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."

Comments

Breaking news from our reporter Roland Piquepaille

[JamesD_UK]

Lots of computers use lots of power which costs lots of money!

Amazing!

[poopdeville]

The Wellcome Trust Sanger Institute is amazing it will-

- optimize seamless communities
- generate vertical e-services
- everage synergistic convergence

and best of all

- engage e-business content Perfect solution

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.

Decoding the gnome?

[LiquidCoooled]

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!"

Re:Decoding the gnome?

[Anonymous Coward]

How about decoding KDE?

Re:Decoding the gnome?

[Fred_A]

I misparsed the title as well and figured they had to resort to a super-computer to try and make sense of the Gnome dependencies...

emerging gnome, package 3 of 46438847...

That's... interesting

[Anonymous Coward]

I think I'm immune to large numbers. This article summary has absolutely no effect on me whatsoever.

Who owns the results?

[Dancin_Santa]

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?

Re:Who owns the results?

[Hittite Creosote]

The centre is funded by the Wellcome Trust and the UK's Medical Research Council. The Wellcome Trust Sanger Institute is a non-trading, non-profit making registered charity. And they tend to make their results open - these are the people who said that the genome should belong to no one individual or company. In other words, if you want to keep your rights without sacrificing the progress of science - we need more places like the Sanger centre.

Re:Who owns the results?

[Gurdy]

> "it also raises the spectre of a single large company owning all these combinations."

You might be interested to read our data release policy http://www.sanger.ac.uk/Projects/release-policy.sh tml which describes how the finished data is made publicly available, to all, no charge.

(I work at the Sanger Centre.)

Dave

Re:Who owns the results?

[dan dan the dna man]

Well the nice thing about the Wellcome Trust is that they are an independent charity and the largest non-corporate non-governmental source of biomedical research funding in the UK.

Maybe you'd like to read their constitution: here

Sure theres a chance that things can get tied up in the hands of companies - but lets look at the human genome project. The best data came out of the academic sector, the private data (held by Celera) didn't turn out to be too profitable after all (or even better quality) and is now in the public domain. I worry about the commercialisation of science as much as the next man, but lets face it, business just doesn't care unless there's a drug to sell at the end. Data is still just data.

Re:Who owns the results?

[Petersson]

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.

This way of genome decoding is much more spectacular. It attracts investors. And doing it the hard way will definitely bring some results.

But bunch of boring sciencists, writing boring equations, can also result in zero success. On the other hand it could save whole lotta money for power, hardware and time. But it's bit risky.

And when the job is finished, this cluster will become national monument.

Re:Who owns the results?

[Anonymous Coward]

A lot of the analysis software used is also freely availible as it most of the web display code

http://www.ensembl.org/

another sangerite

Re:Who owns the results?

[perdu]

A lot of the analysis software used is also freely availible as it most of the web display code

Is the browser freely available to commercial users?

Re:Who owns the results?

[sugarmice]

Yes. It's GPL. Anyone can use it.

Re:Who owns the results?

[ckd]

As noted, the Sanger, like the rest of the public HGP centers, makes their data accessible to everyone for free. You're thinking of Celera, who got out of the business.

(Claimer: I work at another of the centers. Similar scale, but those folks at Sanger have more server room floor space...sigh.)

Exchange Rate

[squoozer]

I wish I could get the submitters exchange rate. I'd be rich rich rich. It's currently around 1.9 dollars to the pound meaning anual running costs are more line $260k which could rise to around $1m.

Having said that everything is cheaper on the US side of the pond so the submitter is probably about right. Sigh.

Re:Exchange Rate

[smithberry]

I think the prices quoted are Euros.
Currently 1 Euro = 1.23 USD, so I think the article is about right.

Re:Exchange Rate

[Gwyn_232]

The trouble is, the poster was too lazy to a) look up the ascii code for or b) type EUR in front of the figures (as in EUR400,000).
Both sterling and euros are used when quoting costs in Britain.

Re:Exchange Rate

[Gwyn_232]

Ok, I'll revise that

The trouble is, Slashdot is too shit to handle the Euro symbol.

