Wednesday, April 29, 2009

Swine flu

The world is in a critical time now, the swine flu is spreading fast, the biggest impact is my loved country Mexico, reporting thousand of cases and more than 150 deceases. Other countries have been reported positive cases around the globe.

Many things isn't clear, are the numbers real?, when did exactly this started?, why is this virus so different?, why are the cases in Mexico lethals?

A good review of the situation is in the Germán's Blog, he is a graduate student of the UNAM in the faculty of biomedics. (My apologizes, it's is in Spanish and I don't want to translate).

By the moment, you can watch the spread with this Google Maps Mash-up:

View H1N1 Swine Flu in a larger map

Remember, the best prevention is the hygiene and medial attention as soon as you feel bad.

Thursday, April 23, 2009

GeneTitan video

Yes, it's a not so good commercial, it shows the new Affymetrix GeneTitan with toys!

Tuesday, April 21, 2009

Scary Email

Just imagine when the spam arrives ...

Image from:

Sunday, April 12, 2009

Real science on TV

Image from:

I admit, some times I'm watching a TV shows and put a smile in my face when I catch some big mistakes in the scientific/technical plot. Anyway I'm a fan of science fiction series.

Saturday, April 11, 2009

Bigger tiny memory

Today I had received my new pendrive, I found it few days ago surfing in tech-news sites. It's amazing how technology decreases the size and increases the performance, for example I compare my old pendrive with the new:

As you see, the old drive is bigger as a finger, and the new one is half of this size, but with 32X more storage capacity and faster. The bad thing is I received it inside a big letter-bubble-envelope for this, I understand package protection but the size of the envelope is ridiculous. The good thing is the price, as much as a movie ticket.

Besides my Dropbox account, some times I need a bigger drive to move my data, I'm not the typical guy with Gigas of music, movies or pictures, when you work with large biological data as genomes, you never have enough space in your drive. Now my workstation is processing 70 Gb in images, I'm using a random sampling inside the images to reduce the computer time.

My kingdom for a personal supercomputer!

Wednesday, April 8, 2009

We're Linux video contest

The Linux Foundation launched the video contests for a "We're Linux", last day they announced the finalists, but I like this one (probably because my biological background):

I hope this wins.

Update: Origin is second place, the winner is

Tuesday, April 7, 2009

Green Supercomputing

There are 3 big problems when you want a supercomputer (besides the cost, of course), the first one is the space, a cheap and common approximation is to use a cluster design which you wire, as many as you can, independent computers. So you need to reserve an adequate space for the equipment, if you're not using servers racks, the space is a problem.

The second problem is the calorific power generated by the computers, a single desktop computer can be really hot in intensive use, so imagine when you put many machines in a same room together. I remember the first cluster of the bioinformatic lab, the provider installed the hardware one day before they installed the software, but when the guy turned-on the systems, all the RAMs were burned. The provider changed all the RAMs for a more heat resistant brand. After some time and after some expansions in the cluster, the cooling systems also was required to be changed for an industrial equipment, in summer it feels like an oven.

The third problem is the electricity cost, because many energy is loose in form of calorific transformation, the system is not efficient.

Last day reading the Icaza's blog, I noted a company named SiCortex, who is selling a green supercomputer solution, based in multi-CPU towers, they have from desktop size with 72 processors, a mid-size configurable with 324 to 1,458 processors and up to 1.9 terabytes of memory, and the "I-want-of-this"-size: the SC5832 with up to 8.2 TFlops of compute power in a single, self-cooling cabinet and configurations range from 1,944 to 5,832 processors and up to 8 terabytes of memory. I did not see prices, except for the desktop version which cost ~$24k usd (a special offer can reduce the price to $16k), I cannot imagine how much cost the others.

The secret is the tower design and the type of processors used, the system use very few space, few energy and don't need A/C. Of course it runs GNU/Linux (RedHat) and support common tools (GCC, Fortran, MPI, ...). For more technical details check the Architecture Tour.

Friday, April 3, 2009

Robot scientist

Amazing, I know about the use of robotics systems to manage high throughput experiments, for example when you need to prepare reactives dilutions in plate series of 96 or 384 (some time ago I hacked one of these equipments using reverse engineering and Perl), or picking bacterial colonies and extract the DNA.

Now a couple of reports in Science (this and this) are describing the use of a robotic system to study yeast mutants in media deprivation, and after run 1000 experiments every day, the system report some insight about the results. Check the video and more information in NewScientist.

Thursday, April 2, 2009

Face gestures in Opera

The best joke for April 1st in my opinion was this: