Linxe's eye

The old battle of Mac vs PC, in this video the fight is with Transformers laptops ... cool concept. Link: http://www.youtube.com/watch?v=uLbJ8YPHwXM By the way, the Linux Foundation has a contest for "I'm Linux" tv-commercial, full rules here .

From: http://xkcd.com/519/

So do you have some PS3 and you're boring of play and watch Blue-Ray movies? You must know the PS3 is the most accessible CELL- based machine, why not use this computer problem in other areas beyond entrainment . In this PS3 ClusterGuide you can build step-by-step your own cluster with PS3, the receipt: 1. Take some PS3. 2. Interconnect it in a LAN. 3. Install Fedora PPC in each one. 4. Install cluster utils . 5. Learn to code in CELL- SDK for a better experience and performance . I accept some PS3 for scientific probes ... really I just want one to play ...

This presentation is a good think-deep-later for anyone in this area, some quotes are fantastic and many points are well focused, others I can't agree. Must watch and think. The Seven Deadly Sins of Bioinformatics View SlideShare presentation or Upload your own. (tags: ismb web service )

DNASIS SmartNote is an on-line service for bioinformatic analysis integration, currently it's like Google Docs but specific for bioinformatic, it looks good and very expandable, it includes some basic tools: Similarity Blast - NCBI Statistics Codon Usage CpG Islands DNA Stats Hetero Dimer - IDT Oligo Analyzer Oligo Analyzer - IDT PCR Primer Stats Protein Stats Translation/complement Reverse Complement Reverse Translation Translate Tool - ExPASy Alignment ClustalW - EBI Multiple Alignment Editor - Jalview MUSCLE - EBI Pairwise Alignment - EBI EMBOSS T-Coffee - EBI Annotations/search Blast - NCBI CpG Islands DNA Pattern Find Fuzzy DNA Search Fuzzy Protein Search Neural Network Promoter Prediction ORF Finder Primer Map Protein Pattern Find ...

I found this text,copy and paste because it's an advice and must be in every biological laboratory. ADVICE FOR POTENTIAL GRADUATE STUDENTS We currently have room in the lab for more graduate students. But before you apply to this lab or any other, there are a few things to keep in mind. First, be realistic about graduate school. Graduate school in biology is not a sure path to success. Many students assume that they will eventually get a job just like their advisor’s. However, the average professor at a research university has three students at a time for about 5 years each. So, over a career of 30 years, this professor has about 18 students. Since the total number of positions has been pretty constant, these 18 people are competing for one spot. So go to grad school assuming that you might not end up at a research university, but instead a teaching college, or a government or industry job. All of these are great jobs, but it’s important to think of all this before you go to school...

I'm starting to be bored with this comparisons, I've not report the last one comparing "apples with pears" between Ubuntu vs. OpenSolaris vs. FreeBSD benchmarks , but this is a more realistic comparison, take the new shinning Fedora 10 and Ubuntu 8.10 for benchmarking , the results: nearly identical perfomance in 32 and 64 bits. Not surprises here. Yes, U-fans claim better hardware support and more user-friendly-desktop, I don't believe that 'cause Fedora is a really good Linux distribution, I had tested and used before. Whatever, for test and compare distros you can use the Phoronix Test Suite . I'm still waiting openSuse 11.1 and maybe try gOS , while I'm saving for an Acer Aspire One.

The " Metagenome Annotation Using a Distributed Grid of Undergraduate Students " is a nice article in PLoS Biology, it remind me than the annotation of sequences is a common problem and hard to implement automatically by programs and a human can "decide" better than a machine (what about AI for sequence annotation?). I like the article tittle using "distributed grid" terms, maybe it is also considered as "heterogeneous nodes". LOL So, the strategy is to mix some students, computers with internet access, sequences and a control version system (validated by a supervisor), the work flow is: Step 1: screen a sequence Step 2. Validate the annotation And the best part you can resolve 2 problems in one hit: 1. annotate your sequences, 2. teach the students how to use bioinformatic tools and annotation. Some years ago, I participate in a similar version of " annotathon ", more simplistic because was based in the sequence homology in DBs , b...