Re:Exchange Rate

[Gwyn_232]

, , It may be that it can't handle if it's a euro keyboard (like mine is)

Re:Exchange Rate

[Anonymous Coward]

Ways to put the Euro symbol in webpages:

• Hex code 0xA4 (decimal 164) in codepage 8859-15 is what you get when you press AltGr+e. This happens to be the general currency symbol in 8859-1, so it's not a good choice if you can't make sure that the document comes with the correct encoding declaration. ""
• HTML entity € "€"
• Unicode character reference € ""
• Hexadecimal unicode character reference € ""

As you can see, Slashcode filters all but the html entity, so that's your only choice here if you have to have the symbol. Most people simply use EUR.

Enough to power a thousand homes

[jurt1235]

Doing some quick math here: 2000 processors+1petabyte, divide by 1000=
2 processors + 1TB per house.
In processors: Way past it
In storage: Getting there (quick count of harddisks lying around= 750GB at least)

Since my energy bill is lower, even with the hardware running 24/7/365, are they buying their energy to expensive or what?

Re:Enough to power a thousand homes

[teknofyl]

Sounds good in theory, however I doubt that either the environment agencies or the local residents would support this. In the case of Wind Turbines we'd be hit by a sudden fit of NIMBY. As for solar panels, well some of the new buildings here have been designed with grass roofs in order to make them blend in with the environment. Again, I doubt we'd get permission to start decking the roofs with solar panels.

(I work at the Sanger Institute)

Re:Enough to power a thousand homes

[hcdejong]

The computing power density of 1000 homes is a lot lower. 1000 homes + the ground they sit on also cost more to buy/build than the one datacenter.

Re:Enough to power a thousand homes

[jurt1235]

It is more about the power consumption. It just seems to expensive. I just tried to compare it in a way which makes their claims just sound to big.

I do not propose a shared/distributed infrastructure, especially not for the storage (if they use up my 750GB, where do I leave my own data? Offline on DVDs?)

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:Enough to power a thousand homes

[ciroknight]

It's simple really. They have to power more stuff than your house does.

Whereas one computer doesn't really produce enough heat to cause a problem in the house (well, dependingly...), 2000 do. This requires an inbuilding airconditioning system to vent the heat, which adds a LOT to the energy bill.

The computers themselves are usually a small load when it comes to the utilites of the building. Oh, of course there are monitors, and things you'd find in an ordinary home (well, probably microwaves, coffee pots, crew comforts, florescent lighting..).

Re:Enough to power a thousand homes

[stilwebm]

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.


Actually you that is backwards. Residential power is usually more expensive. Think of it as buying in volume. Additionally, some businesses and many industrial power users negotiate lower rates with the stipulation that in case of a certain stage of power consumption/power shortage, their power will be cut. Many large power consumers, such as automotive plants own their own transformers and receive power directly from the wholesaler (say, TVA) rather than the local distributor.

For example, compare rates for my area:
Business
Residential

Re:Enough to power a thousand homes

[BranMan]

You have to add in the 'other' stuff too - network boxes, firewalls, routers, switches, etc. Also lights and AC for it all in one place. Not all the processors in the houses will be top of the line either, which adds to the AC bill. Maybe factor in redundancy in the network too - I wouldn't want a SPOF in an array that large. Stuff adds up...

Re:Enough to power a thousand homes

[jurt1235]

The stuff in my house adds up too:
My wife (means the average temperature in winter needs to be 5 degrees Celcius higher than without a woman
TV set
Of course lights
Fridge
Cooking on electricity (>2000 Watt for about 30 to 40 minutes a day on average)

24 hour airco is pretty destructive on the energy bill for these datacenters apparently, but looking at the outside temperature, it might not be needed all the time.
I still think they can get some more efficiency.
Spend a few days of CPU time on that, and you can buy yourself some extra machines from just the savings on the energy bill.

Re:Enough to power a thousand homes

[teknofyl]

24 hour airco is pretty destructive on the energy bill for these datacenters apparently, but looking at the outside temperature, it might not be needed all the time.

No matter what the temperature outside, without the aircon we have about a half hour before we have to start shutting kit down. Any longer than that and the temperature gets high enough to start causing damage to disks and other components.

(I work at the Sanger Institute)

Re:Overkill

[hjo3]

> Unfortunately, I am not Wil Wheaton [slashdot.org]. Thank god. I don't think I'd want to live in a world with two of him.

Windows

[Elshar]

They must be using Windows ClusterFun edition.

Re:Windows

[gstoddart]

They must be using Windows ClusterFun edition.

I think you mis-spelled that. :-P

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.

