Linxe's eye

Phoronix had prepared a second test, now is testing also Fedora 7 to 10 and compare the results with the big U. In my consideration, Fedora became slow in some parts, but there are some results showing big problems with the U like this: So, if you improve your user-friendly don't means you need better hardware every release. Testing many version of a same distro can show its evolution. Whatever, I'm happy with my Mandriva 2009.

Last day, I need to download some sequences from NCBI GenBank, I have a list of ids, typically I used BioPerl to connect and get the fasta sequence of each one, with a code like this: #!/usr/bin/perl -w use strict; use Bio::DB::GenBank; my $gb = new Bio::DB::GenBank; open F, "gene_list" or die "cannot open genes_list\n"; while (<F>) { chomp; my $seq = $gb->get_Seq_by_id($_); print $seq->seq; } Because Broadcast with Mac OS X 10.5.X cannot compile the BioPerl modules (I found many problems when you try to compile from source code, because many dependencies are broken). So, I take a look to BioPython , install it (with some warnings and missing optional packages), and use the next script: #!/ usr /bin/python from Bio import Entrez Entrez .email = "mymail@something.org" # Always tell NCBI who you are f = open("genes_list", "r") while True: myid = f. readline () if not myid : break handle = Entrez . efetch (db="n...

I will not comment this article, I still want to conserve my U-emo-friends, so please read the original in Phoronix: Ubuntu 7.04 to 8.10 Benchmarks: Is Ubuntu Getting Slower? Yes, but still looks nice in brown/gold ;)

Are my computers happier? Source: Abstruse Goose

This week in one of most famous scientific journals has been published this report: Camara CG, Escobar JV, Hird JR, Putterman SJ, "Correlation between nanosecond X-ray flashes and stick–slip friction in peeling tape.", Nature 455, 1089-1092 (23 October 2008) | doi:10.1038/nature07378 http://www.nature.com/nature/journal/v455/n7216/abs/nature07378.html Abstract: Relative motion between two contacting surfaces can produce visible light, called triboluminescence. This concentration of diffuse mechanical energy into electromagnetic radiation has previously been observed to extend even to X-ray energies. Here we report that peeling common adhesive tape in a moderate vacuum produces radio and visible emission, along with nanosecond, 100-mW X-ray pulses that are correlated with stick–slip peeling events. For the observed 15-keV peak in X-ray energy, various models give a competing picture of the discharge process, with the length of the gap between the separating faces of the tape b...

From: http://hackaday.com/2008/10/20/bjork-teaches-you-about-electronics/

Bioinformatics Zen had released the results in a text-file of the Bioinformatic Career Survey 2008 , the survey include data from ~650 people from academia and industry, it's interesting to take a look in the data, I summarize this in some graphics: Career Background Bioinformatics area Computer Language

Do you know what is a Perl Golf problem? It's a general problem formulated and you try to resolve with a minimal number of characters in a perl script, who writes less win. Some times is a good habit to see, admire and think in this beautiful pearls. Commonly there are a lot in the Perl Monks website. Today I was looking for a more simple and effective subroutine to translate a DNA/RNA sequence into the corresponding peptide version using the typical genetic code, I used the typical solution with a hash storing the code and call the sequence in block with substr or pop/shift. I found this solutions in a Perl Golf challenge : # Typical solution hashing the codes: sub f0 { #by tadman my %g = ( # . - Stop 'UAA'=>'.','UAG'=>'.','UGA'=>'.', # A - Alanine 'GCU'=>'A','GCC'=>'A','GCA'=>'A','GCG'=>'A', # C - Cysteine '...

Last week, Mandriva released the 2009 version, because I'm a mandriva fan, immediately I downloaded the One- KDE ISO, burn it and installed in my old HP laptop ( PIII 1 Ghz , 256 Mb RAM, 20 Gb HD , Wi - fi card). The LiveCD run perfectly, show me the new KDE 4 desktop and made a clean install without problems (many others Linux LiveCD have problems just to boot in old hardware like this). I like to use a different partition for the /home, so my partition table looks like: / 5GB swap - 512 MB / geexbox - 100MB /home - rest Yes, I want to install the GeeXBoX , it's great for watch movies. Some good points are the new design, fast boot, the best hardware detection and many friendly menus to configure all. Remarkable is the improved URPMI , it is fast, now support simultaneous package download and the best part is the --auto-orphans option, this check for unused or broken packages and suggest uninstall , cleaning the systems even the kernel, removing unused drivers or m...

Inspired by this article " al 3 x's rules for computing happiness " of Alex Payne, I want to extend this theme to my areas: bioinformatic , computational biology and systems biology. Software Use as little software as possible. Use software that does one thing well. Do not use software that does many things poorly. Try to understand how a software works before to use. Do not use web applications that should be desktop applications. Do not use desktop applications that should be web applications. Do not use software that isn't made specifically for your operating system. Use a plain text editor that you know well. Not a word processor, a plain text editor. Do not use your text editor for tasks other than editing text. Do not use software that's unmaintained. Do not use software unpublished. Try to use Open Source code. Be in touch with the developers or users in forums, mail-list, ... If you don't have a formal IT department, learn to maintain your systems....

Last day I received this email, fortunately the spam engine detected it, but is different the content, other times I had receive similar emails for proprietary software, specially MS Office Suite, which is so expensive and many people want a cheap (an illegal) version. But this time the reference is a Free Software office suite, OpenOffice which in few days will release the new version 3.0. This is the infamous message: From Suite 2009 To XXXXXX@XXXXXX.XXX Date October 6th 2008 18:55 Subject Download Open Office 2009 Open Office Suite 2009 Open, Create & Edit Your Files Download Office Suite 2009??Here Edit Word, Excel & Power Point files- 100% MS Office Compatible. Read and write PDF files just like Adobe. Here's how to download Open Office 2009: 1. Go to: Download Page 2. Download Open Office 2009 3. Receive access immediately This software package is the best way to edit your documents. Publish all of your documents online in the HTML format. Thank you for choosing ...

Today I install 2 more add-ons, both are to improve my GMail accounts. 1. Better Gmail 2 . This utility modify a little (pimp probably) the normal view and use of Gmail, attachments are symbolic images describing the content, colorize the pointed message and more options are available. An excellent job of Gina Trapani from LifeHacker.com https://addons.mozilla.org/en-US/firefox/addon/6076 2. Gmail S/MIME . Talking about privacy, this add-on allow us to sign and crypt messages, a must-have for every-one, you cannot know who's watching in the upper cloud. https://addons.mozilla.org/en-US/firefox/addon/592