Archive for the ‘San Diego’ Category

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.


Dreams End

July 1, 2007

Eleven days of climbing, swimming, writing, dancing, and laughing: one of the best vacations of my life.

TRAGEDY AVERTED: In Kings Canyon National Park, a recent rockslide transformed my easy class-2 route into a treacherous class-4 climb. Potluck Pass was particularly unsafe. On several occasions, I lowered my pack with rope and free-descended exposed granite faces.  I was most terrified when I tumbled off a ledge and broke my trekking pole. In hindsight, this trip was reckless! The route from Dusy Basin to Palisade Lakes is not advisable to people without helmets and training. (Pictured below: the price of bad decision-making).

WONDERFUL PEOPLE: After my dance with danger, I vacated to San Diego. Annie and Erik are generous hosts, and leaving was difficult. I wish I could remain in the fantasyland of beach trips, graduate student parties, and perfect weather. . . but dreams end.

  • Annie never fails to make me smile. She has a talent for building empires.
  • Erik and his friends are beyond superlatives, but here are a few: gregarious, provocative, and perspicacious.
  • I’m not sure which is more awesome: Grant’s endless supply of positive energy, or his coiffed hair.

(Pictured below: Erik rocks the summit of Mount San Jacinto.)

(Pictured below: My MacBook sports a label for Grant and Erik’s homebrew: Government Standoff Ginger IPA. Photo credit to Erik Pukinskis).