Re:Roland

[eclectro]

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.

have they heard of the petabox?

[itsme]

http://www.archive.org/web/petabox.php

it uses only 60kW for 1 Peta byte

Re:have they heard of the petabox?

[Lucractius]

Certainly a very impressive little rack they have there.

Shame if ive got a petabyte id rather have my system running a real os

VMS forever!!!

Hows them uptime records going eh?

Re:have they heard of the petabox?

[goneutt]

What structure do they use do manage the data?

Petafiles

If you didn't laugh, say it out loud.

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?

Re:Whats with the emphasis on power and its costs?

[jonoton]

You're quite right - the costs of the science far outway the costs of the IT.

Within the IT budget the cost of maintaining the equipment & running it (including power & cooling) far outstrip the original purchase price.

[I work here too]

Math

[Alphanos]

Cost of 0.75 MW: ~$170K
$/MW: ~$227K

Cost of 1.4 MW: >$600K
$/MW: >$429K

Why the difference?

Re:Math

[Hittite Creosote]

Part of it is probably inflation, but personally I'm hoping my electricity bill isn't going to double in the next three years...

Re:Math

[Walkiry]

>Why the difference?

Presumably, the infrastructure to get 1.4 MW safely inside the same building and distribute it is more complcated and expensive than what two independent .75 MW would be. Things tend to go down in price when you buy in bulk, until you reach a point where the amount you're asking for is giving more trouble than what is usually dealt with.

Re:Math

[Average_Joe_Sixpack]

Maybe it's a cleaner grade of electron ... you know the stuff audiophiles use

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.

Some computers use more power and do less

[Colin Smith]

I don't know which is the best in the ix86 market at the moment, possibly Via, possibly Intel, used to be Transmeta.

It's one of the things many geeks tend not to consider when they're dreaming up their ideal ultra powerful, ultra cheap beowulf cluster. The fact that you need a megaWatts worth of power and a megaWatts worth of cooling to go along with those $400 1U high density servers running the latest 4GHz AMD CPUs. Suddenly those cheap servers don't look so cheap.

Re:Some computers use more power and do less

[jordie]

Good to see you've got your facts straight before you posted.

AMD does not have a CPU running anywhere NEAR 4GHz, you're thinking of Intel.

As far as power consumption..
"Even the Athlon 64 X2 4800+ consumes less power than all single core 90nm Pentium 4 CPUs" - Anandtech

For more information please see this and this

For less power, better performance use AMD.

Re:Some computers use more power and do less

[ckd]

If you're doing this seriously, 1U servers are too big. IBM BladeCenter: 14 dual-processor blades in a 7U chassis, 6 of which fit in a rack. The power cables look like garden hoses.

Re:Breaking news from our reporter Roland Piquepai

[Anonymous Coward]

Quit badmouthing my man Roland! He provides a valuable service to slashdot, and he even gave me a blowjob for only $10! Roland will do ANYTHING for many, god bless his 'im.

Re:Fuck Roland

[frakir]

Mod parent up.

Just have a look on http://www.google.com/search?query=Roland+Piquepai lle&as_sitesearch=slashdot.org/ or search slashdot articles on roland piquepaille.

Real whore here is Timothy. I bet he'll post an ad for your site for some change, too.

Re:Breaking news from our reporter Roland Piquepai

[matt me]

enough to power 1000 homes with the equivalent power of distributed computing software?

probably not.

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.

Re:Units

[Gwyn_232]

No, MW is the correct way to express it.

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:Units

[Hank Chinaski]

mod parent insightful.

Re:Units

[tempest69]

Megawatts is correct, it the amount of energy that is being pulled continuously. So if you want to multiply the MW*24*365.25 you can get a total MWH/ YEAR, but it's a little silly.

Saying we use 75 MW Hours/Hour seems a bit retarded.

Storm

Alpha!

[Pegasus]

It seems all their boxen are based on Alpha processors. Why? Simply, because even today, you can get the most flops per clock tick out of Alpha. It's a shame such a wonderful architecture was burried.

Anyway, I think I'll be the first in line when they deceide to retire their gs320 servers :)

Re:Alpha!

[grouse]

I use the compute farm the AC refers to and I can confirm that the vast majority of it consists of x86 blades.

Re:Alpha!

