Marshall's IT Plan for Janelia Farm -- Bio IT World

Might be useful to think about in terms of future high-performance computing purchases. See extracted snippets below.

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http://www.bio-itworld.com/issues/2006/oct/janelia-farm/
Oct. 2006 
Marshall's IT Plan for Janelia Farm
By  Kevin Davies
Oct. 16, 2006 |  Driving north from Washington Dulles Airport towards the Potomac River, it's easy to miss Janelia Farm. The only road sign faces the opposite direction, belatedly guiding lost taxi drivers retracing their route in search of the campus. Outside a makeshift hut in the middle of a construction site, the security guard waves a visitor's taxi down a long, winding dirt road appropriately named Helix Drive. Around a corner, however, the scene changes dramatically.....
The data center is completely fiber and boasts a multi 10-Gb network. "That's a constant question," says Peterson. "Am I going to get the data to my desktop fast? If I can't, then I'm going to start having people buying their own supercomputers and sliding it under their desk. I don't want that - it's not cost effective, and you can't manage it." He adds: "We're going to have very high-resolution graphics, and people are going to see it very fast. Just one set of microscopes will be generating 500 GB data/day. 24x7x365."....
With some 1,200 64-bit Intel Xeon processors in all, cooling was a major concern. Peterson explains: "We ended up going with Dell and Xeons, which are hot, but we did a calculation: given the price we got with them and given the increased power requirements, it still came in price effective. Having said that, we're very interested in the new generation of Intels and obviously AMD." ...
Everything in the data center is designed to be ripped out and replaced if needed. "The idea is to design infrastructure that is cost effective and easy to replace. We try to be open source - everything is Linux-based, low stress. It helps hugely with the maintenance."....
Peterson selected three tiers and 150 TB of spinning disk storage from EMC. "We started small... seriously!" Peterson smiles. Tier 1 is 30 TB of SAN. Tier 2 is 70 TB of NAS. Tier 3 - the archive - consists of more NAS on disk plus tape. Peterson wants to expand tier 3. "We have capability of over 1 PB of tape," says Peterson. "I can grow to multi petabytes without adding another cabinet." He opens one of a long row of EMC cabinets to show rows of vacant racks....

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements -- Nature Biotech

Might be good to use as benchmark to judge tiling arrays and protein chips

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16964229&query_hl=5&itool=pubmed_docsum
Nat Biotechnol. 2006 Sep;24(9):1151-61.
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Great Example of Spring Minimization

http://java.sun.com/applets/jdk/1.4/demo/applets/GraphLayout/example2.html

original URL
http://www.javasoft.com/applets/jdk/1.0/demo/GraphLayout/example2.html

How to get on the Farmington Canal Heritage Trail in Hamden

How to get on the Farmington Canal Heritage Trail in Hamden

Official Info.
http://www.ct.gov/dot/cwp/view.asp?a=1390&q=259678
Hamden – Farmington Canal Heritage Trail
http://www.ct.gov/dot/LIB/dot/documents/dbikes/024.pdf
Cheshire – Farmington Canal HeritageTrail
http://www.ct.gov/dot/LIB/dot/documents/dbikes/026.pdf
http://www.railserve.com/jump/jump.cgi?ID=8240

Useful maps
Looking at map on
http://www.farmingtoncanal.org/
Looks like approximate entry point is at:
http://maps.google.com/maps?q=41.365182,-72.917729&spn=0.025348,0.05446

Some Distances
Farmington Canal Greenway:
Simsbury-Avon section; 8 mi
Avon-Farmington section; 2.3 mi
Hamden-Cheshire section; 8 mi

Global variation in copy number in the human genome -- Nature

Assume everyone has seen this. Might be nice to start using this data.