The BASIC Stamp supercomputer is a cool project of humanoido , the system is a small portable cluster with batteries, he remarks the advantages: Smaller Lighter Portable Field operable Runs on batteries Has the greatest number of (I/O) Has the greates number of sensors/variety Lower power consumption Lower unit cost Easy to program The nodes are 12 Parallax Basic Stamp microcontrollers , many wires and some LCD screens. I love the motivations: Learning experiences & challenges Expanding education & knowledge Gaining useful background for career Research Benefits Extending Basic Stamp power Creating new inventions, ideas, applications Own your own, prestige School project, credit Involvement, sense of great accomplishment Psychological relaxation, Symbolic Value Sharing, making new friends And the video is the coolest part (great sound!):

I know it! Original in XKCD: http://xkcd.com/224/ What's your favorite programmer computer cartoon?: http://stackoverflow.com/questions/84556/whats-your-favorite-programmer-cartoon

#!/usr/bin/perl -w use strict; =head1 NAME oligoGenerator.pl =head1 DESCRIPTION Perl script to generate all possible combinations of size k using an alphabet @a, we use function recursion. My intention is to create all possible oligonucleotides (DNA alphabet or ACGT) but can be extended to any other field using a different alphabet. Output also can be printed in other forms, you can put other delimiters in the push function or in the final array printed. =cut my ($k) = 4; # definition of the word size my @a = qw/A C G T/; # definition of the alphabet my @words = createWords($k, @a);# main function print join("\n", @words), "\n"; # print output sub createWords { my $k = shift @_; $k--; my @old = @_; my @new = (); if ($k < 1) { return @old; } else { foreach my $e (@old) { foreach my $n (@a) { push @new, "$e$n"; # add new element } } createWords($k, @new); # recursion c...

This is an environment like "Minority Report", some actions are just visually stunning but video editing and 3D molding are fantastic. The gloves looks very weird. g-speak overview 1828121108 from john underkoffler on Vimeo .

Last commercials from Windows show us a "real PC guy", because the "I'm a Mac" from Apple, this Spanish-English video show the PC but with Linux. Personally, I'm a complex mix of Linux/Windows/Mac/Solaris.

This week the new fastest and most powerful computer of the world is the NCCS's Jaguar , a big cluster build by Cray and AMD, with a 1.64 petaflops of peak capacity. This means the return of the king of super-computers, Cray Inc . who was the reference for many years of the most powerful systems for computing. Now, with AMD build a cluster system (with Linux of course) and reclaim the Top 1. The cabinets also looks cool:

See more funny videos and funny pictures at CollegeHumor . From: http://www.collegehumor.com/video:1886349

Again Phoronix had tested the big U, now the rival is MacOS X. They used a MacMini and installed Ubuntu 32b and 64b with BootCamp . Ok , some rounds Ubuntu won , like this: but others MacOS X was the best: Just one comment, remember than MacOS X is still in 32b, some parts are migrated to 64b but the kernel and base system is 32b native. Should MacOS X in 64b native be a big difference? Only the Snow Leopard knows and I predict: Yes.

Last week my good friend M asks me to create a script to draw some sequences, the main problem is to visually see differences in transcript orientation (sense and antisense), some time ago I created similar tools for mapping short sequences like 454 pyro or siRNAs. Now the big problem is to have a good assembly, many regions can extend a "contig" to the left or the right, so internal coordinates change every time you add a new element, with short sequences you have a target well defined and the extension is relative to it. After thinking a little, I decide not extend my code to the assembly (yes, I'm lazy) and use Phrap to perform the job. A parser read the output and extract the alignment information. Second problem was the fasta naming convention, the original fasta file is a mixed names of other sequences, so I decided to create and tag an unique ID, "seq_##". Extending the problem, M asks me to be possible to add more sequences, based in the sequence homolo...

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

The Defense Advance Research Projects Agency ( DARPA ) is offering support for resolve 23 mathematical problems, you can read the full rules here (sorry it's a DOC). This is the problems they want to solve: The Mathematics of the Brain . Develop a mathematical theory to build a functional model of the brain that is mathematically consistent and predictive rather than merely biologically inspired. The Dynamics of Networks. Develop the high-dimensional mathematics needed to accurately model and predict behavior in large-scale distributed networks that evolve over time occurring in communication, biology and the social sciences. Capture and Harness Stochasticity in Nature. Address Mumford’s call for new mathematics for the 21st century. Develop methods that capture persistence in stochastic environments. 21st Century Fluids. Classical fluid dynamics and the Navier -Stokes Equation were extraordinarily successful in obtaining quantitative understanding of shock waves, turbulence an...

