30 March 2006

Bra-ket notation - Wikipedia


27 March 2006

David MacKay: Information Theory, Inference, and Learning Algorithms: Home

Fantastic book!


22 March 2006

Virtual globes: The web-wide world (google earth) -- Nature [clip]

Describes the huge impact that Google Earth is having on the science. Here's a letter I wrote on this:

I was very impressed with Declan Butler's recent article on the impact that Google Earth is having on the scientific community. I have found this program extremely exciting to use and exhilarating as far as viewing common locations. I would like to point out that the success of this program underscores the importance of open standards for data and having easy interoperation between information resources.
    To some degree, this same success has been achieved in the macromolecular structural world, where there are many programs giving people the ability to easily look at macromolecules in 3D and layer information on them.
    Clearly, a good visualization program and open "browsing" system can catalyze a lot of interesting science. I would like to urge the development of comparable
browsing applications for other newly emerging areas in the biological sciences -- in particular, for visualizing the vast landscape of the genome and for navigating through complex biological networks.

Nature articles by Declan Butler

Published online: 15 February 2006; | doi:10.1038/news060213-7
How does Google Earth work?
Short cuts bring the globe to your screen without crashing your computer.

Published online: 15 February 2006; | doi:10.1038/439776a
Virtual globes: The web-wide world
Life happens in three dimensions, so why doesn't science? Declan Butler discovers that online tools, led by the Google Earth virtual globe, are changing the way we interact with spatial data.

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20 March 2006

http://ongenetics.blogspot.com/2006/03/from-hapmap-to-selection-map.html [url]

Interesting reference to selection maps and PLOS bio. article

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How Do I Love Thee? -- The Atlantic Monthly [clip]

Interesting article talks about the pseudoscience of rigorously determining "Briggs-Myers" personality types and compatibility metrics between people. Personally I think this is more of an art than a science. In anycase, it appears that there will be a vast amount of "social" data mining on the internet in years to come!

The Atlantic Monthly | March 2006
How Do I Love Thee?
by Lori Gottlieb

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http://proteinatlas.org/ [url]

Antibody database indicating proteins present in different cancers and tissues -- and also in different sexes!

Science. 2005 Aug 26;309(5739):1310. 
Proteomics. New database to track protein locations.
Service RF.

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http://www.gnetbrowse.org [url]

perhaps useful to investigate again... contains many nets

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http://rnai.org [url]

perhaps useful to investigate for connecting phenotypes to genotypes

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15 March 2006

emPAI -- MCP [clip]

Useful to refer to in relation to quantifying protein abundance. (Note earlier paper too.)

Mol Cell Proteomics. 2005 Sep;4(9):1265-72.
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein.
Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M.
To estimate absolute protein contents in complex mixtures, we previously defined a protein abundance index (PAI) as the number of observed peptides divided by the number of observable peptides per protein (Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome. Res. 12, 1231-1245). Here we report that PAI values obtained at different concentrations of serum albumin show a linear relationship with the logarithm of protein concentration in LC-MS/MS experiments. This was also the case for 46 proteins in a mouse whole cell lysate. For absolute quantitation, PAI was converted to exponentially modified PAI (emPAI), equal to 10PAI minus one, which is proportional to protein content in a protein mixture.....

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McPherson Clathrin Vesicle Protein Abundance Set [clip]

Papers and person below associated with ~200 protein abundance values with can
be compared with brain mRNA expression levels.

Girard, M., Allaire, P.D., McPherson, P.S., and Blondeau, F. (2005).
Non-stoichiometric relationship between clathrin heavy and light chains revealed
by subcellular proteomics of clathrin-coated vesicles from brain and liver. Mol.
Cell Prot. 4:1145-1154.

Blondeau, F., Ritter, B., Allaire, P.D., Wasiak, S., Girard, M., Hussain, N.K.,
Angers, A., Legendre-Guillemin, V., Roy, L., Boismenu, D., Kearney, R.E., Bell,
A.W., Bergeron, J.J.M., and McPherson, P.S. (2004) Tandem mass spectrometry
analysis of brain clathrin-coated vesicles reveals their critical involvement in
synaptic vesicle recycling. Proc. Natl. Acad. Sci., USA 101:3833-3838.


13 March 2006

http://channingdaughters.com/ [url]

Thought this might be a nice drink to keep an eye out for....

The Tasting Room is open 7 days a week for visitors from 11am-5pm. We taste 6 different wines each day, and provide very informative tastings.
Starting July 4th, we will be open every day from 11-6pm. However, please note that on Sunday, July 6th we will close for tastings at 4:30 in preparation for our fabulous Salsa Party, which begins at 5pm.
1927 Scuttlehole Rd    PO BOX 2202    Bridgehampton, NY 11932
phone: 631-537-7224    fax: 631-537-7243
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11 March 2006

HealthText Audio, Audio Books for Your Health


09 March 2006

potassium iodide + Prussian Blue [url]

Thoughts for those in stress... perhaps useful for the paranoid (potassium iodide + Prussian Blue)! Wonder if a doctor would perscribe these....

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08 March 2006

http://bio.chip.org/mapper [url]

Interesting DB of TFBS, with new extensions to ENCODE regions and SNPs. Based on building HMMs from TRANSFAC and then running these against genomes.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D91-7.   
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.
Marinescu VD, Kohane IS, Riva A.
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Two recent microarray platform evaluation manuscripts from Kohane

Thought these might be good to refer to in relation to the platform
comparison work we are doing. The 2nd one is a glass slide vs. Affy study.

BMC Bioinformatics. 2003 Jun 25;4:27. Epub 2003 Jun 25
Reproducibility of gene expression across generations of Affymetrix
Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH,
Kohane IS.

Bioinformatics. 2002 Mar;18(3):405-12.
Analysis of matched mRNA measurements from two different microarray
Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS.