[rubycodez]

not any more: the Itanium2 is 2 times as fast by that metric. Alpha @ 833MHz: SPECfp2000 644 SPECfp_base2000 571. Itanium2 @ 1.6 GHz: SPECfp2000 2675 SPECfp_base2000 2675. Alpha was cool in its day, some of those ideas went into Itanium. Itanium will "flop" in market for same reasons 8D

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:Genome - the dog chasing its tail?

[J. Random Luser]

To correct the kid's kids, you need to make the correction in the gamete, before the original kid is conceived. Maybe I'm not reading enough lately, but from Huxley to Gattaca, I don't recollect anyone actually trying that method...

Re:Genome - the dog chasing its tail?

[mikael]

Every person has about 7 major genetic defects in their DNA, which only become apparent when two parents with the same defective gene have children.

Dealing with genetic diseases relies on three stages:

1. Identify which genes cause the problem and how they are passed on through the generations; whether they are dominant or submissive.

2. Create a test which determines which genes each parent has. From this information, it is possible to determine whether the disease will be passed on to their children.

If there is a risk, then they can undergo further genetic screening to prevent the gene from being passed onto their children.

Re:Overkill

[Ziviyr]

Thank god. I don't think I'd want to live in a world with two of him.

Really, there wouldn't be any decent ST: TNG episodes if that were the case... :-)

Password

[jlebrech]

Dont bother decoding the thing!! ask God for the password!!

Re:Password

[loose_cannon_gamer]

Why ask? It is obviously 42. Somebody should have talked to Him about easily cracked passwords. *prepares to dodge lightning*

Research target

[readerVoice]

I wonder what the target of this research is. Daily I hear news on TV about people dying of hunger in Africa and other parts of the world. Can't this money be used there? Or am I nuts to think that way.

Re:Research target

[Anonymous Coward]

The human genome is only one of the many genomes being studied at the Institute.

One of the organisms being actively studied at the Sanger Institute is Paramecium falciparum, the organism that causes malaria, and Anopheles gambiae, a mosquito. Study of both of these will hopefully reap huge benefits in the treatment, prevention and perhaps eventually eradication of malaria.

The Pathogen Sequencing Unit that's doing that is also studying other major third world diseases, such as plague.

And much of what we do is developing technology and software tools which other researchers, both commercial and academic, can apply to their various areas of disease, pharmacology and agricultural research

Re:Research target

[LWATCDR]

So could every dime you spend on CableTV, eating out, video games, video cards, and anything else that you do not need to survive. You could also stop waisting time and get a second job and donate all that money to feed the poor. Remember that when you say "they" should do something about it... You are they.
That rant aside this research could lead to cures for all sorts of diseases that are currently killing people. So yes you are nuts to think that way.

Re:Research target

[XMyth]

Brand new trolling account?

Re:Research target

[Hognoxious]

people dying of hunger in Africa and other parts of the world. Can't this money be used there?

Yes, I'm sure $FAVOURITE_KLEPTOCRAT could find the space to squeeze another Mercedes in.

Re:Research target

[psylent]

I do not remember my high school biology very well but isn't it "plasmodium falciparum"?

Whoa

[grimhammer]

That remark should be sufficient here. I mean... whoa...

Cure your piquephobia

[Bemmu]

Do YOU hate Roland Piquepaille? It doesn't have to be so. With my scientifically proven brainwashing program, you can rid yourself of piquephobia forever!

http://www.bemmu.com/pique/

Re:Cure your piquephobia

[Maian]

Haha awesome game :p

Big deal!

[Anti Frozt]

My car requires 1.21 jigawatts and a flux-capacitor.

Re:Fuck Roland

[MrNonchalant]

According to the Google ads the joke might be on him:

Roland On Sale
Low Prices, Free Shipping
12 Months To Pay, Always In Stock
www.SamAsh.com

Roland in stock
Roland sale
up to 80% off Liquidation Sale
www.infinitemarketplace.com

Anyone else want to buy Roland and make him shut up?

Re:Fuck Roland

[jemfinch]

I'll take stories like this (Roland and all) over the consistently boring "Here's what Apple/Microsoft/SCO/Sony/USPTO is doing today!" stories we're inundated with otherwise.

At least this story is interesting. Why does it piss you off so much that someone makes some money off finding this story? If Roland makes some coin because he's bothered to pay attention to news sites I don't read and report interesting articles to a site I do read, by all means, more power to him! I'm glad he's doing the legwork so I don't have to.

