11 December 2006

Cycling Around NYC

Top of Manhattan

Route on Google maps

Summary Data
Total Time (h:m:s) 3:41:08 10:46 pace
Moving Time (h:m:s) 2:33:33 7:28 pace
Distance (mi ) 20.53
Moving Speed (mph) 8.0 avg. 24.5 max.
Elevation Gain (ft) +7,875 / -8,006
Avg. Heart Rate 74 bpm Zone 0.8
Temperature (°F) 50.4°F avg. 51.8°F high
Wind Speed ( mph) S 3.7 avg. S 5.8 max.

Central Park to Prospect Park

Route on Google maps

Summary Data
Total Time (h:m:s) 5:09:31 11:24 pace
Moving Time (h:m:s) 4:02:56 8:57 pace
Distance (mi ) 27.14
Moving Speed (mph) 6.7 avg. 49.2 max.
Elevation Gain (ft) +2,803 / -2,833
Avg. Heart Rate 84 bpm Zone 0.9
Temperature (°F) 63°F avg. 64.4°F high
Wind Speed ( mph) SSE 6.2 avg. SSE 8.1 max.

Up West Side to NJ

Route on Google maps

Summary Data
Total Time (h:m:s) 3:12:13 16:19 pace
Moving Time (h:m:s) 1:38:16 8:20 pace
Distance (mi ) 11.78
Moving Speed (mph) 7.2 avg. 17.6 max.
Elevation Gain (ft) +4,407 / -4,375
Avg. Heart Rate 83 bpm Zone 0.9
Temperature (°F) 45.8°F avg. 46.4°F high
Wind Speed ( mph) N 1.9 avg. N 5.8 max.

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10 December 2006

Metcalfe's Law is Wrong -- IEEE Spectrum

Thought this social networking analogy gave some nice intuition about the power-law network structures.

Metcalfe's Law is Wrong
By Bob Briscoe, Andrew Odlyzko, and Benjamin Tilly
Communications networks increase in value as they add members—but by how much? The devil is in the details

Of all the popular ideas of the Internet boom, one of the most dangerously influential was Metcalfe's Law. Simply put, it says that the value of a communications network is proportional to the square of the number of its users....The foundation of his eponymous law is the observation that in a communications network with n members, each can make (n–1) connections with other participants. If all those connections are equally valuable—and this is the big "if" as far as we are concerned—the total value of the network is proportional to n(n–1), that is, roughly, n^2.... We propose, instead, that the value of a network of size n  grows in proportion to n log(n)....To understand how Zipf's Law leads to our n log(n) law, consider the relative value of a network near and dear to you—the members of your e-mail list. Obeying, as they usually do, Zipf's Law, the members of such networks can be ranked in the same sort of way that Zipf ranked words—by the number of e-mail messages that are in your in-box. Each person's e-mails will contribute 1/k to the total "value" of your in-box, where k is the person's rank. The person ranked No. 1 in volume of correspondence with you thus has a value arbitrarily set to 1/1, or 1. (This person corresponds to the word "the" in the linguistic example.) The person ranked No. 2 will be assumed to contribute half as much, or 1/2. And the person ranked kth will, by Zipf's Law, add about 1/k to the total value you assign to this network of correspondents. That total value to you will be the sum of the decreasing 1/k values of all the other members of the network. So if your network has n members, this value will be proportional to 1 + 1/2 + 1/3 +… + 1/(n–1), which approaches log(n). More precisely, it will almost equal the sum of log(n) plus a constant value. Of course, there are n-1 other members who derive similar value from the network, so the value to all n of you increases as n log(n). Zipf's Law can also describe in quantitative terms a currently popular thesis called The Long Tail.....

To Probe Further
David P. Reed argues for his law in "The Sneaky Exponential" on his Web site at http://www.reed.com/Papers/GFN/reedslaw.html.
Several additional quantitative arguments are made for the n log(n) value for Metcalfe's Law on the authors' Web sites at http://www.cs.ucl.ac.uk/staff/B.Briscoe and http://www.dtc.umn.edu/~odlyzko.
Chris Anderson's article "The Long Tail" was featured in the October 2004 issue of Wired. Anderson now has an entire Web site devoted to the topic at http://www.thelongtail.com.
An article in the December 2003 issue of IEEE Spectrum, "5 Commandments," which can be found at http://www.spectrum.ieee.org/dec03/5com, discusses Moore's and Metcalfe's laws, as well as three others: Rock's Law ("the cost of semiconductor tools doubles every four years"); Machrone's Law ("the PC you want to buy will always be $5000"); and Wirth's Law ("software is slowing faster than hardware is accelerating").

03 December 2006

cycling fast loops in Central Park

4 fast (for me) loops in Central Park. Some stats and images below.

route on Google Maps
Total Time (h:m:s) 2:08:16 5:08 pace
Moving Time (h:m:s) 1:55:04 4:36 pace
Distance (mi ) 24.96
Moving Speed (mph) 13.0 avg. 30.9 max.
Avg. Heart Rate 133 bpm
Temperature (°F) 53.6°F avg. 53.6°F high
Wind Speed ( mph) WNW 8.0 avg. WNW 12.6 max.


Cycling Around New Haven

Route on Google Maps [static cached image]
Elevation Profile

Total Time (h:m:s)7:36:5110:54 pace
Moving Time (h:m:s)4:52:576:59 pace
Distance (mi )41.91
Moving Speed (mph)8.6 avg.20.0 max.
Elevation Gain (ft) +3,583 / -3,586

Avg. Heart Rate88 bpm Zone 1.0

Temperature (°F)48°F avg.57.2°F high
Wind Speed ( mph)SSE 5.1 avg.SSE 8.1 max.


25 November 2006

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.

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

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


original URL

How to get on the Farmington Canal Heritage Trail in Hamden

Official Info.
Hamden – Farmington Canal Heritage Trail
Cheshire – Farmington Canal HeritageTrail

Useful maps
Looking at map on
Looks like approximate entry point is at:

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


24 November 2006

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

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

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


13 November 2006

Machine Over Man: Stock Pickers' Woes -- WSJ

Appears indexing maybe back in fashion....

Machine Over Man: Stock Pickers' Woes
November 6, 2006; Page R1
Stock pickers' recently healed egos are about to be battered anew....

ooo[clip]ooo ooo[general]ooo ooo[finance]ooo

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

What I always thought...

After the Sale
The Word on Warranties: Don’t Bother
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.

ooo[clip]ooo ooo[computers]ooo ooo[purchases]ooo

07 November 2006

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

Interesting article pointing to the future of misinformation

Gaming the Search Engine, in a Political Season
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.....

ooo[clip]ooo ooo[computers]ooo ooo[search]ooo

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