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Chinese Lab Speeds Through Genome Processing With GPUs

Posted by timothy on from the looking-for-the-reset-button dept.

Eric Smalley writes "The world's largest genome sequencing center once needed four days to analyze data describing a human genome. Now it needs just six hours. The trick is servers built with graphics chips — the sort of processors that were originally designed to draw images on your personal computer. They're called graphics processing units, or GPUs — a term coined by chip giant Nvidia. This fall, BGI — a mega lab headquartered in Shenzhen, China — switched to servers that use GPUs built by Nvidia, and this slashed its genome analysis time by more than an order of magnitude."

104 of 408 comments (clear)

  1. The Future Is Here!! by mastershake82 · · Score: 5, Funny

    Sounds like these newfangled "GPUs" are gonna change the world.

    1. Re:The Future Is Here!! by MollyB · · Score: 4, Insightful

      If one reads to page 2 of tfa, they only claim the technique works well in this instance. They go on:

      Even for computer-intensive aspects of analysis pipelines, GPUs aren’t necessarily the answer. “Not everything will accelerate well on a GPU, but enough will that this is a technology that cannot be ignored,” says Gollery. “The system of the future will not be some one-size-fits-all type of box, but rather a heterogeneous mix of CPUs, GPUs and FPGAs depending on the applications and the needs of the researcher.”

      and

      GPUs have cranked up the speed of genome sequencing analysis, but in the complicated and fast-moving field of genomics that doesn’t necessarily count as a breakthrough. “The game changing stuff,” says Trunnell, “is still on the horizon for this field.”

      So yes, the article is a bit breathless, but if utilizing GPUs helps cure my potentially impending genetic disorder, I'm all for it.

    2. Re:The Future Is Here!! by davester666 · · Score: 1

      Yes, unfortunately, you will be unable to pay for that cure, unless you own the business you work for.

      --
      Sleep your way to a whiter smile...date a dentist!
    3. Re:The Future Is Here!! by Anonymous Coward · · Score: 1

      I used to work with Texas Instruments TMS34010/32020/34082 processors in the 1990's. These were surface mounted onto a VGA graphics board, along with a number of TMS34082 vector processors and a few megabytes of memory (Hercules Graphics Station Card as an example). They had this really neat feature where you could cross-compile, download and execute programs on these boards as "extensions". You could do anything from encryption/decryption, image-processing to drawing lines and rendering triangles.

      Initially, these were known as "graphics accelerators", though they quickly became "graphics deaccelerators" as motherboard bus and CPU clock speeds increased so rapidly - those days PC clock speeds were 20 - 25MHz, graphics card clock speeds were 60 - 90 MHz.

    4. Re:The Future Is Here!! by Stormthirst · · Score: 3, Insightful

      Unless you are fortunate to live in a civilised part of the world with a universal healthcare system.

    5. Re:The Future Is Here!! by davester666 · · Score: 1

      You stinking communist!

      Don't think you can keep giving away the cures to your patients that we develop so we can gouge our victims er patients.

      --
      Sleep your way to a whiter smile...date a dentist!
    6. Re:The Future Is Here!! by Stormthirst · · Score: 1

      Your point? *snicker*

  2. News for nerds by Anonymous Coward · · Score: 5, Funny

    I always wondered what GPUs are. Thanks Slashdot!

    1. Re:News for nerds by galanom · · Score: 5, Funny

      No, it's "Guinea Pig Units"

    2. Re:News for nerds by Anonymous Coward · · Score: 1

      And there I was thinking there was a chance it could be "Guanxi Publicity Units".

    3. Re:News for nerds by maxwell+demon · · Score: 1

      Genome Processing Unit

      --
      The Tao of math: The numbers you can count are not the real numbers.
    4. Re:News for nerds by formfeed · · Score: 1

      German Pilsner untergärig

    5. Re:News for nerds by nevillethedevil · · Score: 3, Funny
      I thought it was 'Gnomes Processing Underpants' and that we finally had that elusive missing step

      1. Steal underpants
      2. Process underpants
      3. Profit

      --
      Be gone from my sight or prepare to feel my flaming wraith!
    6. Re:News for nerds by supremebob · · Score: 1

      We know what they are, but we've been using them to play Battlefield 3 or create phony "untraceable" currency for drug dealers instead.

    7. Re:News for nerds by SeaFox · · Score: 1

      I always thought it stood for General Processing Units!

      Didn't you read the summary title? It's obviously Genome Processing Unit.

    8. Re:News for nerds by virgnarus · · Score: 1

      I thought it was 'Gnomes Processing Underpants' and that we finally had that elusive missing step

      1. Steal underpants 2. Process underpants 3. Profit

      I knew Bitcoin mining smelled funny...

    9. Re:News for nerds by Forty+Two+Tenfold · · Score: 1

      You made my day, Mr Stewart.

      --
      Upward mobility is a slippery slope - the higher you climb the more you show your ass.
  3. Summary dumbed down enough for you? by Anonymous Coward · · Score: 3, Insightful

    Explaining what a GPU is in a slashdot summary? Come on.

    This is similar to someone telling you a story about something funny happening to them while shopping at the store, pausing mid-story to inform you that a 'store' is a business where goods are displayed and exchanged for a papery substance called 'money'.