Jeremy

Re:Roland

[metlin]

Awww, he's just French... =)

Compression, people, compression!

[seven of five]

Don't tell me endlessly repeated combinations of the same four base pairs needs 300 TB...

Re:Compression, people, compression!

[fbartho]

Don't tell me endlessly repeated combinations of the same four base pairs needs 300 TB...

I think it needs more than 300TB infact, it probably needs an infinite amount of space

Re:Compression, people, compression!

[ciroknight]

Compression would add to the need for a) greater data redundancy (because compression errors DO happen from time to time), b) more computational time (unless someone made a Gzip chip and stuck it on an HD controller.. *ponders*), and c) would be terribly cost-inefficient.

HD's are a dime a dozen. CPUs are not. If you have to have more costly CPUs running your File servers, that means less costly CPUs to run your Genetic Algorithms (pardon the pun).

Re:Compression, people, compression!

[confusednoise]

But they're storing MUCH more than just raw NT sequence -- they're storing all the annotation data around the sequence (which includes what genes are where, what papers have been written about those genes etc.) as well as a massive amount of data generated from experiments aiming at figuring out exactly what everything does and how it can be affected.

It adds up quickly. The nucleotide sequence is just the starting point.

How true

[kilodelta]

Friend of mine manages a cluster that models the worlds oceans. One thing they forgot about when planning it was the cooling needs. That added a nice chunk to the budget.

I doubt they even looked at the power requirements.

But it is cool to have access to a super computing cluster.

It's not *that* special

[photon317]

Those stats sound roughly comparable, if anything slightly lower, than what a private company I know of runs for seismic data processing.

We can do either

[cookie_cutter]

Will these kids inheric the original bad gene of their parent?

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.

Re:Roland

[tomhudson]

Aggh! I clicked on the link w/o looking! It was worse than goatse.cx. I am SO ashamed :-(

Seriously, I'm putting "127.0.0.1 primidi.com" in my hosts file TODAY.

Oh well.

[CAIMLAS]

So much for the whole, "only as complex as a fruit fly" blurb which people use to say humans are simple creatures.

I haven't a clue...

[Martin Spamer]

as to what they are actually doing with all this computing power.

OK I broadly understand 'sequencing the human genome' is mapping out all the combinates of genes. 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.

So why does it take so much computing power ?

What are the really doing with it ?

Why do they dum down these stories down so much ?

Facts and figures dont make a science story/article!

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:I haven't a clue...

[nounderscores]

I don't really know what these guys are doing with their computing power, but one cool free bioinformatics resources that allow you to browse the genome is

http://www.ensembl.org/

User interface is fairly intuitive and well documented.

You can see that serving this information is a non-trivial engineering problem.

Re:I haven't a clue...

[Misanthropy]

OK I broadly understand 'sequencing the human genome' is mapping out all the combinates of genes.

Sort of. Sequencing is really just finding the sequence of the DNA bases. (i.e. if a certain piece of DNA is ACCGT that is it's sequence)

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 pairs of chromosomes. Each human cell (besides sperm/eggs) have 46 chromosomes.
Each chromosome has many genes. There are about 30,000 estimated genes in the human genome. Each gene can be hundreds or thousands of DNA bases (not "one of four"). There are around 3 billion bases in the human genome. Think your desktop computer will handle that?

And your math is wrong. Even if you just had four bases, that is 256 combinations not 16.

So why does it take so much computing power ?
That is a lot of data to process and analyze.

What are the really doing with it ?
Analyzing the raw genome data. Trying to locate genes by itself is a pretty tough job. Trying to match protein sequences with their original gene. This can be very hard because the original DNA sequence does not always match the protein it ultimately codes for. Basically there is a lot of data and a lot of processing of that data.

Why do they dum down these stories down so much ?
Do some google searches on DNA, genes, bioinformatics, or gene mapping. You'll find plenty of articles that aren't so "dum".

Re:I haven't a clue...

[tempest69]

No, no! 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 other strand is cruical to act as a template to repair errors. The best analogy would be a raid-1, there are mechaisms to figure out which strand went bad, so then the information is recovered from the good copy. BTW each chromosome averages 4" in length, calling it immensely long might be a bit of a overcompensation. 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! The big thing that wasnt explicitly pointed out is that each chromosome has around a thousand genes. Genes are sets of hundreds to thousands of base pairs AT TA GC or CG.

not to knock, but listen carefully to what the person has a clue about, you skipped to the end part without correcting the original assumptions.. so even with the Now do the Math, the guy should assume that desktop power is fine. because you've said that the chromosome is immensly long, but didnt explain a base.. so he assumes that an A is an immensly long molecule composed of billions of bases, connected to an G A T or C also composed of billions of bases.

