Archive for August, 2007

Blog Day 2007

August 31, 2007

Apparently today is Blog Day, a day in which we write about five new/favorite blogs.

In no particular order:

(1) “The Tree of Life” by Jonathan Eisen. Jonathan is on faculty at UC Davis, researching evolutionary biology. He recently co-authored this textbook, which I’m currently reading (and very much enjoying).

(2) PLoS Computational Biology. This isn’t really a blog, per se. Actually, it’s just the RSS feed for the journal of the ISCB. So why did I pick this “blog”? Answer: The Public Library of Science (PLoS) is a great example of open-access research. Because PLoS is open-access, I can read scientific publications FOR FREE in Google Reader, instead of paying monthly/annual subscriptions.

(3) “Imbibable: the world’s most comprehensive beverage review source”, by Abi Jones. Abi’s latest consumer blog is basically hilarious. Abi has a talent for combining practical consumer information with witty humor. Other Abi Jones projects include: Heat Eat Review, The Impulse Buy, and Stupid Wedding Crap.

(4) “A Softer World”. Sometimes humorous, sometimes painful, always inventive.

(5) “TracyFood”, by Tracy van Cort. Tracy cooks delicious food, and writes about it.

Enjoy. Happy Blog Day 2007.


Spectral Network Analysis

August 29, 2007

This video is exciting:

Pavzner and his team address the challenge of determining a protein’s sequence, given mass spectrometry data. This problem is challenging because every protein undergoes translational modifications, and therefore mass-specs actually measure proteins which deviate (slightly) from their non-translated nucleotide sequences.

An unsolved challenge is to correctly infer a protein’s sequence, given mass-spec data. However, we CAN compare mass-specs against a database of existing (and known) mass-specs in order to guess the sequences. This process is computationally expensive because it requires a linear search of the database for every queried mass-spec search key.

Pavzner present a more efficient algorithm for “guessing” a protein’s sequence, given its mass-spectrum. His technique involves constructing a network of spectral data, and then using that network as the basis for a search. This is remarkably faster than traditional database searches. Pavzner, et al, apply this technique to whole-genome spectrometric data, and yield promising results.

My obscure notes:

17:00 – Why is the signal-to-noise ratio reduced “six-fold” ?

18:01 – Look-up reference for “anti-symmetric pass approach” to solving an alignment between two sequences of unequal length. Can we use this storage technique for other information domains: phylogenetic trees? Electroencephalographic data?

28:07 – The use of “snake venom” makes any science project sound cool.

The Power of Myth

August 21, 2007

Joseph Campbell (1904-1987) was a living encyclopedia of world mythology.  He is best known for “The Hero with a Thousand Faces,” “The Masks of God,” and other writing.  Campbell’s work illuminates the spiritual common-ground between all world religions.  As Joseph Campbell said, “if you want to understand Jesus, you have to go beyond Jesus.  If you want to understand Buddha, you have to go beyond Buddha. . . ”

Before Campbell’s death, he filmed six conversations with Bill Moyers.  The episodes (linked below) were aired on PBS.  If you don’t have six hours to spare, my favorite episodes are #4 and #6.  Enjoy.

Episode 1 of 6: introduction

Episode 2 of 6: the message of the myth

Episode 3 of 6: the first storytellers

Episode 4 of 6: sacrifice and bliss

Episode 5 of 6: love and the goddess

Episode 6 of 6: masks of eternity

Mount Tallac und Ebbetts Spitze

August 19, 2007


Bernhard und ich kletterten Tallac Berg und Spitze Ebbetts. Fotos können hier angesehen werden.

Obscure notes for the future:

  • We reached the Tallac summit in two hours, fifteen minutes. That’s pretty fast.
  • Highway 4 is a single lane over Ebbett’s Pass: scenic, but very slow
  • The Pacific Crest Trail connects with the eastern parking lot at Ebbett’s Pass (not the western lot)

Playing with new themes

August 8, 2007

More improvisation. The MP3 file is here.

(To avoid excessive traffic from web-bots: user=sharing, password=isgood)

Voices in my head

August 7, 2007

Two minutes of improvisation. . .

A high-quality piano, but a low-quality microphone.

Click here for the MP3.

(To reduce traffic from web-bots: user=sharing, password=isgood)

ART version 1.4

August 6, 2007

A new version of ART (an ancestral reconstruction tool) is available for release. This software package is a labor of love, and lately consumes my “spare” time. I have big plans for ART (including a web interface and visualization tools), but in the meantime this project is stable and functional.

What does ART do?

  • ART wraps CodeML into an easier-to-use and error-safe tool.
  • ART calculates the maximum a posteriori (MAP) ancestor. The MAP concept is a new statistical practice currently being developed in Joe Thornton’s lab.
  • ART manages your phylogenetic reconstruction projects in a SQL database.

Coming up for air, #3

August 5, 2007

I spent the night on Clouds Rest with Isaac. Sunset was sublime; Sunrise was transcendent. For more photos, click this image:

Obscure notes for the future:

  • There is good camping along the final ridge to the summit. There is also good camping on the summit itself.
  • Before the summit, the last water source is about 1/4 mile after “the pond.”
  • The summit can be windy – bring a windscreen for the stove.

Introduction to Computational Proteomics, latest issue of PLoS

August 1, 2007

Here is a TERRIFIC article in the recent issue of PLoS:

“Introduction to Computational Proteomics” by Jacques Colinge and Keiryn L. Bennett.

I like this article because it summarizes a large body of research, and it’s written for a non-CompBio audience. Introductory articles in CompBio are rare. Well-written introductory articles are even rarer. Enjoy.