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Tuesday, August 29, 2006

Folding@Home, but speedy than Blue IBM Gene/L System, supercomputer.

Cell specs. BBC courtesy.
I have just attended a conference of digital journalism, organized by the UNMSM, of Lima, in which a central topic was the horizontal/participatory/ interactive journalism, promoter of close collaborations among people/advanced technology/journalists of vast reach. Now it is that this complicity surpasses journalistic boundaries and invades related and until now distant fields (games, science, illnesses). The digital games (Wii of Nintendo, Playstation, Xbox 360 of Microsoft), before the users' demands, are forced to be constantly renewed thanks to the employment of superspeedy processors (chips), each time but complex. To someone (statistical, mathematician, biologist) happened, to suggest SONY Playstation, to adapt a graphic interface of advanced game, to the need of calculation and graphic view of certain medical/biology/epidemic investigations. The biochemists know that normal human protein foldings is critical to maintain the health. On the contrary, a misfolding can condition :cancer, Alzheimer's disease, Huntington, Parkinson, mad cows disease, CJD, imperfect osteogenesis, etc. To simulate in a PC, human protein foldings and analyzing them critically would help to establish the causes of several illnesses. Distant objectives for the time being, in reason of the slowness of the current processors. Usually, a complete normal human protein folding, is executed in a few microseconds, in a simulation, it delays about 26 years.

Then here is SONY Playstation 3 (PS3), that has just developed an ultraprocessor (chip/cell/cell specs: 256 million calculations/second, 2,5 MB of memory, 20/60 GB of entrance and exit speed, 234 million transistors, images (Nvidia + RSX, of high definition of advanced game, 60 images/second), 10 times but speedy that anyone of the current chips), to be thrown to all the world, in November of the 2006. The good thing is that the CPU of PS3, has interactive controllers able to generate 3D graphics in realtime, of virtual protein foldings, being possible view them from any angle. Of another side, Sony in alliance with Folding@home (http://folding.stanford.edu) and 10 000 biologists, each one with their PC, have begun to study protein foldings in collaborative form. Kind of an extensive thinking net, that never existed before. After download a piece of folding software from the net, each PC works under certain rules, then send the results forwards to Internet or to a central integrative PC, hoping in this way to overcome in 4 times (1000 trillion calculations/second), the capacity of the supercomputer, but speedy of the world: the IBM BlueGene/LSystem of California. To tell the truth the simulations with PCs, began some years ago (October/2000), not alone for protein foldings, but also to calculate patterns of dissemination of malaria and smallpox, in front of possible bioterrorist attacks. Another collaborative project Seti@Home sponsored by Search Extraterrestrial Intelligence (SETI), is about capturing possible signals of extraterrestrial intelligence, employing radiotelescopes and hundred of PCs distributed all over the world. In the future, it is hoped to use 1 000 000 of PCs, in collaborative projects of vast reach.

Folding@Home, mas velóz que la IBM Blue Gene/L System.

Acabo de asistir a una conferencia de periodismo digital, organizada por la UNMSM, de Lima, en la que uno de los temas centrales fue el periodismo horizontal/participativo/interactivo, promotor de estrechas colaboraciones entre usuarios/tecnología de punta/periodistas de nuevo cuño. Ahora resulta que esta complicidad rebasa linderos periodisticos e invade ambitos conexos y hasta distantes (juego, ciencia, enfermedades). Los juegos digitales (Wii de Nintendo, Playstation, Xbox 360 de Microsoft), ante exigencias de los usuarios, son forzados a renovarse merced al empleo de procesadores (chips), ultraveloces, c/vez mas complejos. A alguien (estadisticos, matematicos, biologos), se le ocurrio entonces, sugerirle a SONY Playstation, adecuar una plantilla grafica de juego avanzado, a las necesidades de calculo y visualizacion grafica de ciertas pesquisas medico/biologo/epidemiologicas. Los bioquimicos conocen que el plegamiento normal de las proteinas humanas es critica para mantener la salud. Por el contrario, un plegamiento inadecuado puede condicionar : canceres, enfermedad de Alzheimer, de Huntington, Parkinson, de las vacas locas, CJD, osteogenesis imperfecta, etc. Simular plegamientos proteicos en una PC y analizarlos críticamente ayudaria a establecer las causas de varias enfermedades. Objetivos distantes por ahora, en razon de la lentitud de los procesadores actuales. Normalmente, el plegamiento completo de una proteina humana, se ejecuta en unos cuantos microsegundos; en una simulación, demora unos 26 años.

He aquí, que SONY Playstation 3 (PS3), acaba de desarrollar un ultraprocesador (chip/cell/cell specs: 256 millones de calculos/segundo, 2,5 MB de memoria, 20/60 GB de velocidad de entrada y salida, 234 millones de transistores, imágenes (Nvidia + RSX), de alta definición de juego avanzado, 60 imágenes/segundo, 10 veces mas veloz que cualquiera de los chips actuales), listo a ser lanzado a nivel mundial en Noviembre del 2006. Lo bueno es que el CPU del PS3, cuenta con controladores interactivos capaces de generar a voluntad graficos de 3D, en tiempo real, de plegamientos virtuales proteicos, siendo posible visibilizarlas desde cualquier angulo. De otro lado, Sony en alianza con Folding@Home y 10 000 biologos, c/uno con su ordenador personal, han empezado a estudiar plegamientos proteicos, en forma colaborativa. Una especie de red extensa pensante, como nunca ha existido antes. Tras bajar una pieza de software de plegamiento la net, c/ordenador trabaja bajo ciertos canones y luego reenvia los resultados a Internet o a un ordenador central integrador, esperando superar en 4 veces (1000 trillones de calculos /segundo), la capacidad de la supercomputadora, mas veloz del mundo :la IBM BlueGene/LSystem, de California. A decir verdad las simulaciones con ordenador, se iniciaron hace algunos años atrás (Octubre/2000), no solo para plegamientos, sino tambien para calcular patrones de diseminación de la malaria y viruela, frente a posibles ataques bioterroristas. Otro proyecto colaborativo (Seti@Home), patrocinado por el Search Extraterrestrial Intelligence (SETI), trata de captar posibles señales de inteligencia extraterrestre, mediante el empleo de radiotelescopios y cientos de ordenadores distribuidos a lo largo y ancho del mundo. En el futuro, se espera emplear 1 000 000 de PCs, en proyectos colaborativos de vasto alcance.
Technorati tags (Playstation/PS3, protein folding, misfolding, Folding@home).

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