    1. Re:Summary dumbed down enough for you? by galanom · · Score: 1

      It might have some use. "store" is chiefly American English. British would prefer "shop", though they should definitely be able to understand what you are talking about. But in both BE and AE "store" would also mean "to keep".

    2. Re:Summary dumbed down enough for you? by Anonymous Coward · · Score: 1

      I don't mind the explanations in the submitter's summary too much: it's better than some of the jargon/acronym laden summaries that totally obfuscated some summaries, and abstracts need to avoid jargon in order to pull in interested readers. I do, however, mind that the summary just plagiarizes the first few sentences of the Wired article. I'm also unhappy with the watered-down article; summaries and abstracts need to avoid jargon for clarity, but articles need to use the right words to convey their points, and they need to have more depth to them than this one does.

      As for Wired's the repetition of Nvidia, which is really tangental to the main point (BGI's accomplishment), makes this look like a case study taken out of Nvidia's marketing literature. The BGI story ends at the second paragraph (the extent of submitter's summary), and the rest of the article is like a jumble of press releases from Nvidia and Amazon. My guess is that someone was facing a deadline, had no ideas, and ransacked some press releases (not astroturfing, just laziness in the face of deadlines).

  4. This article is almost painfully dumbed down... by tiffany352 · · Score: 2

    Submitter couldn't find a more technically-oriented one?

    1. Re:This article is almost painfully dumbed down... by gman003 · · Score: 2

      Hell, even the summary is condescending.

      This is Slashdot. You don't have to explain what a GPU is.

    2. Re:This article is almost painfully dumbed down... by Anonymous Coward · · Score: 1

      I'd say there are too many summaries that fail to explain the acronyms used. Not all readers have the exact same knowledge.

    3. Re:This article is almost painfully dumbed down... by Zakabog · · Score: 5, Informative

      The summary is pulled directly from the top of the article.

      Here's the article from HPC Wire and some details from nvidia as well as the nvidia press release

    4. Re:This article is almost painfully dumbed down... by SomePgmr · · Score: 1

      Sure, as they often are. I thought it was funny though. Usually I shake my head at the silly use of BS, jargon-of-the-week phrases in the summaries without any effort to define them.

      And then we get a verbose definition of "GPU"... one everyone is familiar with. The lack of consistency might be explainable, but it's kinda funny. ;)

    5. Re:This article is almost painfully dumbed down... by tiffany352 · · Score: 1

      Not all readers know how to use google either, apparently.

    6. Re:This article is almost painfully dumbed down... by heironymous · · Score: 1

      That's an unfair comment. Acronyms can stand for more than one thing, and a good writer's intent is not to show how much smarter they are than their readers.

    7. Re:This article is almost painfully dumbed down... by heironymous · · Score: 2

      I agree, and it would be a better policy to define acronyms the first time they are used. The same could be said about the names of software packages in other summaries. I'm mystified that so many commenters are miffed that GPU is explained.

  5. Reader's Digest by Anonymous Coward · · Score: 1

    It reads like some Reader's Digest piece. I can't believe timothy published it like that. :)

  6. A reminder by Mannfred · · Score: 5, Insightful

    It's hardly news that GPUs can be used to speed up parallel tasks/computations, but even so this article is a useful reminder of two things; 1) there are still many important processes that can be sped up by using GPUs, and 2) this can be achieved pretty much anywhere in the world.

    1. Re:A reminder by peragrin · · Score: 2

      The only reminder should bethat processors designs for different types of math can do that math faster than processors designed for other types of math.

      I don't understand why companies don't realize that. Running graphics on a floating point processors is like using a train to go across an ocean. Sure you can do it doesn't mean that it is a good idea.

      --
      i thought once I was found, but it was only a dream.
    2. Re:A reminder by blahplusplus · · Score: 2

      "The only reminder should bethat processors designs for different types of math can do that math faster than processors designed for other types of math."

      Not all kinds of math can be parallelized.

    3. Re:A reminder by purpledinoz · · Score: 1

      I always wondered why FPGA's aren't used for this kind of stuff, or if they already are. I would imagine they would even be faster because you can design a circuit specifically optimized for the problem. But now that I think about it, NVidia and AMD put considerable amounts of resources into making them super fast and cheap. I guess price/performance ratio would be pretty damn good on a GPU vs FPGA.

    4. Re:A reminder by the+gnat · · Score: 2

      I always wondered why FPGA's aren't used for this kind of stuff, or if they already are. I would imagine they would even be faster because you can design a circuit specifically optimized for the problem.

      I think they are to some degree, but there is a major barrier to adopting them: they require specialized programming knowledge which you won't find in most genomics centers. GPUs are commodity technology and APIs like CUDA are easier to tackle (and more transferable to other fields) than FPGA programming. (Or such was my impression - I know a lot about bioinformatics, but much less about FPGAs.)

      There is at least one company that sells hardware specially accelerated for bioinformatics, CLC bio. I don't know if they use FPGAs or some kind of ASIC.

    5. Re:A reminder by gmhowell · · Score: 1

      you have proof of this ?

      I don't have room to write it in the margins of this website. The borked .js keeps killing it.

      --
      Jesus was all right but his disciples were thick and ordinary. -John Lennon
    6. Re:A reminder by Vegemeister · · Score: 1

      The versatility of FPGAs comes at a steep price in die area, power consumption, and operating frequency. If your design goal is "We want to do this specific kind of math Real Fast.", and somebody already makes an ASIC that does that kind of math Real Fast, the ASIC is generally a lot more cost effective than using FPGAs.