The I havent a clue as the headed should have clued you in.

Storm

listen next time.

Re:I haven't a clue...

[Rikurzhen]

At the start, one chromosome is maternal, the other is paternal. But over time, they actually swap bits around until there's a mixture. close... they don't swap bits in our body cells, only in the formation of sperm and egg cells. so, for example, the chromosomes your mother gave you thru her egg were a actually a combination of sequence originaly from your maternal grandparents. each body cell carries 2x genomes. each sperm or egg cell gets a randomly mixed 1x version. because the 1x genome is 3e9 bases, any two sperm or egg cells from a single person are totally unlikely to be identical. that's why siblings aren't normally identical.

Roland Piquepaille Arrested

[FidelCatsro]

Unfortunatly im lying

Re:Roland Piquepaille Arrested

[tomhudson]

I heard it wasn't an arrest, but that he volunteered to be a defense witness at the Michael Jackson trial. The deal Piquepaille offered was that in return for testimony admitting to being the real owner of Michael's porn mags, he'd get an exclusive interview on primidi.com, complete with pix of Michael's detachable nose collection, and banner ads from Crazy Glue. Or was it 3M duct tape?

The defense lawyers said they'd wait and see - they want to hear back from a rebuttal witness (the goat.cx guy) first, because they think he'd have more credibility with a jury.

Re:Roland Piquepaille Arrested

[Roland Picky-Pail]

I resemble that remark

Who is Roland Pipaquelle?

[eno2001]

Only one person in the world has ever claimed to have met him - in the pressroom at Microsoft Devshed Conference in Boston complete with a Roland Pipaquelle badge - and described him as a fortyish reddish-blonde who giggled a lot.

Oh yeah? Wonder what cold crème he uses. Rolland Pipaquelle is a 61-year-old Jehovah's Witness who lives in a shabby genteel garden apartment in desperate need of an interior decorator on a heavily trafficked commercial road at nnnn XXXXXXXXX XXX. XXXXXX, New York. XXXXXX is in XXXXXXXXXXX and XXXXXXXXXXX is Microsoft territory.

[snip]

Stop that! This is silly! Really! There is no room for this kind of silliness on Slashdot! Now... go home! And stop it! ;P

Re:Who is Roland Pipaquelle?

[Roland Picky-Pail]

And don't you forget it

humans are simple creatures

[nounderscores]

and so are fruit flies.

An arabadopsis plant on the other hand, that like most plants survives by modifying its cells rather than running away from danger, that's complex.

Sad...

[KoReE]

It's kind of sad that the datacenter I work in does nothing anywhere near as important as genome number crunching.....yet uses a TON more power, and has WAY more storage than this genome DC in this story...

a petabyte?

[austad]

I have a sony DMS-8400 petabyte storage array sitting in storage. They should buy it from me.

You wouldn't believe how hard it is to sell something like this. It seems like any of the companies that need it have the money to purchase it new. Argh!

genes run in both directions

[nounderscores]

and overlap. please see my other post linking to the http://www.ensembl.org/ genome browser.

if you want to see a very dense genome, try looking at some viri. they take advantage of the fact that each amino acid that is used to make the protein machinery are encoded using three bases, and so can put three genes almost on top of each other. It's on the level of funkyness of a programmer writing a sequence of bits in machine language where 8 fully functional programs could be derived depending on whether you shift out one to eight bits from the start of the "program" before loading the program onto the stack of a cpu that has an 8 bit opcode system.

Uh Oh

[ReidMaynard]

Be careful not to get a Flux Capacitor to close to this

hummm

[MutteringMonkey]

The Wellcome Institute... I wonder how they get their samples?

Clearance on low power chips, Aisle 3

[AirDave]

They should check out the going-out-of-business sale at Transmeta. Pick up a few dumpsters of low power chips.