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http://www.nature.com/nature/journal/v444/n7118/abs/nature05329.html
Nature 444, 444-454 (23 November 2006)
Global variation in copy number in the human genome
Richard Redon1, Shumpei Ishikawa2,3, Karen R. Fitch4, Lars Feuk5,6, George H. Perry7, T. Daniel Andrews1, Heike Fiegler1, Michael H. Shapero4, Andrew R. Carson5,6, Wenwei Chen4, Eun Kyung Cho7, Stephanie Dallaire7, Jennifer L. Freeman7, Juan R. González8, Mònica Gratacòs8, Jing Huang4, Dimitrios Kalaitzopoulos1, Daisuke Komura3, Jeffrey R. MacDonald5, Christian R. Marshall5,6, Rui Mei4, Lyndal Montgomery1, Kunihiro Nishimura2, Kohji Okamura5,6, Fan Shen4, Martin J. Somerville9, Joelle Tchinda7, Armand Valsesia1, Cara Woodwark1, Fengtang Yang1, Junjun Zhang5, Tatiana Zerjal1, Jane Zhang4, Lluis Armengol8, Donald F. Conrad10, Xavier Estivill8,11, Chris Tyler-Smith1, Nigel P. Carter1, Hiroyuki Aburatani2,12, Charles Lee7,13, Keith W. Jones4, Stephen W. Scherer5,6 and Matthew E. Hurles

Machine Over Man: Stock Pickers' Woes -- WSJ

Appears indexing maybe back in fashion....

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Machine Over Man: Stock Pickers' Woes
By IAN MCDONALD
November 6, 2006; Page R1
Stock pickers' recently healed egos are about to be battered anew....
http://online.wsj.com/article/SB116276713084613902.html

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The Word on Warranties: Don’t Bother -- NY Times

What I always thought...

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http://www.nytimes.com/2006/11/01/technology/circuits/01warr.html
After the Sale
The Word on Warranties: Don’t Bother
By DAVID S. JOACHIM
Published: November 1, 2006
IT may be tempting to buy extended warranties with all those high-tech gadgets on your holiday list, but the experts say they are almost always a waste of money.

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Gaming the Search Engine, in a Political Season -- NY Times

Interesting article pointing to the future of misinformation

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http://www.nytimes.com/2006/11/06/business/media/06link.html
Gaming the Search Engine, in a Political Season
By TOM ZELLER Jr.
Published: November 6, 2006
A GOOGLE bomb — which some Web gurus have suggested is perhaps better called a link bomb, in that it affects most search engines — has typically been thought of as something between a prank and a form of protest. The idea is to select a certain search term or phrase (“borrowed time,” for example), and then try to force a certain Web site (say, the Pentagon’s official Donald H. Rumsfeld profile) to appear at or near the top of a search engine’s results whenever that term is queried.....

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A loss-of-function RNA interference screen for molecular targets in cancer -- Nature

Interesting datasets related to cancer and phenotypes

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16572121&query_hl=6&itool=pubmed_docsum
Nature. 2006 May 4;441(7089):106-10. Epub 2006 Mar 29.
A loss-of-function RNA interference screen for molecular targets in cancer.
Ngo VN, Davis RE, Lamy L, Yu X, Zhao H, Lenz G, Lam LT, Dave S, Yang L, Powell J, Staudt LM.

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The Connectivity Map: using gene-expression signatures to connect

Interesting dataset related to cancer and phenotypes

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17008526&query_hl=4&itool=pubmed_docsum
Science. 2006 Sep 29;313(5795):1929-35.
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP,
Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ,
Clemons PA, Wei R, Carr SA, Lander ES, Golub TR.