    7. Re:A reminder by Pseudonym · · Score: 1

      What the article doesn't say:

      • BGI is late to the party when it comes to using GPUs to process genomic data.
      • "Processing" could mean just about anything.
      --
      sub f{($f)=@_;print"$f(q{$f});";}f(q{sub f{($f)=@_;print"$f(q{$f});";}f});
    8. Re:A reminder by blahplusplus · · Score: 1

      http://en.wikipedia.org/wiki/Amdahl's_law

    9. Re:A reminder by Asmodae · · Score: 1

      Are any researchers really looking for skilled FPGA designers? It's a pretty dedicated skillset, but work on research would be more interesting than my current job. Also, it should be noted that the devices themselves (FPGAs), and the tools needed for the design flow (particularly synthesis tools) are expensive, and computationally intensive in and of themselves. Unfortunately we don't have the open source tools of the software world available to us.

  7. Wonder the speed for using AMD by witherstaff · · Score: 2

    I wonder if the AMD use of more cores, whereas Nvidia uses faster cores, would change the time. I have no idea how genetic algorithms work. I do know simple hashes like bitcoins are best on AMD.

  8. A better article by arielCo · · Score: 4, Informative
    http://hpcwire.com/hpcwire/2011-12-15/bgi_speeds_genome_analysis_with_gpus.html

    Excerpt:

    At BGI, he says, they are currently able to sequence 6 trillion base pairs per day and have a stored database totaling 20 PB.

    The data deluge problem stems from an imbalance between the DNA sequencing technology and computer technology. According to Dr. Wang, using second-generation sequencing machines, genomes can now be mapped 50,000 times faster than just a decade ago. The technology on track to increase approximately 10-fold every 18 months. That is 5 times the rate of Moore's Law, and therein lies the problem.

    Obviously it would be impractical to upgrade one's computational infrastructure at that rate, so BGI has turned to NVIDIA GPUs to accelerate the analytics end of the workflow. The architecture of the GPU is particularly suitable for DNA data crunching, thanks to its many simple cores and its high memory bandwidth.

    --
    This post contains no rudeness or derision of any kind. All arguments are friendly. Terms and exclusions may apply.
    1. Re:A better article by Samantha+Wright · · Score: 4, Informative

      ...countering this stunning and exciting revelation is BGI's stunning and exciting reputation for producing stunningly and excitingly low-quality raw data from said stunning and exciting second-generation sequencing machines. This is a little like the biology equivalent of being told that your least-favourite Slashdot editor (please pick just one) has just gotten a brain implant so he can spam the front page with dupes, typo-ridden summaries, and fallacy-laden opinion pieces ten times an hour.

      --
      Bio questions? Ask me to start a Q&A journal. Computer analogies available for most topics!
    2. Re:A better article by mapkinase · · Score: 1

      The problem with next generation sequencing is that it produces a lot of garbage as well. There is no free lunch. And that is why a lot is passed on computers to handle that garbage. Also, computation speed hours per genome annotation does not make sense without reference to what exactly and at what reliability is being annotated,

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  9. c'mon intel by Cyko_01 · · Score: 1

    I get that programmers are offloading certain tasks to the GPU because they are able to perform specific tasks faster, but why is this even necessary. If the GPUs are so good at it then why can't there be a dedicated part of the CPU to perform these same computations in parallel streams the same way the GPU does?

    1. Re:c'mon intel by wbr1 · · Score: 1

      Both modern Intel and AMD CPUs come in flavors that include a GPU core. I am currently running a laptop with an AMD E-450 that has a GPU core. Admittedly this core is stripped down, but it is there, and functional, and probably better than many higher end GPUs of 4-6 years ago. There are two other issues surrounding the use of GPUs for processing. One, competing APIs, and two, few programs make use of the availability. I believe some Adobe software (either Premiere or some Photoshop filters) are now written to take advantage of certain brands and models of GPU. There isalso A/V transcoding software that does as well. Why not more? One there used to be no unified API. You had CUDA for Nvidia and Firestream (I think) for AMD/ATI. OpenCL is supported by both, but I do not know if it has limits that the proprietary APIs do not. Second, just as more and more software has been rewritten to take advantage of multiple cores/CPUs (still have a long way to go there), the same will be true of software written to take advantage of GPUs. Not being a programmer (beyond a little scripting) myself, it seems logical that if it has taken this long for programmers (and compilers) to really start to take advantage of 2-8 processors, then learning what tasks can be broken down to several hundred or thousand smaller cores, and how to do it may take a while too. Hell, running a search in regedit in Windows 7 still takes 100% of one core, and only has one thread.

      --
      Silence is a state of mime.
    2. Re:c'mon intel by Macman408 · · Score: 1

      First question: Why do you want it from Intel, versus anybody else? They've always struck me as moderately evil - the Microsoft of the chip world, looking out for their own sales numbers and not much else.

      Second question: Which do you want in your chip; a fast CPU that can run your web browser and E-mail client, or a fast parallel computing unit that's good for gene sequencing, multimedia processing, etc? You can't have both. Well, you can, but both parts will be slower. The top-of-the-line chips you get these days are as big as can be reasonably manufactured, and produce as much heat as can be reasonably removed from the chip (without requiring you to supply a source of liquid nitrogen). You can combine them, but you won't get great performance from either the CPU or the GPU/"parallel unit" in that case. You're better off buying two chips. And Intel has a pretty poor history at making graphics chips with reasonable performance.

