Driving Directions to Claire's in New Haven

Here's how to get from GW bridge to Merritt.

Here's how to get from Merritt to Claire's.

Entrace to parking garage is between Chapel and Crown on College St.

Thunderbird issues

"Thunderbird can't use the profile because it is in use to continue close the running instance of thunderbird"
In relation to the above error message found the only thing to cure this is to restart windows and re-run thunderbird.

The lock file that often gums up a thunderbird session is:
D:\vmshared\PERS\mailstuff\mbg\parent.lock

My other thunderbird hints are at: http://del.icio.us/mbgmbg/Link_ThunderbirdFixes

Some Ipod Notes

Notes on water proofing an iPod
http://www.waterproofcases.net/headphones.html
http://ilounge.com/index.php/reviews/comments/otterbox-for-ipod-4g-photo-ipod/
http://www.ilounge.com/index.php/reviews/comments/h2o-audio-sv-imini-underwater-housing-ipod/
B0009I2M7C
B0009IZSAK
http://www.slicsound.com/ss001.asp

To reset an iPod with a Click Wheel
(below extracted from a page on the web)
Including the following:
* iPod mini
* iPod mini (Second Generation)
* iPod with color display (iPod photo)
* iPod (Click Wheel)
* iPod nano
* Fifth Generation iPod (also known as iPod with video)

1. Toggle the Hold switch on and off. (Slide it to Hold, then turn it off again.)

2. Press and hold the Menu and Select buttons until the Apple logo appears, about 6 to 10 seconds. You may need to repeat this step.

Tip: If you are having difficulty resetting your iPod, set it on a flat surface. Make sure the finger pressing the Select button is not touching any part of the click wheel. Also make sure that you are pressing the Menu button toward the outside of the click wheel, and not near the center.

If the above steps did not work, try connecting iPod to a power adapter and plug the power adapter into an electrical outlet, or connect iPod to your computer. Make sure the computer is turned on and isn't set to go to sleep
http://docs.info.apple.com/article.html?artnum=61705

let. to ed. ("23andMashup") re. "23AndMe Will Decode Your DNA for $1,000" -- Wired

Here's a letter to the Wired that was published:
23andMashup
I enjoyed the article about personal genomics company 23andMe ("Your DNA Decoded," issue 15.12). I was especially interested in the visionary and somewhat whimsical idea of connecting social networking with understanding one's genome. We can take this idea a step further and combine it with another phenomenon — the rise of easy-to-make consumer mashups. People could use Web services to share their genomic information in meaningful ways. For instance, friends on a social networking site might look beyond external characteristics like hair and eye color and instead search for sequence variants they have in common. Alternatively, you could mash up genomic profiles with marathon times and highlight common characteristics of fast runners. However, people will only share genomic information if it's done in a way that doesn't reveal too much about themselves: To be viable, genomic mashups should be interesting, but not too specific about future health implications.

---

Citation of the Letter:
http://www.wired.com/culture/culturereviews/magazine/16-02/rants
Wired Magainze, Issue 16.02, Pg. 17 (Feb.)
Mark Gerstein, New Haven, Connecticut
Rants Section

Article letter is in response to:
Wired Magainze, Issue 15.12
23AndMe Will Decode Your DNA for $1,000. Welcome to the Age of Genomics
By Thomas Goetz
http://www.wired.com/medtech/genetics/magazine/15-12/ff_genomics
At the age of 65, my grandfather the manager of a leather tannery in Fond Du Lac, Wisconsin, suffered a severe heart attack. He had chest pains and was rushed to the hospital. But that was in 1945, before open heart surgery, and he died a few hours later. By the time my father reached 65, he was watching his diet and exercising regularly. That regimen seemed fine until a couple of years later, when he developed chest pains during exercise, a symptom of severe arteriolosclerosis. A checkup revealed that his blood vessels were clogged with arterial plaque. Within two days he had a triple bypass. Fifteen years later (15 years that he considers a gift), he's had no heart trouble to speak of.....

Text that was submitted to the magazine (before editing):
I enjoyed the recent article about the new personal genomics company, 23andMe, and was especially interested in their visionary and somewhat whimsical idea of connecting social networking with understanding one's genome. We can take this idea a step further and combine it with another emerging phenomenon of the past year -- the creation of easy-to-make consumer mash-ups (such as Yahoo Pipes). Then, we can begin to imagine people using web services to interrelate and give personal meaning to their genomic information, just as we currently see discrete bits of apparently meaningless data related to location come together into an emergent whole when they are mashed up with a map service such as Google's -- think of collecting all the photos taken near Times Square on Flickr to get an overview of the neighborhood. However, unlike the case of vacation photos, people will only be willing to share genomic information if they are not worried that it reveals too much about themselves. That is, to be viable mash-ups of genomic information should be interesting, but not too specific about future health implications.

