csbio (biocs tumbled)

"So often people are working hard at the wrong thing. Working on the right thing is probably more..."

Wed, 30 Sep 2009 15:08:00 +0200

“So often people are working hard at the wrong thing. Working on the right thing is probably more important than working hard.”

- Caterina Fake, also pointing to Watson & Crick who discovered the structure of the DNA not working 24/7.

Handle non-UTF8 character in Perl

Thu, 06 Aug 2009 16:34:52 +0200

use Encode;
decode("utf8", $line, Encode::FB_HTMLCREF);

"Genes do not respect disciplinary boundaries."

Tue, 30 Jun 2009 17:14:50 +0200

“Genes do not respect disciplinary boundaries.”

- Lawrence Hunter in his talk at ISMB/ECCB 2009. Some genes that have been studied in certain clinical areas might be relevant in other areas as well, e.g. relaxin I.

"You can predict the neural activity in your brain when you think about a word based on how that word..."

Tue, 14 Apr 2009 22:58:00 +0200

“You can predict the neural activity in your brain when you think about a word based on how that word is used on the web.”

- Tom M. Mitchell in a most excellent Google Tech Talk: Brains, Meaning and Corpus Statistics.

migrate to Django 1.0 with sed

Thu, 05 Mar 2009 14:37:21 +0100

Doesn’t cover everything, but works for me:

find -name '*py' | xargs sed -i -e 's/maxlength/max_length/' -e 's/FloatField/DecimalField/'

Date regex for grep

Wed, 28 Jan 2009 16:02:13 +0100

(January|February|March|April|May|June|July|August|September|October|November|December) *([1-9]|[1-3][0-9]), *[12][0-9][0-9][0-9]|([1-9]|[1-3][0-9]) *(January|February|March|April|May|June|July|August|September|October|November|December) *[12][0-9][0-9][0-9]

This matches dates like:

12 October 1993
29 June 1982
31 March 2008
4 July 1980
April 21, 2008
February 12, 2007
March 31, 2008
May 27, 2002
November 16, 2006

If you drive too fast (and go over a hill)…

Mon, 26 Jan 2009 14:10:59 +0100

If you drive too fast (and go over a hill)…

…you’ll end up in the roof of a church [context]

Mon, 26 Jan 2009 14:10:00 +0100

…you’ll end up in the roof of a church

[context]

Test if file exists and is not empty (for Makefile)

Mon, 26 Jan 2009 14:07:41 +0100

In case some of your scripts in a Makefile silently fail (e.g. because they’re running on a cluster):

test -s file

(file exists, not empty)

stripping HTML tags in Python

Tue, 09 Dec 2008 18:31:47 +0100

from BeautifulSoup import BeautifulSoup
''.join(BeautifulSoup(page).findAll(text=True))

source: Euan

"Let’s put someone else’s money where your mouth it."

Fri, 28 Nov 2008 23:23:34 +0100

“Let’s put someone else’s money where your mouth it.”

- ibid.

"Physicists are really clever, unlike biologist."

Fri, 28 Nov 2008 23:19:00 +0100

“Physicists are really clever, unlike biologist.”

- Luca Turin (tongue in cheek) in an entertaining talk about the molecular mechanisms of the sense of smell. (Though I’d still call BS on his theory.)

Clean up whitespace in LaTeX

Wed, 26 Nov 2008 14:37:00 +0100

Correct whitespace around abbreviations and references (on a Mac). Don’t hyphenate “p-value(s)”.

sed -inplace -E -e 's/ \\(ref|cite)/~\\\1/g' -e 's/(e\.g\.|cf\.|et al\.|i\.e\.) /\1\\ /g' -e 's/([^{])(p-values?)([^}])/\1\\mbox{\2}\3/g' *.tex

"You can only do two things a day, one before lunch and one after."

Wed, 26 Nov 2008 13:48:43 +0100

“You can only do two things a day, one before lunch and one after.”

- Roland Krause, attributed to a German scientist.

Use Mac OS X 10.5 screen sharing for any VNC

Tue, 25 Nov 2008 15:14:51 +0100

Finder, Go: Connect to server

vnc://server:590x

where x is the display port

Ignore tweets from Friendfeed in Twitterific

Mon, 24 Nov 2008 16:30:00 +0100

defaults write com.iconfactory.Twitterrific \
    tweetTextFilter -string 'ff\.im'

Ugly hack to fold path names into file names

Mon, 24 Nov 2008 16:23:00 +0100

I want to go from ../www.fda.gov/medwatch/SAFETY/2003/03AUG_PI/Advair Diskus_PI.pdf to 2003_-_03AUG_PI_-_Advair Diskus_PI.pdf

I came up with this hack:

find ../www.fda.gov/ -name '*_PI*pdf' > names_a 

find ../www.fda.gov/ -name '*_PI*pdf' | \
sed -e 's/.*safety\/\(.*\)/\1/gi' -e 's/\//_-_/g'> names_b

paste names_a names_b | ~/src/misc/to_tsv.py -0 \' | \
xargs -l1 ln

(The to_tsv.py script is used to wrap the filenames in quotes.) I guess a quick Python script would have been better…

This is so funny, but… in German dialect. In (almost) my...

Tue, 18 Nov 2008 00:13:37 +0100

This is so funny, but… in German dialect. In (almost) my dialect.

prototype-based classification

Tue, 18 Nov 2008 00:08:12 +0100

(or: prototype-based active classification by Uni Konstanz)

"Take large unbiased data to find new components of well-studied pathways"

Mon, 17 Nov 2008 22:51:00 +0100

“Take large unbiased data to find new components of well-studied pathways”

- Nevan Krogan, 4th EMBO Conference: From Functional Genomics to Systems Biology, referring to Roguev et al. (Science, 2008)