    3. Re:c'mon intel by Xrikcus · · Score: 1

      There is: AVX. The difference is that to cope with the workloads GPUs are NOT good at, a lot of the CPU transistors are dedicated to things other than AVX units and registers so the peak is lower.

  10. SIMD for the Win! by adharma · · Score: 1

    SIMD chips will always show computational gains to any class of problem that makes significant use of matrix multiplication or linear algebra. So graphics, crypto, etc..

    --
    What word rhymes with buried alive?
  11. Re:first by Pieroxy · · Score: 4, Insightful

    So, a site dedicated to nerds needs to explain what a GPU is? Are we not nerds anymore?

    --
    Write boring code, not shiny code!
  12. Re:first by Samantha+Wright · · Score: 1

    Yeah, Wired, what gives?

    (Hint: the summary is a direct quote from the enterprise-y TFA.)

    --
    Bio questions? Ask me to start a Q&A journal. Computer analogies available for most topics!
  13. I've been Folding for years on GPUs by unassimilatible · · Score: 1

    And other assorted distro-computing tasks. Hell, my old x1800's stopped being supported for the current Folding software years ago.

    A nice list of distro computing projects.

    Another nice list of such projects.

    --
    Slashdot "libertarians": Small government for me, big government for those I disagree with. -1, I disagree with you
    1. Re:I've been Folding for years on GPUs by RicktheBrick · · Score: 1

      I have been volunteering for more than a decade now. I first started with united devices. They have stopped now for about 5 years. I started with single core computers. About 4 years ago I bought my first 4 core computer and last year I bought two 6 core computers. The 6 core computers do twice as many results than the 4 core computers. The 4 core computers do 6 times as many results as the single core. Therefore I think a single 6 core computer would pay for itself in electricity costs in less than three years I would think that this would continue with a super computer that has thousands of cores. Here is a link to a super computer that cost only $1,4000,000 http://www.eng.vt.edu/news/virginia-tech-s-wu-feng-unveils-hokiespeed-new-powerful-supercomputer-masses. Now if only 100,000 volunteers donated just $20 each for a total of $2,000,000 someone could purchase that super computer and have $600,000 for their expenses. $20 a year is probably far less than the average volunteer is paying for the extra electricity. I think that this super computer would do more results than the over 500,000 members of World Community Grid do now.

  14. The Answer Lies in Parallel Computation by turkeyfish · · Score: 1

    Genomic analysis involves extensive use of recursive techniques, which are well suited to parallel processing and combinatoric problems. GPU's are small independent components originally designed to handle large matrices of pixel elements for video programming very quickly for video display and refresh. Thus, they can when suitably programmed, for example using CUDA, in parallel to compute solutions required to map problems of high combinatoric dimensionality onto a one dimensional space (sequence) very quickly compared to a CPU that would require serial computation on an extremely large combinatoric space. Effectively, it puts massive supercomputers in the petabyte and exabye processing speeds to be built with standard components at modest prices.

    The amazing thing about this technology and the responses of the supposedly technologically sophisticated responses on a site such as slashdot, is that the Chinese are picking up on the technology and on genomic data mining far faster and with more intensity than is the broader US tech community. Given the size of their brainpower base and the rate at which they are adapting the technology the Chinese are well on their way to dominating the drug development and physiological/functional genomic sciences in the next 10 years. The race will largely be over before most American tech types even know it happened.

    The even more amazing thing is the potential of unlocking the genetics which control human intelligence, memory and learning capacity. Once these are patented and developed for a host of applications all other forms technology will become increasingly inconsequential. While the US is putting its most powerful computers to use cracking into and reading people's email, the Chinese have a more ambitious agenda.

    Actually, this is a good thing, since the Chinese are far more cognizant of the dangers posed by imminent global warming due to carbon dioxide pollution to their economy and the the stability of their political system. If you have any doubts about the Chinese propensity to use their wits, I suggest you see the movie Red Cliff, which very dramatically displays the remarkable triumph of wits over shear military superiority. Its based on a true story.

    1. Re:The Answer Lies in Parallel Computation by the+gnat · · Score: 2

      the Chinese are picking up on the technology and on genomic data mining far faster and with more intensity than is the broader US tech community.

      You're forgetting that the vast majority of countries actually developing this technology, and making it available to consumers, are based in the US (and Britain, to some degree). One recent article about the BGI that I read last year noted the irony of seeing several crates of sequencing machines stamped "MADE IN THE USA" waiting to be unloaded in Shenzhen. The Chinese government is certainly willing to spend large amounts of money advancing their capabilities, but I haven't seen any evidence that they're significant surpassing the US in anything other than sequencing capacity. (And the machines they're using are very good for generating large quantities of data, but the quality of said data is somewhat suspect.)

      Given the size of their brainpower base and the rate at which they are adapting the technology the Chinese are well on their way to dominating the drug development and physiological/functional genomic sciences in the next 10 years.

      Except that genomics has as of yet proven minimally useful for drug development. Until they actually develop significant amounts of homegrown technology (which, to be fair, they are actually doing in the bioinformatics arena, as opposed to sequencing), I'm not convinced that they're that much of a threat. What they will certainly accomplish, I think, is a record of high-profile scientific output and the ability to compete on even terms with the rest of the industrial superpowers. No mean feat considering where they were 40 years ago, and certainly some cause for concern given their large and inexpensive labor force, but it's not the same thing as suddenly eclipsing the USA in technology that they're still mostly importing or stealing.