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http://www.returnpath.net/ [url]

perhaps useful to investigate for re-routing hotmail to gmail (and other similar combinations).....

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07 March 2006

jccmanhattan.org [url]

Might have interesting activities

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Infamous email writers aren't always killing their careers after all -- WSJ [clip]

A true email exchange and was the subject a WSJ article.

Read from the bottom up.

-----Original Message-----
From: David Breen
Sent: Friday, February 10, 2006 9:54 AM
To: Stacey G. Bloom
Subject: FW: Thank you

Read from the bottom to the top.there was an intervening exchange of
voice mails as well.as <http://well.as/> you can imagine, they were
as unprofessional as
her e-mails.

-----Original Message-----
From: William A. Korman
Sent: Friday, February 10, 2006 9:55 AM
To: 'David Breen'
Subject: RE: Thank you

You can e-mail this to whomever you want.

-----Original Message-----
From: David Breen
Sent: Friday, February 10, 2006 9:47 AM
To: 'William A. Korman'
Subject: RE: Thank you


Where to begin?

First of all, how unprofessional, and secondly, it is "reap what you
'sow,'" now "sew". If she is going to use a cliche, couldn't she at
least spell it right? And WTF is with her "blab la bla"? Does she not
read your e-mail about it being a small community?! So, finally, can I
forward this along to some folks? I am sure they would love to see how
the up-and-coming lawyers are comporting themselves! (Clearly she did
not go to BU!!!) J

-----Original Message-----
From: William A. Korman
Sent: Friday, February 10, 2006 7:59 AM
To: 'David Breen'
Subject: FW: Thank you

Did I already forward this to you?

-----Original Message-----
From: Dianna Abdala
Sent: Monday, February 06, 2006 4:29 PM
To: William A. Korman
Subject: Re: Thank you

bla bla bla

----- Original Message -----

From: William A. Korman
To: 'Dianna Abdala'
Sent: Monday, February 06, 2006 4:18 PM
Subject: RE: Thank you

Thank you for the refresher course on contracts. This is not a bar exam
question. You need to realize that this is a very small legal
especially the criminal defense bar. Do you really want to start
pissing off more experienced lawyers at this early stage of your

-----Original Message-----
From: Dianna Abdala
Sent: Monday, February 06, 2006 4:01 PM
To: William A. Korman
Subject: Re: Thank you

A real lawyer would have put the contract into writing and not exercised
any such reliance until he did so.

Again, thank you.

----- Original Message -----
From: William A. Korman
To: 'Dianna Abdala'
Sent: Monday, February 06, 2006 12:15 PM
Subject: RE: Thank you

Dianna -

Given that you had two interviews, were offered and accepted the job
(indeed, you had a definite start date), I am surprised that you chose
an e-mail and a 9:30 PM voicemail message to convey this information to
me. It smacks of immaturity and is quite unprofessional. Indeed, I
rely upon your acceptance by ordering stationery and business cards with
your name, reformatting a computer and setting up both internal and
external e-mails for you here at the office. While I do not quarrel
with your reasoning, I am extremely disappointed in the way this played
out. I sincerely wish you the best of luck in your future endeavors.

- Will Korman

-----Original Message-----
From: Dianna Abdala
Sent: Friday, February 03, 2006 9:23 PM
To: William A. Korman
Subject: Thank you

Dear Attorney Korman,

At this time, I am writing to inform you that I will not be accepting
your offer.

After careful consideration, I have come to the conclusion that the pay
you are offering would neither fulfill me nor support the lifestyle I am
living in light of the work I would be doing for you. I have decided
instead to work for myself, and reap 100% of the benefits that I sew.

Thank you for the interviews.

Dianna L. Abdala, Esq.

06 March 2006

A Ray of Hope for Diabetics -- Times [clip]

Interesting article about a drug that slows digestion of food (making you feel fuller). It pointed out how doctors might be under pressure to prescribe off-label.

A Ray of Hope for Diabetics
Peter DaSilva for The New York Times
Byetta, a diabetes drug that was approved for marketing last April, has shown strong growth in the number of prescriptions written.
Published: March 2, 2006
The users call the drug Lizzie, the Big Brother or sometimes Gilly. On blogs they rave over its uncanny ability to melt away pounds, although some are wary of its side effects, which can include nausea and strange welts. The users are not fad dieters or methamphetamine addicts, but people with diabetes. And the subject of their rhapsodies is not a gray-market diet pill sold on late-night television but Byetta, a federally approved diabetes medicine, available only by prescription, whose popularity and sales have soared since its introduction last June....
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04 March 2006

Yale Information Society Project Lunches


Taking Snooping Further; Government Looks at Ways To Mine Databases -- Times [clip]

Thought this was an interesting article about the practical value of data mining. It seems that of the big applications of mining -- e.g. genomics, credit-card fraud, marketing, anti-terrorism -- mine is the only one that's open and not shrouded in secrecy...

Taking Snooping Further; Government Looks at Ways To Mine Databases
Published: February 25, 2006
PALO ALTO, Calif., Feb. 23 - A small group of National Security Agency officials slipped into Silicon Valley on one of the agency's periodic technology shopping expeditions this month.On the wish list, according to several venture capitalists who met with the officials, were an array of technologies that underlie the fierce debate over the Bush administration's anti-terrorist eavesdropping program: computerized systems that reveal connections between seemingly innocuous and unrelated pieces of information.The tools they were looking for are new, but their application would fall under the well-established practice of data mining: using mathematical and statistical techniques to scan for hidden relationships in streams of digital data or large databases.Supercomputer companies looking for commercial markets have used the practice for decades. Now intelligence agencies, hardly newcomers to data mining, are using new technologies to take the practice to another level...
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