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Letter ("Programming Pedigrees") responding to "The Semicolon Wars" -- American Scientist

Resurrected one of my favorite letters, which might be good to follow up on. Viz: :
I read with great interest Brian Hayes's recent column "The Semicolon Wars" on the genealogy of computer languages (Computing Science, July-August). I was struck by the first figure that shows how many well-known languages are related to each other in a tree-like structure. Mr. Hayes carefully compared the development of computer languages to that of spoken languages. This is, of course, quite appropriate. However, another illuminating comparison is to the development and evolution of genomes in biology.
The genome has often been compared to an organism's operating system, and in this sense, its underlying genetic coding is the ultimate computer language. The triplet codons in the literal genetic code have not changed much over time. However, the specific features they encode in different genomes have changed dramatically since life first appeared.
One of the nice things about biology, moreover, is that the main mechanisms underlying this evolution can be studied experimentally. It is believed that the genome evolves through a variety of processes duplicating and copying chunks of DNA, and then further variation happens to these copies. One also sees, most often in bacteria, whole genetic elements horizontally transferred from one organism to another.
The parallels to computer languages in the operation of these mechanisms are quite strong: In a specific lineage of languages (such as that for Algol60, C and Java) one sees the duplication and variation of basic control structures for such items as loops and subroutines, and horizontal transfer of new structures (such as the object-oriented constructions from Simula67).

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Citation of Letter:
Programming Pedigrees
http://www.americanscientist.org/template/AssetDetail/assetid/54089
Volume 94, Number 6 (November-December 2006)
Mark Gerstein
Yale University
New Haven, CT

Article Commented on:
http://www.americanscientist.org/template/AssetDetail/assetid/51982
The Semicolon Wars
Every programmer knows there is one true programming language.
A new one every week
Brian Hayes
American Scientist, July-August 2006
If you want to be a thorough-going world traveler, you need to learn 6,912 ways to say "Where is the toilet, please?" That's the number of languages known to be spoken by the peoples of planet Earth, according to Ethnologue.com. If you want to be the complete polyglot programmer, you also have quite a challenge ahead of you, learning all the ways to say: printf("hello, world\n") ;.....
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The Thin Pill -- Wired

Interesting article on how medicines are labelled and targeted

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Issue 14.10 - October 2006
WIRED magazine
The Thin Pill
http://wired.com/wired/archive/14.10/thin.html
FOR PATIENTS, disease puts a name to an affliction. It answers that question we all face at one time or another: What's the matter with me? If there is a clear and precise explanation for what's wrong, then surely there is an equally clear way to get better.....

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A limited universe of membrane protein families and folds -- Prot Sci

Yang Liu et al. part II

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=16815920&dopt=Abstract
Protein Sci. 2006 Jul;15(7):1723-34. 
A limited universe of membrane protein families and folds.
Oberai A, Ihm Y, Kim S, Bowie JU.

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Cyberface: New Technology That Captures the Soul -- NY Times

Thought this was an interesting fusion of science and art -- biophysicists go to Hollywood.  Got to check out the video.

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http://www.nytimes.com/2006/10/15/movies/15waxm.html
Cyberface: New Technology That Captures the Soul
By SHARON WAXMAN
Published: October 15, 2006
THERE’S nothing particularly remarkable about the near-empty offices of Image Metrics in downtown Santa Monica, loft-style cubicles with a dartboard at the end of the hallway. A few polite British executives tiptoe about, quietly demonstrating the company’s new technology....

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Structural biology: proteins flex to function -- Nature

Nice cartoon of protein motions, related to order-disorder transitions. Might be useful in expanding classification.

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16267540&query_hl=2&itool=pubmed_docsum
Nature. 2005 Nov 3;438(7064):36-7.
Structural biology: proteins flex to function.

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http://zoho.com

Zoho might be nice in a similar way to Google Spreadsheet.

A Letter in response to "Inspired by the Cell, With Mitochondrial

Here's the letter I wrote in response to this article (which was never published):
I read with great interest the recent article in Science Times about the new biomedical research center in China with architecture inspired by the cell. It's a great thing having man-made creations inspired by fundamental molecular and cellular architecture. It's ironic that this hasn't happened to a greater degree. Many of the shapes in scientific structures are particularly interesting. Good examples would be the famous double helix of DNA and lipid bilayer of the cell membrane. Moreover, a key aspect of post-modern architecture is referring to and playing with evocative shapes and forms borrowed from non-architectural contexts. Thus, the irony in why famous pieces of post-modern architecture -- such as the AT&T building in New York, which makes reference to a grandfather clock or a Chippendale highboy -- seem to ignore the fundamental designs of nature.