    2. Re:The Answer Lies in Parallel Computation by turkeyfish · · Score: 1

      Sounds a lot like wishful thinking to me. I agree that virtually all technology is global these days. Its just the rate of uptake that is astounding. About 35% of all US PhD students are Chinese an other 35% are Indian, while US grads are diminishing as a percentage. Major cutbacks in the UK now as well, but China is growing in double digits in most technology areas. I don't read Chinese myself, but the number of journals in the genomics area for Chinese readers is growing fast.

      Beg, borrow, steal, collaborate it all comes down to the same effect. The momentum is shifting and shifting quickly, while our politicians sleep and throw cocktail parties to raise campaign dollars. Not necessarily a bad thing, especially given what sad shape planet earth is in, but when the reality does start to set in a lot of people are going to have nervous breakdowns and lots of unrealistic expectations. Keep in mind much of that importing is done on our dime given our otherwise large trade imbalance on most other commodity goods.

      In any event, the throughput for NVIDIA's Tesla product lines are quite impressive. They really are revolutionizing computational biology, where there are many NP complete and NP Hard problems that can only be tackled with very past processors (in parallel) and with heuristic rather than exact algorithms. Do you know if these are manufactured here or in Asia?

    3. Re:The Answer Lies in Parallel Computation by turkeyfish · · Score: 1

      Like much of science, we often only see the small pieces that we are most familiar with. Biology is not rocket science, the underlying mathematics is much more difficult than rocket science. A small combinatoric problem in a biological context can contain a larger solution space than all the electrons in the known universe.

      I'm at the other end of Biology myself, Systematics (at the intersection of Taxonomy, Morphology and Machine Vision). The bridge between the two is where the action is in terms of functional genomics, its just that it is very hard to frame, much less compute, the equations needed to solve problems that unify both ends of the spectrum at once. Most biological problems don't lend themselves to ready statistical analysis because evolution is largely a long sequence of many nearly random events involving incredible complex interactions of encompassing extraordinary diversity and because statistical techniques have great difficulty factoring out the effects of phylogeny.

      I just wish I only paid more attention to mathematics at a much earlier age. Without it, making the connections is hopeless. I guess that's why I see the potential for parallelism in GPU computing revolutionizing most biological disciplines. What worry about is that given the difficulty of these problems and the time it will take to get solutions carbon dioxide pollution and human population growth will largely have exterminated much of the biodiversity we will need to obtain answers. Maybe with luck our Chinese colleagues will push the frontiers faster than we are. I guess they better hope so as their environmental problems are often much larger than our own on a local and regional level, although all this talk of eliminating the EPA may get us quickly there as well.

    4. Re:The Answer Lies in Parallel Computation by the+gnat · · Score: 1

      In any event, the throughput for NVIDIA's Tesla product lines are quite impressive. They really are revolutionizing computational biology, where there are many NP complete and NP Hard problems that can only be tackled with very past processors (in parallel) and with heuristic rather than exact algorithms. Do you know if these are manufactured here or in Asia?

      I don't know where they're manufactured; my impression was that most of the really powerful chip-fabrication technology was still essentially based in the US. This is one area in which China is still substantially behind, although they're certainly not stagnant.

      I agree that GPUs are making a significant contribution to the biomedical sciences, but once again, most of the progress has been in the US and Europe. Moreover, there are still limits to what they're useful for; in my specialty, X-ray crystallography, they don't gain us much. In any case, any organization with enough money can buy a rackful of GPUs, write a few dozen lines of CUDA, and brag about its newfound processing might and cutting-edge software. I'm not impressed until I see major innovations that truly surpass the work being done in the First World. I'm sure China is working on this, but I haven't seen anything yet that makes me fear for my job (especially not in my field). The most frightening aspect is China's willingness to throw large amounts of money at boosting their scientific output - because many interesting problems are limited as much by expense as by experimental details.

  15. So the visiting politician asks, "What are GPUs?" by PolygamousRanchKid+ · · Score: 1

    "GPUs . . . ? . . . I was informed that this project was powered by GNUs . . . ?"

    ". . . now where is that Apple MAC chip that generates the GPL number that allows the PC to connect to the Internet . . . ?"

    --
    Schroedinger's Brexit: The UK is both in and out of the EU at the same time!
  16. Re:yes' but... by galanom · · Score: 1

    Only if you have a Beowulf cluster of them!

  17. Re:bad article by Anonymous Coward · · Score: 1

    Turns out I've been wrong about you all this time. It's the goats having sex with you isn't it?! You just love the burn of a hot goat cock in your tender brown bud don't you. HA, no lube for you!

  18. Part of the problem is Low Standards by MaizeMan · · Score: 3, Informative

    Although at least in my field the problem is that no one ever thought to set lower limits on the quality of what you can call a genome. So now we get "genomes" made up of 100,000 contigs (many only a couple of hundred base pairs long) and even counting all of those, the total sequence might account for only 70% of the total size of the genome. But it's still a "genome" paper, which is still an instant ticket to Nature Genetics (or Nature Biotechnology if the assembly is REALLY bad).

    BGI is certainly one of the biggest offenders (Cucumber and Pigeonpea are both examples of the sort of terrible genomes-in-name-only BGI puts out) but I think the real problem is that Illumina sequence data is so cheap people keep trying to use it to sequence genomes, thinking if they throw enough raw data and enough mate-pair libraries at the problem it'll eventually make up for the fact that Illumina reads are so short. Illumina data is great for a lot of things. Calling SNPs, measuring gene expression, studying methylation patterns.

    But, at least for any genome significant transposon content, it simply does not work.

    1. Re:Part of the problem is Low Standards by Samantha+Wright · · Score: 1

      Incidentally, ABI claims you can do de novo with SOLiD systems (which have read lengths of only ~20 bp!) but they say you need to get about 300x coverage just for a bacterial genome. That's not a lot of saved money when you work out all the numbers. It looks like we've nearly found a state function for dollars-per-high-quality-nucleotide.

      --
      Bio questions? Ask me to start a Q&A journal. Computer analogies available for most topics!
    2. Re:Part of the problem is Low Standards by the+gnat · · Score: 1

      you need to get about 300x coverage just for a bacterial genome

      OUCH. Wasn't the original high-quality human genome sequence (using Sanger technology) only about 10x? And doesn't having only 20bp per read basically rule out de novo sequencing of any eukaryote? Even for bacteria that sounds tricky without a closely-related reference sequence.

    3. Re:Part of the problem is Low Standards by Samantha+Wright · · Score: 1

      Yes, yes, and yes. To be fair, these are comparatively cheap and fast runs, but the numbers are still ridiculous, I agree. Hopefully third-generation sequencing technologies (not counting Pacific Bio's implausible promises of "3.1 billion flying pigs in 30 seconds flat!") will do better at pandering to us poor underfunded evolutionary biologists.

      --
      Bio questions? Ask me to start a Q&A journal. Computer analogies available for most topics!
  19. Now where are the HTX slots / HTX GPU cards by Joe_Dragon · · Score: 1

    Just thing how cool it will be to have cards that can do this on the CPU BUS.

  20. For the curious... by Cow+Jones · · Score: 5, Funny

    ... this is what a Chinese lab looks like.

    --

    Ah, arrogance and stupidity, all in the same package. How efficient of you. -- Londo Mollari
  21. From the article..... by Doubting+Sapien · · Score: 1

    According to Jackson Lab’s TeHennepe, the feat BGI and NVIDIA pulled off was porting key genome analysis tools to NVIDIA’s GPU architecture, a nontrivial accomplishment that the open source community and others have been working toward.

    Can anyone familiar with current efforts shed more light on this? Who is working on open source bioinformatics and how much work has been done?

    --
    ========== "Hello World" in my programming language of choice: ATG - LET THERE BE LIFE - TAG ==========
  22. Re:NOT coined by Nvidia by nedlohs · · Score: 1

    Commodore didn't. The C64 had the "VIC-II" (video interface chip II). The Amiga had Agnus and Denise and later the AGA.

    I'm don't think Atari did either. Sure they had a Blitter chips and there was graphics accelerators and so on. But I don't think the term "GPU" was used.

    I don't recall anyone arguing with it at the time either: http://www.tgdaily.com/hardware-brief/18947-nvidia-launches-worlds-first-gpu.

    Still PU was common enough already.

  23. Re:first by Tubal-Cain · · Score: 1
    So why not:

    "The world's largest genome sequencing center once needed four days to analyze data describing a human genome. Now it needs just six hours. The trick is servers built with...GPUs — a term coined by chip giant Nvidia. This fall, BGI — a mega lab headquartered in Shenzhen, China — switched to servers that use GPUs built by Nvidia, and this slashed its genome analysis time by more than an order of magnitude."

  24. Re:NOT coined by Nvidia by russotto · · Score: 2

    A search of Usenet reveals the Atari Jaguar had a unit called a "GPU" in 1993, considerably before NVIDIA's "first GPU" in 1999. The Amiga unit was also called a GPU.

    The term's generic, and NVIDIA knows it... they don't have it registered as a trademark.

  25. What if they pull an Apple? by ibsteve2u · · Score: 1

    Except that genomics has as of yet proven minimally useful for drug development. Until they actually develop significant amounts of homegrown technology (which, to be fair, they are actually doing in the bioinformatics arena, as opposed to sequencing), I'm not convinced that they're that much of a threat.

    What if they simply avoid competing by patenting the sequence for Caucasians and then pulling an Apple and suing us out of existence? ;^)

    --
    Orwell: "In a Time of Universal Deceit, telling the Truth is a Revolutionary Act"
  26. Re:Show Me the Monkey by turkeyfish · · Score: 1

    That seems to be the general attitude across the board in the US, but it seems unlikely to be warranted any more. They keep growing their economy at between 8-10% per year. Estimates are their GDP will overtake that of the US in about 2025, if not sooner. The days of resting on laurels will have been gone by then. In any event if we are that far ahead, it seems hard to get a sense of that on slashdot judging from the sophistication of most comments.

    Besides, I be curious to know what specific research has been falsified? Its not as if the US fossil fuels industry hasn't been doing the same here with respect to climate science.

  27. Re:first by Pieroxy · · Score: 1

    First, I didn't read the AC's comment. Then I thought the FP in question was pretty relevant to the quality of the summary. Not a troll in my view and I explained why.

    Of course, it depends your point of view I guess. My post was probably badly worded.

