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."

Big computers = big power

[goneutt]

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.

Whats with the emphasis on power and its costs?

[manavendra]

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?

Units

[Hank Chinaski]

They use Megawatts as a measurement of energy consumption? Should't that be Megawatt/hour ? P.S.: Dont click the link. Editors could at least include as "Signup required" warning.

Genome - the dog chasing its tail?

[Wayne247]

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...

Re:Units

[Anonymous Coward]

They use Megawatts as a measurement of energy consumption? Should't that be Megawatt/hour ?

No. Didn't you pay attention in high school? A megawatt is a unit of power. Power is energy divided by time. A watt is one Joule per second. A joule is a unit of energy.

So, watts means joules per second. When you get your household electric bill it is in kilowatt-hours, which is the number of watts multiplied (not divided) by the time you consumed that many megawatts.

So, since a watt is energy/time, a kilowatt-hour is energy/time x time, which is a unit of energy.

And while household energy use is normally billed per kilowatt-hour (energy used) when you get to be a large commercial customer, you are billed not only for kilowatt-hours (energy used), but for the maximum kilowatts you draw.

Example: when a factory starts up at 9 am, it takes a lot of power to start up the all the machinery. To keep the machinery running takes much less power. Drawing all that power from the grid at 9 am will create a big spike and possibly lead to brownouts. To compensate & prevent that big spike isn't cheap, so you're billed for max. power.

Re:Amazing!

[Anonymous Coward]

The Trust also believes that the basic DNA sequence of humans and other organisms as such should be placed in the public domain as soon as is practical, without any fees, patents, licences or limitations on use, giving free and equal access to all. Subject to this, the Trust is supportive of patents encompassing genes and their products when there is research data or information indicating that a particular DNA sequence has a utility such that the legal criteria for patenting can be met.

Exactly the same bullshit is used by European software patent proponents when they say that "software 'as such' will not be patentable". It's such a victory for the public that the wellcome trust does not support patents on DNA sequences, just the practical application of those sequences.

Wellcome trust, bunch of halfwits or deceptive front for big business? You decide.

Re:I haven't a clue...

[oneandoneis2]

No, no!

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!

Re:Enough to power a thousand homes

[Tassach]

It is more about the power consumption

Yep.

First off, utility companies generally charge a higher rate for business/industrial power than they do for residential power; so even if all things were equal, they'd still be paying more per KW/H than you.

Secondly, you can't compare a couple of desktop machines running in a home office to a datacenter with multiple fully-populated 72U racks. Running 2 or 3 computers in a 120 ft^2 room isn't going to require any additional cooling. Running 2000 mahines in (say) a 1000 ft^2 data center is going to require heavy-duty air conditioning. Finally, remember that enterprise-grade hardware generally has redundant power supplies, 15000K rpm SCSI disks, and more powerful fans -- all of which draw more power (and throw off more heat) than a typical desktop system.

Re:Math

[Renraku]

Diminishing returns.

You've gotta have a lot of infrastructure outside the facility to be able to support 1.4MW. Infrastructure that is probably taken care of by the power company, for a fee.

And the more power you push down the line, the more power that is lost to the environment. Especially if you're overcharging the lines, which causes acceleration of the loss the more power you pump into them.