput sequencing technologies, with quotes below from 454 people and on cost of storing a Solexa's run of data, estimated at ~$15K/run .

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http://www.bio-itworld.com/issues/2007/may/cover-story
http://www.bio-itworld.com/issues/2007/may/cover-story-sidebar1/
http://www.bio-itworld.com/issues/2007/may/cover-story-sidebar2/
The Drive for the $1000 Genome
By Kevin Davies
May 15, 2007 | J. Craig Venter recently made his Comedy Central debut on The Colbert Report. Asked by host Stephen Colbert "What makes you think you can do a better job with life and genetics than God?" Venter shot back: "We have computers!" rendering Colbert momentarily (and uncharacteristically) speechless.....
SOLiD Storage
A potential downside of the SOLiD setup is the premium it puts on compute power and storage. The complete SOLiD system including compute and workflow pieces, could push the price above $600,000....
"No-one stores the [Sanger] images when they're small, so who's going to store them when they're large? So we want to get you past the images and into analyzing the data," says Rhodes.
By contrast, a typical 454 FLX run produces a paltry 13 GB of raw image data After data extraction, namely base calling, we're at a final of just less than 20 GB in total. That's actually quite manageable, especially nowadays with 500-GB hard drives," says Harkins. "We're looking to compress that down so potentially you could burn a DVD for one drive. You could store an instrument run for a few dollars."
Harkins notes that other next-generation sequencing platforms are talking about terabytes per run. "We're talking about pushing the science, but these other companies have a dilemma. It could cost more in computer hardware than reagents for an instrument run," says Harkins.
While Illumina's Smith agrees that, "The really big data is in the images," Illumina offers customers the opportunity to store all of their images, "because there will be people who want to do that. The issue is you get into hundreds of GB or even 1 TB [per run]." And that will only increase in the future. "The customer may decide to store a subset of the images for quality control purposes, or store images for a particularly important run and archive them to a tape backup."
The question for the market, Harkins reckons, is: Do you want to save your raw data? 454 allows users to re-evaluate their raw data. "We had one customer who re-processed his raw data using the updated GS FLX software and is seeing improvements," says Harkins. "When you're talking about 1-2% error down to 0.5%, that leads to tangible improvements for downstream analysis."
But Rhodes dismisses such criticism. With an instrument potentially pumping out 4 Megabases each second over three days, "People don't need the images, they need the data. What you really want is the result," says Rhodes.
During a panel discussion at CHI's Next Generation Sequencing conference, Rhodes said: "Back of the envelope calculations say that if you wanted to store the raw image data, it's 6 TB a week... that could require you to spend $1 million on storage, backup, and stuff. So unless you think you're going to want to go back to every image, it's cheaper to do the experiment again." Rhodes can see certain situations for storing images, say for a precious cDNA clone. "But as a routine workaday measure, no."
"Once you've got to that stage, you still have a large dataset — if you're going to generate 1 billion bases per run, you've got to have quite a lot of bytes as well as bases," says Smith. "But you're no longer in the TB of data, you're back down in the 100 GB or so. So you can reduce the data quantity by not storing the images." Smith says many customers already have the necessary compute infrastructure. ...
But Harkins says the market hasn't come to terms with the dilemma of paying $10,000-20,000 to save a single instrument run's data. "That's going to put the market into a bind," he says. "Throwing raw data away is a paradigm shift I don't think people are ready for yet."