    --
    Write boring code, not shiny code!
  28. Even faster by aprdm · · Score: 1

    Imagine if the calculus were processed in a FPGA, it would be another magnitude faster :P

  29. Re:http://www.youtube.com/watch?v=lW7fZ0etra0 by MichaelKristopeit551 · · Score: 1

    i should really get a life.

  30. Re:ROFL! clone53421=MichaelKristopei330=pudge=LOL by MichaelKristopeit497 · · Score: 1
    ur mum's face're a joke, and have been LIBELLING. (i'm not sure what LIBELLING is... but if it's anything like libeling, it sounds like you can't cope with being an ignorant hypocrite).

    clone53421 = stephen alongi... i am not stephen alongi... i am michael kristopeit. you don't understand the difference, because you're an idiot.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  31. Re:Show Me the Monkey by c6gunner · · Score: 1

    Besides, I be curious to know what specific research has been falsified?

    Here's a decent summary of the problem:
    http://www.nature.com/news/2010/100112/full/463142a.html

    Its not as if the US fossil fuels industry hasn't been doing the same here with respect to climate science.

    "Microsoft has put out some faulty software, so I'm gonna buy my next operating system from VaporWare Inc"

    They keep growing their economy at between 8-10% per year

    That's part of the problem:

    A new study from Wuhan University, for instance, estimates that the market for dubious science-publishing activities, such as ghostwriting papers on nonexistent research, was of the order of 1 billion renminbi (US$150 million) in 2009 - five times the amount in 2007.

  32. Re:ROFL! clone53421=MichaelKristopei330=pudge=LOL by MichaelKristopeit497 · · Score: 1
    ur mum's face're both mental trolls.

    clone53421 is stephen alongi. i am michael kristopeit. stephen alongi =/= michael kristopeit. you can't comprehend that simple application of the transitive property because you're an idiot.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  33. Re:ROFL! clone53421=MichaelKristopei330=pudge=LOL by MichaelKristopeit497 · · Score: 1
    ur mum's face need to get a life.

    clone53421 is stephen alongi. i am michael kristopeit. stephen alongi =/= michael kristopeit. you can't comprehend that simple application of the transitive property because you're an idiot.

    you're also an ignorant hypocrite.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  34. Re:I believe U Mike (they TRY impersonate me too) by MichaelKristopeit497 · · Score: 1
    so, by your ignorant logic, if someone responds to you in a timely fashion, and then i respond to you in a timely fashion, then i must be that someone. you're dumber than i thought.

    if you believe you're being attacked, you're even dumber than that... but considering i merely responded to your idiocy with a statement of fact concerning it's idiotic content, it's already clear you're an idiot and an ignorant hypocrite.

    you are not defending yourself. you are denying the existence of yourself. you don't understand the difference because you're a moron.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  35. Re:ROFL! clone53421=MichaelKristopei330=pudge=LOL by MichaelKristopeit498 · · Score: 1
    clone53421 is stephen alongi. i am michael kristopeit. michael kristopeit =/= stephen alongi. you can't comprehend the difference, because you're an idiot.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  36. Re:first by Qwertie · · Score: 1

    The explanation isn't even correct. When I wrote a Super Nintendo emulator in the 90s, various documents referred to its GPU as a, er, GPU. The SNES predates NVidia itself, so let's not call it a "term coined by chip giant NVidia".

    GPUs are nowhere near new. What's relatively new is GPGPUs (General-Purpose computation on Graphics Processing Units).

  37. Re:ROFL! clone53421=MichaelKristopei330=pudge=LOL by MichaelKristopeit498 · · Score: 1
    ur mum's face is waldo.

    you're an ignorant hypocrite.

    clone53421 = stephen alongi. i am michael kristopeit. stephen alongi is no-one's ma. michael kristopeit =/= stephen alongi... you don't understand the difference because you're an idiot.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  38. Re:clone53421=clone52431 lol by MichaelKristopeit487 · · Score: 1
    still living in the bushes in the middle of shantytown, alex?

    you're worthless.

  39. Re:Depends on the needs of the problem by MichaelKristopeit489 · · Score: 1
    still living in the bushes in the middle of shantytown, alex?

    you're worthless.

  40. Re:MichaelKristopeit's only Man of 500 faces by MichaelKristopeit491 · · Score: 1
    still living in the bushes in the middle of shantytown, alex?

    you're worthless.

  41. Re:Editing my posts & impersonating me? LOL! by MichaelKristopeit490 · · Score: 1
    ur mum's face DON'T DARE.

    alex, p, k?... is that what your mom tells you to when you've been alone in the basement too long without a potty break?

    still living in the bushes in the middle of shantytown, alex?

    you are NOTHING

  42. Re:http://science.slashdot.org/comments.pl?sid=261 by MichaelKristopeit490 · · Score: 1
    still living in the bushes in the middle of shantytown?

    you are NOTHING

  43. Re:Yes, I own my own home MichaelKristopeit by MichaelKristopeit499 · · Score: 1
    in every way how, you're an idiot.

    cower in my shadow in your paid in full shanty some more, feeb.

    you're completely pathetic.

  44. Re:Right: I own my own home MichaelKristopeit by MichaelKristopeit498 · · Score: 1
    in every way how, you're an idiot.

    cower in my shadow in your paid in full shanty some more, feeb.

    you're completely pathetic.

