Linxe's eye

I have used Perl for my projects for more than 6 years, when I used the Arabidopsis genome it was easy to load a full chromosome into a string variable, but now I work mining bigger genomes, like human or mouse, and I had the habit to pass direct variable or references to subroutines, bad idea. The point is when you are using many subs to perform calculations inside the sequences, the memory increase exponentially, one of my scripts takes the sequences, divide into blocks and perform calculation by each block, and store in a hash ( O-O programming), first time I made a mistake and create an infinite loop and sucks the entire memory, including the SWAP, our server has 32 GB in RAM and 32 GB in SWAP, fortunately the server survive to my error. Next I fixed it, and now the script require about 3 GB , so much ... After think a little I decide to not pass nothing to the subs, declare globally access for principal variables and this reduces the memory needed to 300 MB for the same proc...

Yesterday I was disturbed of my coding-state to answer a basic problem, which's the best font to display a sequences alignment? First introduce the concept of sequence alignment, if you want to compare 2 or more sequences in their composition of nucleic bases (for DNA or RNA) or amino acid (for peptids ), you must search similar blocks between all the context and try to fix the rest as possible. Many algorithms has been created to perform this task, with different approaches, if you want to know more, please go to Wikipedia or bioinformatics books. Ok , let's consider we have our alignment, really this is a text file with a special structure to easy visualize the blocks found. Some people make the mistake to cut-and-paste in a text document without change the font style, a font is just an image to represent letters or symbols, some are very artistic but generally the font does not conserve a proportional aspect in size, so the beautiful alignment changes its proportion and vi...

Next July 24th a special event marks the 25th Anniversary of the release of War Games , some theaters will have the 1983's movie. I noticed that a second version was filmed, and after the anniversary will be available but the release is direct to DVD, I'm curious to watch how they actualized the technical material, because now you have wireless networks instead the dial access, or better security schemes to make invisible your network and also high-level encrypted, besides the monitor systems which are hard to break. Ok, Hollywood generally doesn't show reality, but some movies are spectacular (or simply stupid) to show the computer world, some times looks like magic ... I miss the sound of a modem connecting to the internet, or a monocromatic screen with plain text (well, not so much this last because sometimes my X11 crash and you need to fix in the terminal mode). $ logout

Bioinformatic: Which is the best blast E-value?

If you are in biosciences related work many times you have seen a fabulous but meaning-less image in the sci papers, typical error to represent data with wrong visuals perceptions, M. E. J. Newman named "Ridiculograms" (you can see the related video in Youtube). A ridiculogram can be defined as: Visual stunning Scientifically worthless Published in Nature or Science After a group discussion and a no so good seminar about text mining for disease terms, some agree that the last point can not be required, I want to extend this concept to other parts in bioinformatics. Many people are working in the user interaction part, novel technologies have large and heavy output and require some tools to show the results, but many of this tools are redundant (yes, many people want a desktop/web/network interfaces or some programs for Linux/Windows/Mac or versions in Java/C#/Python/Perl) and while the developers think "in the user experience", they forget the concept of the tool: ...

These days I had working on web interfaces for some Perl scripts, the server is an 8-cores Linux box with CentOS with Apache as web server, but some tests didn't work well and some probably fall into an infinite loops. The problem was I can not kill these process, because I must not know the admin password and I can not have access for the web server, the scripts are created in my home and when activate the process is submit by the apache user. So the solution was a script which ask the PID and send a termination signal. Here is the code, maybe someone can use it: #!/tools64/bin/perl -w use strict; =head1 NAME reaperl.pl =head1 DESCRIPTION Web service to stop some uncontrolled process created by the Perl::CGI. Simply presents a web form to indicate the PID and call a system termination. =cut use CGI::Pretty qw/:standard/; print header; print start_html(-title=>'reaperl.pl'); print start_form; print p('Kill this process: ', textfield(-name=>'proc')); pr...

I suppose you have listen about Second Life or games like WoW , these sites are known as virtual worlds where you can be anyone, even yourself. Few days ago, Sun announce its solution for virtual meetings named Project Wonderland , a evolution of their experiments with Looking Glass (I made an article for GLiB ). This approach create a virtual enviroment where people can be reunited with 3D avantars and talk (also you can be a weird floating ball when you are using a phone communication). Today Google launched Lively a personal "world" (maybe more like a personal room). Lively is like Second Life but small and owned by yourself, the bad point is that requires MS Vista/ XP at this moment. The concept is good, take the good things in SL and apply for a minimal space and with Google support, it can be big and soon we'll have many variations or improvements. When will be we as close as the Metaverse written by Neal Stephenson in the cyberpunk novel Snow Crash ? By the...

Oh, life is bigger It's bigger than you And you are not me The lengths that I will go to The distance in your eyes Oh no, I've said too much I set it up That's me in the corner That's me in the spotlight, I'm Losing my religion Trying to keep up with you And I don't know if I can do it Oh no, I've said too much I haven't said enough I thought that I heard you laughing I thought that I heard you sing I think I thought I saw you try Every whisper Of every waking hour I'm Choosing my confessions Trying to keep an eye on you Like a hurt lost and blinded fool, fool Oh no, I've said too much I set it up Consider this Consider this The hint of the century Consider this The slip that brought me To my knees failed What if all these fantasies Come flailing around Now I've said too much I thought that I heard you laughing I thought that I heard you sing I think I thought I saw you try But that was just a dream Tha...

Which OS is dominating the SuperComputer world?