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Decoding the Genome: Serious Infrastructure
Roland Piquepaille writes "The Wellcome Trust Sanger Institute is one of the largest genomics data centers in the world. In "The Hum and the Genome," the Scientist writes about the IT infrastructure needed to handle the avalanche of data that researchers have to analyze. With its 2,000 processors and its 300 terabytes of storage, the data center uses today about 0.75 megawatts (MW) of power at a cost of 140,000 per year (about $170K). But the data center will need more than a petabyte of storage within three years, and its yearly electricity bill will reach 500,000 (more than $600K) for about 1.4 MW, enough to power more than a thousand homes. The original article gets all the facts, but this summary contains all the essential numbers."
Lots of computers use lots of power which costs lots of money!
I misread that and thought it involved a spotlight and torture methods to a poor garden gnome :(
"You will tell us what we need to know. WHERE IS THE LAWN MOWER!"
liqbase
The idea behind all this mapping is to find genetic sequences that can be used to mend ailing people. Using a computer to throw every single combination possible against the wall and seeing what sticks is certainly a way to go about this, but it also raises the spectre of a single large company owning all these combinations. This wouldn't be such a terrible thing if there was some sort of actual science involved, but by brute-forcing results, they are doing nothing more complicated than running a counting program with an infinite number of bits.
So each result is directly traceable to a number. Will these companies own these numbers? Can you even take out a patent on a number? In the DeCSS case, it was argued that the decoding algorithm was protected even though some implementations of it were nothing more than a carefully crafted prime number.
I don't like the idea of someone owning numbers any more than I think someone should be entitled to the fruits of their own work. This whole patent "creation/reward" system is getting turned on its head because of the power of computers. What would have been prohibitive even 10 or 15 years ago is possible (even easy) now. How can we keep our rights without sacrificing the progress of science and the arts?
TANSTAFL. This post seems drawn into the spinning power meter dials and not caring about what the computer is. If you want a lot of power, you need a lot of power. Chip scale efficiency could reduce their bill, but its a research foundation crunching numbers all day. If they need more money they just ask their contributors politly.
How's this stack up with google's server farm bill.
Bacardi + slashdot = negative karma.
What's the deal wiht this roland guy
They're trying to decode his genome to find the missing link.
Which will lead to his website, of course.
Take the cheese to sickbay, the doctor should see it as soon as possible - B'Elanna Torres, "Learning Curve"
http://www.archive.org/web/petabox.php
it uses only 60kW for 1 Peta byte
What about the costs of scaling and maintaining such an infrastructure? The routine administrative tasks, reporting, etc? The costs for someone actually looking at the generated results to see if they are meaningful at all, and if it is all going in the right direction?
http://efil.blogspot.com/
Cost of 0.75 MW: ~$170K
$/MW: ~$227K
Cost of 1.4 MW: >$600K
$/MW: >$429K
Why the difference?
Alphanos
Mod parent up.
i lle&as_sitesearch=slashdot.org/ or search slashdot articles on roland piquepaille.
Just have a look on http://www.google.com/search?query=Roland+Piquepa
Real whore here is Timothy. I bet he'll post an ad for your site for some change, too.
The interesting bit about genome research is that suppose we do find what the human genetic code all means. We can then start treatments to correct genetic problems, right? If we do so, and say we correct illness X on some kid. When this kid grows up, becomes an adult and have kids of his own, what kind of genetic heritage will he give his own kids? Will these kids inheric the original bad gene of their parent? If so, we'd be running at our lost since defects would multiply across generations...
I think you mis-spelled that.
Lost at C:>. Found at C.
Anyone else want to buy Roland and make him shut up?
It depends. If you are doing somatic cell genetic engineering, then you only fix those cells in the patient in which the defect manifests itself, and not the germ-line cells (ie, sperm and eggs), so the 'fix' is not passed on to the next generation. If instead you modify the germ-line cells as well, then the 'fix' is passed on to the next generation.
One of the main reasons for doing the somatic fix rather than the germ-line fix is that we're still pretty damned new to this genetic engineering thingy, so it's probably a good idea to not fuck with the genetic heritage of future generations just to cure a patient today. However, as the science and technology develops, and we gain more experience with it, our self-assuredness in our abilities will likely increase, and we'll think we know what we're doing enough to risk making 'permanant' changes to the germ-line. I put 'permanant' in quotes, because if we make genetic changes one way, we should be able to turn them back if and when we decide they are mistakes.
There are 23 chromosomes in the human genome. That chromosomes are a pair of the genes. I understand that each gene is one of four DNA molecules called A,G,C & T. There 16 combinations of those mlecules and I can map those out with a pencil and paper, I can produce all 23 sets with desktop computing power.
There are 23 chromosomal pairs. Each half of each pair contains the same (more or less) information - you could think of it as a genetic back-up system. (Except for the XY chromosomal pair in males). At the start, one chromosome is maternal, the other is paternal. But over time, they actually swap bits around until there's a mixture.
Each chromosome contains one immensely long strand of DNA, a double-helix. This double helix is NOT redundant, only one of the two strands contains genetic information: The other strand is only there to make it easier to copy the helix.
The human genome is approximately 3 billion bases long, and it takes three bases (known as a codon) to code one amino acid. 4 x 4 x 4 = 64 possible amino acids. (Altho they only actually code 20 or so). Then you have to filter out all the codons that don't actually code anything, and are discarded before the gene is transcribed into a protein.
NOW do the math!
So.. it has come to this