Linxe's eye

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...