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http://www.nytimes.com/2006/09/12/science/12find.html
FINDINGS; Inspired by the Cell, With Mitochondrial Pools
Article Tools Sponsored By
By JOHN SCHWARTZ
Published: September 12, 2006
The blob is coming to Chengdu. A biomedical research institute in Chengdu,
China, is planning to show true commitment to scientific principles by erecting
an innovative building inspired by cells. Bulges on the surface are meeting
rooms and are intended to represent the proteins embedded in a cell membrane.
The interior pools, shaped like mitochondria, border on the surreal....

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Connecting the Dots -- Am. Sci.

Nice social network analogies. In particular, discussion of Granovetter paper relates nicely to ‘socio-affinity’ index in Gavin et al. (2006) [http://www.nature.com/nature/journal/v440/n7084/abs/nature04532.html]

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September-October 2006
Connecting the Dots
Can the tools of graph theory and social-network studies unravel the next big plot?
Brian Hayes
http://www.americanscientist.org/template/AssetDetail/assetid/53062
In the five years since that wrenching Tuesday morning when hijacked aircraft sliced into the World Trade Center and the Pentagon, Americans have been living with a new undercurrent of worry and mistrust. Naturally, there's fear of further attacks. But there's also concern that measures taken to forestall such attacks could erode traditional rights and liberties. In recent months, controversy has erupted over reports that government agencies are monitoring Internet and telephone communications as well as financial transactions. Some of the surveillance programs are said to be sifting through gigantic data sets, scanning for patterns that might reveal criminal intent or activity....

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http://babyadenine.blogspot.com/

A baby named for a nucleic acid -- http://adenine.org/
Based on http://en.wikipedia.org/wiki/Adenine , there are many potential
derivative names here: AMP, Deoxyadenosine, &c.

Scenic Routes Bike Routes -- NY Magazine

Thought this was interesting... includes bike trip to Bear Mountain and a route through DUMBO.

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Brooklyn Waterfront
http://newyorkmetro.com/nymetro/urban/strategist/everything/bikes/12336/index1.html
Approximately 24 miles
1. Start at City Hall. Head across Park Row onto the bridge.
2. Take first right off the bridge onto Tillary Street.
3. Left on Cadman Plaza West, quick right on Clark Street. Left on Henry Street, down about a mile.
4. Right on Sackett Street, three blocks.
5. Left on Van Brunt Street, down to the end.
6. Walk bike at Beard Street Warehouse.
7. Go back up Van Brunt Street a block, then left on Van Dyke Street to the end.
8. Take sidewalk to avoid cobblestones.
9. Walk bike down Valentino Pier. Exit on Coffey Street, two blocks.
10. Left on Van Brunt Street.
11. Right on Union Street, quick left on Columbia Street.
12. Right on Congress Street, two blocks.
13. Left on Hicks Street, parallel to highway.
14. Left on Montague Street, to the Promenade.
15. Right on Promenade, walk bike to end.
16. Left on Columbia Heights, down the hill to Fulton Landing.
17. First left on Water Street, two blocks against traffic.
18. Left on Washington Street, quick right on Plymouth Street.
19. Enter park on left for a block, under the Manhattan Bridge.
20. Left back onto Plymouth Street.
21. Right on Hudson Avenue, then merge onto Navy Street for a block.
22. Right on Sands Street, down toward Manhattan Bridge.
23. Follow signs to the bridge entrance across the street on the left.
24. Coast down to the Manhattan exit, cross onto Canal Street.
25. Take Canal Street down to the Broadway subway station.

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