Today when I was in the bus, a girl close to me was reading, she had a small block of cards, the cards had a hole in one side and a key ring attached together, simple and effective mode to keep the notes, the notes are some chemical formulas, the amino acids charts, one side was the formula, in the reverse of the card was the name, 3 letter abbreviation and the polar class. Yes, I remember when in college I learned all this information, also I build some molecules with my atomic-kit, to see the structure, and now I just see the ACGT codes, missing the 3D beauty. Amino Acid Short Abbrev. Side chain Polar pH Alanine A Ala -CH 3 - - Cysteine C Cys -CH 2 SH - acidic Aspartic acid D Asp -CH 2 COOH X acidic Glutamic acid E Glu -CH 2 CH 2 COOH X acidic Phenylalanine F Phe -CH 2 C 6 H 5 - - Glycine G Gly -H - - Histidine H His -CH 2 - C 3 H 3 N 2 X weak basic Isoleucine I Ile -...

Currently I use every day the best on the world browser: Mozilla Firefox , in all my computers (1 Linux laptop with dual Vista/Mandriva, other old laptop with Puppy Linux and 1 Mac with Leopard), some add-ons "cannot-live-without" I commonly install for Firefox are: All-in-One gestures . Control web actions with mouse movements. Download statusbar . Simple download status. Firefox Universal Uploader . To send/receive images from Picasa and Flickr Gmail manager . To check my mail. Link alert . You can "see" the link targets. Foxmarks Bookmarks Synchronizer . To sync my bookmarks between computers. Ubiquity . Great tool in a web2.0 universe. While Google Chrome doesn't support tools like that (and native Linux/Mac versions), I hardly change the Fox.

Killer Tux from Cenek Strichel on Vimeo . Thanks to Xbit for the link.

BABY(1) USER COMMANDS BABY(1) NAME BABY - create new process from two parent processes SYNOPSIS BABY sex [ name ] SYSTEM V SYNOPSIS /usr/5bin/BABY [ -sex ] [ -name ] AVAILABILITY The System V version of this command is available with the Sys- tem V software installation option. Refer to Installing SunOS 4.1 for information on how to install and invoke BABY. DESCRIPTION BABY is initiated when one parent process polls another server process through a socket connection (BSD) or through pipes in the system V implementation. BABY runs at a low priority for approximately 40 weeks then terminates with heavy system load. Most systems require constant monitoring when BABY reaches it's final stages of execution. Older implementations of BABY required that the initiating process not be present at the time of completion, In these versions the initiating process is awakened and notified of the results upon compl...

Now I'm dad of a very cute girl, I'll be off-line the next 2 weeks.

For my work I get some slices of 100 kb from real chromosomes, but I forget to insert in the fasta comment the name and coordinates for each sequences, now I need to know this information for each one, so I tried to map using blast, but in the server a weird error marks "Segmentation fault" (I format the full genome ~3 Gb). I think in the Perl solution and this is the code: #!/usr/bin/perl -w use strict; =head1 NAME mapSeq2Chr.pl =head1 DESCRIPTION Perl script to find and get the position of each sequence in a multifasta file into a big sequence (a chromosome). The comparation is direct, so it only works with sequences in same direction (typical 5' -> 3'). Output is a simple text file with the name of the sequence, the name of the big sequence and the positions where match. Note we match every line with a fasta comment (defined with ">") but the last sequence is omitted, I add a ">" as last line with: echo ">" >> fast...

If you missing the BSOD at the Olympic Games , today is another Windows bad point takes the press, a computer virus is found in some laptops in the ISS , specifically the virus known as Gammima .AG. Apparently the source was a memory flash from a digital camera, infected the laptop and try to infect other computers, obviously NASA filter every transmission with the ISS and the virus is aisled , but the laptop doesn't have an antivirus. The laptops are used to register nutritional data for the astronauts and as personal computer to send email to Earth, nothing special. NASA is very paranoic in the materials which send to space, no dust or particles are allowed, but they need to start checking the computers and other informatic devices too. Or maybe is that a revenge from the Aliens from " Indepence Day "? You know, Jeff Goldblum infected them using a custom virus from his Mac. Source: http://news.bbc.co.uk/2/hi/technology/7583805.stm PD: Today Linux isn't secure al...