WinXP within WinXP with VMware (BlogEntry_VMconfigT60b_Xmg)

This document contains some public notes I've made on the arduous process of getting VMware to run with a Win XP guest on a Win XP host. (One might wonder why I'm trying to do this, but this will take too much text here. I'll let any reader just speculate.) In general see below and some of my relevant del.icio.us links .

## Del.icio.us Links

My central collection of bookmarks around this endeavor is:
http://del.icio.us/mbgmbg/Useful_VMconfigT60b_Xmg

In addition, some extensions that I found useful for Firefox and Thunderbird
http://del.icio.us/mbgmbg/UsefulExtension

## Outlook

Getting Outlook to work with the Palm Treo and VMware

* Have to keep main outlook DB in
C:/Documents and Settings/mbg/Local Settings/Application Data/Microsoft/Outlook

Doesn't seem to work when moving it another location.

* archive stuff to archive.pst and then compacted

* When synching with the VMware and treo, host application often seizes the "context." This happens particularly on the second sync attempt. Have to tell it to "take no action" on a sync on the host application dialog box.

* See treo hints under http://del.icio.us/mbgmbg/useful_vminstalls to work with Verizon wireless sync.

## Blackberry
Works fine in VM

7750M_PBr4.0.0_rel201_PL1.5.0.30_A4.0.0.171.exe
BlackBerry_400_33_desktop_ml.exe
user "mbg"
Select "Blackberry Internet Email" Option

Run desktop mgr
set it to use USB
use default folder
C:/Documents and Settings/mbg/Application Data/Research In Motion/BlackBerry

## Thunderbird
Getting it to run in VM and then have it's mail directory outside.

* Install normally
but then edit c:/Documents and Settings/mbg/Application Data/Thunderbird/profiles.ini
to be thus:

[General]
StartWithLastProfile=1
[Profile0]
Name=default
IsRelative=1
Path=Profiles/knnjxcfu.default
[Profile1]
Name=mbg
IsRelative=0
Path=J:/vmshared/PERS/mailstuff/mbg
Default=1
[Profile2]
Name=mbg2-yahoo
IsRelative=0
Path=J:/vmshared/PERS/mailstuff/mbg2
[Profile2]
Name=mbg-old-rec
IsRelative=0
Path=J:/vmshared/PERS/mailstuff/mbg-old-rec
[Profile3]
Name=mbg-old-sent
IsRelative=0
Path=J:/vmshared/PERS/mailstuff/mbg-old-sent

* To access profiles,
"C:/Program Files/Mozilla Thunderbird/thunderbird.exe" -ProfileManager

* Profile0 was there, now adding profile1
Thunderbird should then come up with full mail setup

* One has to install quicktext manually.
Then all the stuff should be there.

Make sure you check the auto download of messages.

## Google Earth
It runs under VMware but not in directX mode

## Itunes
Key point here is putting iTunes DB in another location and then configuring VMware to access this location with another.

## MS Office

* Installs fine on the VM
* Transferred settings from "office-saved-settings-for-MG-29Dec07.OPS"

However, then ran to documents to go problem -- interface with word was messed by copying over the prefs (see above). Found fix at http://support.dataviz.com/support.srch?docid=12792 , viz:

How to manually uninstall Word Add-In:
1. Open Word
2. Go into Tools menu
3. Click on Templates and Add-Ins
4. Uncheck DVZWDAddin.dot - this menu should then be removed
5. Close Word, then press CTRL-ALT-DELETE to bring up the Task Manager, and check to make sure all instances of WINWORD.EXE are closed
6. Go into the following directory: C:/Documents and Settings/<user name>/Application Data/Microsoft/Word/STARTUP
(NOTE: The Application Data folder is a hidden folder. If you can't see hidden folders, go to Tools > Folder Options, select the View tab, select the option to "Show hidden files and folders" and click OK.)
7. Delete the file "DVZWDAddin.dot" and all of its temp files (i.e. ~$ZWDAddin.dot)

## This doc

Tips in formatting include using ^l (in word) instead of ^p before import into Google Docs. Within GoogleDocs one can just do "shift-return" .

Your fingers are the best comb.... -G Ray

let. to ed. re. "For a Tunnel to Go 16 Miles, No Light Yet" -- NY Times

Here's a letter to the Times that wasn't published:
I was very intrigued by your recent column about a proposed tunnel
connecting Long Island to Westchester. As the piece noted, this
tunnel follows a route long ago advocated by Robert Moses. If such a
tunnel were ever to be built, it would validate one of Moses' original
designs for the road network encircling New York City; thus, in a way,
this proposal revitalizes his original dream. However, it is worth
pointing out that Moses' original plan was for a bridge, not a tunnel.
Moses, in fact, strongly disliked and actively opposed tunnels,
whereas he felt bridges made a stronger and grander statement. Thus,
the interesting twist in the column is how it simultaneously revives
Moses' original dream just as it implicitly criticizes his
stubbornness.

---

Letter in response to:
http://www.nytimes.com/2007/11/29/nyregion/29towns.html
November 29, 2007
Our Towns
For a Tunnel to Go 16 Miles, No Light Yet
By PETER APPLEBOME
GARDEN CITY, N.Y.
A reasonably sane person contemplating the modest proposal of the
developer Vincent Polimeni to build a $10 billion, privately financed,
16-mile tunnel linking Long Island and Westchester the longest
autos-only tunnel in the world and the first to be privately built in
the United States might start with two thoughts.
The first: This might be a brilliant idea or a nutty one, but in an
era of shrunken ambitions, give the guy credit for a big idea that
goes back to Robert Moses, who in the 1960s championed a bridge over
pretty much the same route.....

Cycling in DC (TripBethesda)

Cycling from Bethesda into DC and back

Route taken on Google Maps
Summary: ~40 miles cycling
Geotagged images, served from [P]icassa or [F]lickr (also look at overall flickr map)

Potential alternate terms RFBRs for chIP-chip "hits"

The ENCODE paper coined the term RFBR for "hits" in chIP-chip experiments, viz: "We refer to regions with enriched binding of regulatory factors as RFBRs. RFBRs were identified on the basis of ChIP-chip data in two ways..." Some other terms were considered instead of RFBR. Here's a list of some of them:

CHIRP -- chip hit of regulatory potential
EIGR -- experimentally identified genomic region (like mountain)
GRAF -- Genomic region associated with function
GRAB -- Genomic region associated with binding
MONOD
RELIC -- Regulatory element in living cells
GELC -- Genomic element in living cells
FELC -- Functional event in living cells
MOJO
EDGE -- Experimentally determined genomic element
GEMMS -- Genomic element defined by multple methods
LORE
REIVE -- Regulatory element in vivo
GERP -- Genomic element of regulatory potential
TRE -- transcriptional regulatory element
GIVE -- Genomic in-vivo element
LRE -- long-range element
RFBS -- regulatory factor binding site

Bad MILK. How does milk know when to expire? - Bad Astronomy and Universe Today Forum

Some useful quotes on what makes milk go bad:
"Generally, if kept constantly cold, bacteria in milk will grow at a constant slow rate. The bacteria generally feeds on the lactose, turning it into lactic acid. As it accumulates, it makes the milk taste more and more sour. But our taste buds will generally ignore the small bit of sourness. The milk is considered bad when the sourness becomes noticeable. The proteins in the milk will start to stick to each other in an acid environment. However, for this to happen on a large scale requires the milk to be fairly acid (pH around to 5.5). Our taste buds register sour at a much higher pH (~6)."

Some Durable Indoor Plants (from visiting a nursery)

Pictures of them at http://www.flickr.com/photos/mbgmbg/tags/kw30sep07nurseryvisit

Listing of plants

• Snake Plant - http://en.wikipedia.org/wiki/Sansevieria_trifasciata
• (verabella?) palm plant
• Jade Plant - http://en.wikipedia.org/wiki/Jade_plant
• ZZ plant (durable) - http://en.wikipedia.org/wiki/Zamioculcas
• Rubber Plant (not as durable) - http://en.wikipedia.org/wiki/Ficus_elastica
• Bamboo plants (need to be immersed in water) - http://www.bamboogarden.com/care.htm

Cycling and Walking around Vienna, with Pictures (TripVienna)

Attempted to carefully integrated image and geo data on last summer's vacation to Vienna

Photos
(Geotagged images, served from [P]icassa or [F]lickr)

• All of the photos [P][F] (also look at overall flickr map)
• Various Subsets (sublime to ridiculous):

1. Interesting Architecture [P][F]
2. Street Art [P][F]
3. Generic, non-geotagged shots [P][F]
4. Graffiti [P][F] (alternate picassa with subset map)

