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ScalaBLAST
Jamais Cascio, 22 Jun 05

ScalaBLAST.jpgIt may be awhile before it shows up on your desktop, but the Pacific Northwest National Laboratory has just made a massive leap in the ability to sequence genomes.

ScalaBLAST is a software tool for use with multiprocessor systems, dividing up the work of analyzing biological information. With the PNNL's supercomputer -- number 30 in the latest Top 500 supercomputer list -- the software allows genome sequencing to happen hundreds of times faster than before. Prior to ScalaBLAST, sequencing the DNA of a single organism took 10 days, a remarkably short time compared to the months and years such a process took less than a decade earlier. With ScalaBLAST, the same machine can analyze 13 organisms in 9 hours, or about 42 minutes per organism.

The PNNL scientists are enthusiastic about the opportunities this could provide:

"Access to and understanding the pieces of genome sequences will allow researchers to understand the body's cellular machinery and discover clues to some types of cancer. And it will help in developing drugs or detection methods to be used for particular diseases," said T.P. Straatsma, a PNNL senior research scientist.

And it likely will help in other areas of human health. It's fair to say that, in the realm of human health and disease, if you can solve a problem in one area, you can often solve it in others – that's the nature of human biology," Straatsma said.

Having the ability to process large data sets with this computational tool can also provide new insight into how microorganisms can process toxic pollutants through processes like bioremediation. It also can help understand the components of biological systems, leading to better detection methods for homeland security purposes and making it possible to more quickly identify and respond to threats or develop biological countermeasures.

But the critical element to keep in mind is the rate at which supercomputing is improving, and the reduction in cost of extremely fast systems. The PNNL's supercomputer is #30 now, but last November, it was #16, and it was the fifth fastest supercomputer in the world in November of 2003. By next year, it probably won't be in the top 50. And while we're not likely to see 2,000-processor desktop systems any time soon, we could well see distributed processing arrangements offering equivalent power at a fraction of the cost.

Sequencing an organism in 45 minutes brings individual genome sequencing within reach. We talked a bit about what that means last August, including the Harvard Personal Genome Project. It also makes sequencing the planet and "frozen arks" far simpler, as well -- making it possible to preserve, at least in code, some of the planet's vanishing biodiversity.

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Comments

This leads into garage nano/biotech in a long run.

The implications of garage nano/biotech are not in concordance with the current Foresight Institute guidelines (http://www.foresight.org/guidelines/current.html), since garage tech creates an environment of "uncontrolled circumstances" below, where self-replicating nanostructures and self-replicating genetic viral enhancements will be made very easily.

1. Nanotechnology developers adopt and practice professional guidelines relevant to the responsible development of both near term and advanced nanotechnology.
2. Nanotechnologists attempt to consider proactively and systematically the environmental and health consequences of their specific technologies. They recognize that the scope and magnitude of potential problems are reduced to the extent that they consider the possibilities, and plan to minimize their effects.
3. Nanotechnology research and development is conducted with due regard to accepted principles and practices of environmental science and public health, with the understanding that significant changes in physical and physiological properties may occur when macroscale materials are developed and utilized on the nanoscale.
4. Nanotechnology products are conceived and developed using total product lifecycle analysis.
5. Molecular manufacturing system designs make no use of self-replicating machines.
6. When controversy exists concerning the theoretical feasibility or implementation timing of advanced molecular nanotechnologies, such as specialized molecular manufacturing components or assemblers, researchers address and clarify the issues rapidly, and attempt to resolve any controversy openly.
7. Any use of self-replicating systems is avoided except in approved and controlled circumstances.
8. Any developers who design or build self-replicating machines adopt systematic security measures to avoid unplanned distribution of their designs and technical capabilities. Both potential benefits and risks of alternative technologies are explored actively, in a balanced and rigorous manner.

However, nature is already broad of such self-replicating stuctures, and organisms have build-in procedures to screen themselves from their harmful effects. Some of human invented self-replicating structures could also be valuable for us (like all the billions of bacteria living inside human body, or the retroviruses frozen in the junk DNA), and that should be left for our integrated cellular intelligence to straighten out (it's a very cogent machinery running down there in the DNA level).

Considering that I would say that Foresight Institute should readjust the guidelines more toward Genomic Capitalism, and not into Goverment-Controlled Genomic Communism.

Summarizing this and the rapid technologic advances I would say that self-replicating nanostructure development should be considered as a part of mundane business that benefits both human macroeconomy and our evolutionary DNA code-base.

Pekka


Posted by: Pekka on 23 Jun 05

I've got a very easy to use piece of open-source software that is well-suited (and designed for) genetic analysis by both laypeople and fulltime researchers. It's based on some new data compression mathematics and available at
http://complearn.org/

I think it's important that we have plenty of open-source tools like mine to help everybody who's interested to easily dive into genetic analysis at whatever level they find interesting, whether evolutionary, exploratory, or other. There are some of us who understand that everybody deserves to benefit from the fruits of science. And we can do this now with the internet. I wrote this program years ago before there was so much publicly available sequence data; now it's just amazing how many different experiments you can try. If you use the "cldemo" program, you don't even have to use a keyboard. Just drag and drop your sequence files into the window and watch the 3D tree evolve. Cheers

Rudi


Posted by: Rudi Cilibrasi on 26 Jun 05



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