Cheap electricity

[Stankatz]

That's some cheap electricity. I pay > $600/y for electric in my apartment. They must have their own power plant (no I didn't RTFuckingA, thank you very much.) I wonder how much of that waste heat they use for heating in the winter. ;)

The Relevant Quote Is

[Master of Transhuman]

"A shift from proprietary to commodity hardware will also help keep costs down, as will the planned move away from a proprietary 64-bit operating system to open-source Linux. Though the move chimes with Sanger's open-source ethos for its sequence data, Butcher cites solid practical reasons for the change. "HP [Hewlett Packard] pulled the plug on the Alpha chip," he says, "so we have nowhere to go." Moving to another proprietary system means it could happen again, he says. "I want something we can rely on and have control over our destiny for a good few years into the future.""

Linux rules again, proprietary fanboys!

Hmmm maybe they should call IBM

[Some_Llama]

I just saw a commercial the other day from IBM, int he commercial 2 scientists were looking for computers to help them map the human genome and replicate the folding of protiens.

The IBM representative said "Here is Gene, it is able to fold protiens and map the entire human genome". It was a cluster of IBM systems (maybe 40 total).

I just laughed and tried to explain to my wife how much BS this was (which basically describes all marketing).

Re:Fuck Roland

[TheRealStubot]

Oh, I'm terribly sorry! I clicked the link!

I admit, I wasn't going to, until you and your nazi friends convinced me that this Roland fellow must have something important to say, since everyone wants to repeal his freedom of speech.

Congradulations! You achieved exactly the opposite of your intentions.

Some social pointers:

1. Using bad language does NOT make you cool.

2. If someone has a different point of view than you do, it's NOT OK to assault them, verbally or otherwise.

3. If Roland and Slashdot have a financial arrangement, it's none of your business. Implying that you should have been informed of such an arrangement is conceited.

Remember Slashdot ( like life ) is what you make of it.

cooling

[Dioscorea]

Friend of mine manages a cluster that models the worlds oceans. One thing they forgot about when planning it was the cooling needs. That added a nice chunk to the budget.

I used to work at the Sanger Institute (before they were quite so big). One year after the main building was occupied, there was a fire in the main server room, filling the informatics corridor with black smoke. It turned out to have been started by a fan that had been left on all year...

1.4 MW = over 1000 homes?

[phliar]

That would mean that the mean power consumption of a house is 1.4 kW. A good hair dryer uses that much. Large appliances like air-conditioners, refrigerators, dishwashers, clothes dryers, etc. are all around 1-2 kW.

1.4 kW is about 2 horsepower. At 110 V, 1.4 kW is a current draw of 12 A. (At 220 V, it's 6 A.) I guess "over 1000 houses" sounds much better than "a few hundred houses."

Odd storage requirements.

[jesdynf]

300 terabytes, advancing to a petabyte in three years? I can see it now.

"Yeah! We got it! The whole Human Genome! We scanned that sucker in... wait, what? You meant... /all/ the genome? Okay. Uhm. Well, we already got Alice scanned in. I guess we can have Bob done in another couple years or so, maybe Charlie after that, but I think we're going to need to look at how we're doing this..."

The object (CPU) of my desire (geek lust)

[Moekandu]

Yes, many organizations that "do this seriously" will use blade servers and ridiculous amounts of power.

However, if I were doing this seriously, I would be shopping here.

DS-96
96 CPU's (Efficeon)
230 GFlops
1500W Max Power

Is the hardware cheaper? No. But once you factor in the power and cooling infrastructure and costs, it's definitely the way to go. Especially when you consider that 22 of the above machines will give you 2112 CPU's cranking away with a max power draw of 33,000 Watts, instead of 750,000 Watts.

Granted, with WTSI's setup, there's still the consideration of power and cooling requirements for the storage arrays. Not an insignificant issue.

Exponential Algorithms

[SauroNlord]

I am a comp sci major, just finished my Bsc and continuing towards data mining and bioinformatics for a graduate degree...I do not know as much as I would like to know however I can tell you that the best algorithms are typically brute-force solutions. Why? Because the amount of data and the precision that we require does require all combinations to be processed and analyzed. This all comes back to algorithm efficiency and analysis (big-O a.k.a asymptotic growth rates). Many of these algorithms are of the NP-Hard class, meaning that a polynomial time(read: 'efficient') algorithm in terms of the input (n x m matrix[n dna sequences, each at most m bases long]) are very very very unlikely.

There are proofs showing that the algorithms are the best (even though they are the brute force) that is possible....so one way or another someone will have to do the 'infinate computations'

Might as well get started!