• Shots of People [P] (need auth. key)

Cycling and Walking Routes

• Cycling along Danube near Vienna, ~58 km (13 July 2007);
  Route taken on Google Maps (Garmin HST file)
• Walking through city center (11 July 2007);
  Route taken on Google Maps (Garmin HST file)
• Walking through city outskirts, including Naschmarkt, Palace and Freud museum (12 July 2007);
  Route taken on Google Maps (Garmin HST file)

Useful Links

• Overall, FunVienna1, FunVienna2, FunVienna3, FunVienna4

Cycling near New Haven (BikeCT + BikeOrchard)

BikeCT
Cycling along CT coast near Guilford and Branford, with a lunch in Branford.
Route taken on Google Maps
(kmz colored by course heading)
Associated useful links.
Summary: ~52 miles cycling (7 hrs. of biking time)

BikeOrchard
Cycling to Lyman Orchard, with a lunch there.
Route taken on Google Maps
(kml colored by elevation -- note hills.)
Associated useful links.
Summary: ~41 miles cycling (7.5 hrs. of total time)

Some examples of Cockney rhyming slang

Cockney rhyming slang - Wikipedia, the free encyclopedia:
'plates' means 'feet' ('plates of meat')
'brown' means dead ('brown bread')
'titfer' means hat ('tit for tat')

Some Useful Tidbits on Asthma

The Harvard Medical School Guide To Taking Control Of Asthma

by Christopher H. Fanta (Author), Lynda M. Cristiano (Author), Kenan Haver (Author)
http://www.amazon.com/Harvard-Medical-School-Taking-Control/dp/0743224787/ref=ed_oe_p/104-6142984-5779139?ie=UTF8&qid=1190536146&sr=1-6
http://books.google.com/books?id=ohIbOrVcRBwC

Leukotriene Inhibitors

[From link above:]
"Molecular biology promises to provide drugs that will control our immunologic and biochemical reactions. Several pharmaceutical companies are now producing leukotriene receptor blockers - the first of the new line of agents being developed to control the inflammatory response in asthma. The first agents coming to market in Canada are zafirlukast (Accolate) and montelukast (Singulair). Both act by blocking the most potent of the leukotrienes, L4. Asthma is felt to be due to allergens triggering an inflammatory response. .... Leukotrienes were found to be the active factor in the old SRSA (slow releasing substance of anaphylaxis) first described in 1938. They are 1000x more potent in inducing bronchospasm than histamine. They are part of the lipoxygenase pathway that is also involved in prostoglandin production. These pathways are also used in allergic rhinitis. At the moment, leukotrienes are hoped to be the appendix of the immune system - of no good use, but known to cause problems....."

Beta Blockers & Asthma

[From link above:]
"What is a beta-blocker? A beta-blocker is a medicine used to treat high blood pressure and heart problems. Some beta-blockers are atenolol (brand name: Tenormin), metoprolol (brand names: Lopressor, Toprol XL) and propranolol (brand name: Inderal). A beta-blocker blocks the harmful effects of stress hormones on your heart. This medicine also slows your heart rate. Beta-blockers can also be used to prevent migraine headaches in people who get them frequently. Can I take a beta-blocker if I have asthma or chronic lung disease? Beta-blockers are generally not used in people with asthma. A beta-blocker can cause asthma attacks.... "

Beta-agonists

[From link above:]
"Beta-agonists are bronchodilator medicines that open airways by relaxing the muscles around the airways that tighten during an asthma attack....
Beta-agonists come in many different forms. Some common beta-agonist medicines are: albuterol, Alupent, Brethine, metaproteronol, Metaprel, Proventil, Salbutamol, terbutaline, Ventolin. "

The concept of "Pre-treatment" with beta-agonist

Preventing Respiratory Viruses

[From Harvard Med. Guide above:]
"Most viruses are spread from oral or nasal secretions onto surfaces, are picked up by hand contact, and are then spread from your hands to your nose and mouth. So wash your hands frequently..."

http://en.wikipedia.org/wiki/Purell

Eosinophils: mischief-makers in asthma

[From link above:]
"Whatever are eosinophils?

Eosinophils are a type of white blood cell (corpuscle) and take up the red dye eosin when blood is examined under a microscope by the commonest method.

They accumulate wherever allergic reactions like those in asthma take place. Their natural role is to defend us against parasites. In fact allergies such as asthma are probably a malfunction of our protective mechanism against parasites...."

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