From : http://www.besttechie.net/forums/Linux-Humor-t14545.html

From Ceyusa's blog : "A Pythagorean triplet is a set of three natural numbers, a , for which, a 2 + b 2 = c 2 For example, 3 2 + 4 2 = 9 + 16 = 25 = 5 2 . There exists exactly one Pythagorean triplet for which a + b + c = 1000. Find the product abc ." My Perl solution (ok it isn't a functional programming but works): #!/usr/bin/perl -w use strict; my @n = ( 1 .. 1000 ); foreach my $a ( @n ) { my $a2 = $a * $a; foreach my $b ( @n ) { my $b2 = $b * $b; my $c = sqrt ( $a2 + $b2 ); next unless ( ($a + $b + $c) == 1000 ); next unless ( ($c / int $c ) == 1 ); print "Solution: a = $a b = $b c = $c\n"; exit; } }

A first law in building large systems to High Performance Computing is more processors are better, for many years the development of processors was dominated by the x86 family, beating including the PowerPC (more in cost than in performance in my opinion) and new families emerge like the x86_64 and the multicore chips. Beside the CPU technology advances, other part of the computer had acquired a new task, the graphic card, in early stages of computer evolution, its function was only connect and control the visual output for the system and the monitor. Later computer games demand more intensive usage for the GPU, principally by 3D environments, and new technologies were created to satisfy the demand. Actually a high performance graphic card is like a small but very efficient version of a complete system, including one or more special GPUs, own memory and can share information with the host system or other graphics card very fast (SLI). How do include this computing power? Because apa...

Ok , last time I judged the Ubuntu distribution so hard, later I started to think if there are a perfect Linux. First thing I believe is the Linux versatility, with the freedom of evolve or changing (forking) you can expect everything, so you can choice what to use as desktop, shell, editor, package system, ... Many distributions are open to change the default installation, or simply to allow to try any program in the repositories or just the code. The options are infinite. I remember when you need to decide the parts of your system, in the beginning of many distributions the installation system ask you the packages to include, some times you obtain an unstable systems, but many times you have a personal system. Many problems could be resolved reading manual or asking in the LUGs , but some times you needed to wait until the next release and a programmer or hacker fix it. Later the popularity of LiveCDs allows to install a full system which works fine, because many debuggers tested t...

Many of my linux -friends well know I don't like Ubuntu , yes the " so popular and friendly linux ", this week I had some buddy-support for this bad distro , but these people are fascinating using it! Basic problems include (in order of appearance ): Compile a C code. Why Ubuntu doesn't configure well the dependent libraries for static? I try the code in other Un *x environment and works well, but in Ubuntu I had to delete the static flag and edit the headers in source code. Execute a CGI script under Apache (I'm not 100% sure of Ubuntu systems but I guess). If the system install a httpd . conf file with basic rules to work, you expect this work, if it doesn't, I don't like to read the manual to fix something when many other distros like Mandriva do perfectly fine the first time. Install updates and reboot. Sorry for the similitudes, but this is a Windows feature, why do you need to reboot after the installation of updates? I like to update if I ...

Ok , lets get some conclusions about the image: Time is 9 years, Linux had almost 9 years old in 1999. I don't now the numerical values of the samples. In 1999, the average is in medium size (M), in 2008 is extra large (XL). I think one explanation, many linux users started as very active-skinny young people and later they gain some weight. But really few people, like me, use Linux in 1999, and after the Ubuntu boom in 2005 many new users are converted every year. Are they bigger in size? The anti-MS commentary: If Windows crash every 5 minutes, the BSOD makes you move with your frustration , Linux stability makes you be more static in front the screen. BTW, I'm L since 1995.

From Boston.com : "The Large Hadron Collider (LHC), a 27 kilometers (17 miles) long particle accelerator straddling the border of Switzerland and France, is nearly set to begin its first particle beam tests. The European Organization for Nuclear Research (CERN) is preparing for its first small tests in early August, leading to a planned full-track test in September - and the first planned particle collisions before the end of the year. The final step before starting is the chilling of the entire collider to -271.25 C (-456.25 F)." Here a few amazing pictures, more in the website: