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Showing posts from May, 2009

Installing Ruby on Mac OS X

ftp ftp://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.1-p129.tar.gz
tar -xvf ruby-1.9.1-p129.tar.gz
cd ruby-1.9.1-p129
./configure --enable-shared --enable-pthread CFLAGS=-D_XOPEN_SOURCE=1
make -j4
sudo make install


Installs in /usr/local/bin, make sure to point path there

Those geneticists and their Excel

Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

If you are too lazy to get to the punchline:

"MatchMiner [1] and GoMiner [2] are two bioinformatics program packages we
published recently in another Biomed Central Journal, Genome Biology. When we
were beta-testing those programs on microarray data, a frustrating problem
occurred repeatedly: Some gene names kept bouncing back as "unknown." A little
detective work revealed the reason: Use of one of the research community's most
valuable and extensively applied tools for manipulation of genomic data can
introduce erroneous names. A default date conversion feature in Excel (Microsoft
Corp., Redmond, WA) was altering gene names that it considered to look like
dates. For example, the tumor suppressor DEC1 [Deleted in Esophageal Cancer 1]
[3] was being converted to '1-DEC.' Figure 1 lists 30 gene names that suffer an
analogous fate."

Sourceforge nominations

My choices:
- Matplotlib

- Inkscape

Function definitions in scripts

My MATLAB origins betrayed me. I kept thinking - you can't put function definitions in a script in Python. Man, I gotta write a module and THEN a script that calls the module? But, in Python, you can include function defs in a 'script'. So the following works perfectly well:

def func1():
print '1'

def func2():
print '2'

func1()


Take that MATLAB.