  45. Re:LMAO, perhaps music can soothe the savage beast by Demonoid-Penguin · · Score: 1

    LMAO -> http://www.youtube.com/watch?v=JrUGYT_gl9I = MikeK, lol...

    APK

    P.S.=> How many accounts is that you're up to now? Well, lol, let's see: I said 500 on a guess, & MichaelKristopeit412 looks like your 412th, lmao... I was wrong, but (rotflmao)... who cares?? Why??

    Well - You're the "Man..." (See song above, lol, same quality as you, lol).. /quote)... apk

    Troll fight! Humongous host file vs. pig fucker.

    The only possible winner is - everybody else.

  46. you've obviously never been informed by MichaelKristopeit495 · · Score: 1
    you said you had sex that you didn't want to have. either you were lying or you were raped. are you a liar?

    The Fine Print: The following comments are owned by whoever posted them. We are not responsible for them in any way.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  47. you've obviously never been informed by MichaelKristopeit494 · · Score: 1
    you said you had sex that you didn't want to have. either you were lying or you were raped. are you a liar?

    The Fine Print: The following comments are owned by whoever posted them. We are not responsible for them in any way.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  48. you've obviously never been informed by MichaelKristopeit493 · · Score: 1
    you said you had sex that you didn't want to have. either you were lying or you were raped. are you a liar?

    The Fine Print: The following comments are owned by whoever posted them. We are not responsible for them in any way.

    cower in my shadow some more, feeb.

    you're completely pathetic.

  49. ur mum's FACE're going to regret you by MichaelKristopeit480 · · Score: 1
    having sex without consent is being a party to rape. you claimed, in quotes, that it was your "job"... who said it was your job? are you a registered sex worker? did you have a pimp? either you consented, and stated your desire to engage in wanted sexual contact, and later lied about it; or you were raped. are you a liar?

    cower in my shadow some more, feeb.

    did jay little regret you claiming that he libeled you? you said that he would too, but it seems his website is still up after many years, and no action was ever taken..., as well as many other individuals who you've threatened with libel suits that resulted in no action. you're a demonstrated liar. you're a moronic buffoon. you are completely worthless.

    searching for "Alexander Peter Kowalski" on google responds with the top result "How to Respond When People Threaten to Sue You on the Web"... full of people mocking your pathetic attempts to invoke legal action where none is warranted. why do you think that is?

    cower in my shadow some more, feeb.

    you're completely pathetic.

  50. ur mum's FACE're going to regret you by MichaelKristopeit481 · · Score: 1
    having sex without consent is being a party to rape. you claimed, in quotes, that it was your "job"... who said it was your job? are you a registered sex worker? did you have a pimp? either you consented, and stated your desire to engage in wanted sexual contact, and later lied about it; or you were raped. are you a liar?

    cower in my shadow some more, feeb.

    did jay little regret you claiming that he libeled you? you said that he would too, but it seems his website is still up after many years, and no action was ever taken..., as well as many other individuals who you've threatened with libel suits that resulted in no action. you're a demonstrated liar. you're a moronic buffoon. you are completely worthless.

    searching for "Alexander Peter Kowalski" on google responds with the top result "How to Respond When People Threaten to Sue You on the Web"... full of people mocking your pathetic attempts to invoke legal action where none is warranted. why do you think that is?

    cower in my shadow some more, feeb.

    you're completely pathetic.

  51. ur mum's FACE're going to regret you by MichaelKristopeit487 · · Score: 1
    having sex without consent is being a party to rape. you claimed, in quotes, that it was your "job"... who said it was your job? are you a registered sex worker? did you have a pimp? either you consented, and stated your desire to engage in wanted sexual contact, and later lied about it; or you were raped. are you a liar?

    cower in my shadow some more, feeb.

    did jay little regret you claiming that he libeled you? you said that he would too, but it seems his website is still up after many years, and no action was ever taken..., as well as many other individuals who you've threatened with libel suits that resulted in no action. you're a demonstrated liar. you're a moronic buffoon. you are completely worthless.

    searching for "Alexander Peter Kowalski" on google responds with the top result "How to Respond When People Threaten to Sue You on the Web"... full of people mocking your pathetic attempts to invoke legal action where none is warranted. why do you think that is?

    cower in my shadow some more, feeb.

    you're completely pathetic.

  52. Plenty of nothing was done to Jay Little by MichaelKristopeit478 · · Score: 1
    having sex without consent is being a party to rape. you claimed, in quotes, that it was your "job"... who said it was your job? are you a registered sex worker? did you have a pimp? either you consented, and stated your desire to engage in wanted sexual contact, and later lied about it; or you were raped. are you a liar?

    cower in my shadow some more, feeb.

    did jay little regret you claiming that he libeled you? you said that he would too, but it seems his website is still up after many years, and no action was ever taken..., as well as many other individuals who you've threatened with libel suits that resulted in no action. you're a demonstrated liar. you're a moronic buffoon. you are completely worthless.

    searching for "Alexander Peter Kowalski" on google responds with the top result "How to Respond When People Threaten to Sue You on the Web"... full of people mocking your pathetic attempts to invoke legal action where none is warranted. why do you think that is?

    cower in my shadow some more, feeb.

    you're completely pathetic.

  53. Plenty of nothing was done to Jay Little by MichaelKristopeit479 · · Score: 1
    having sex without consent is being a party to rape. you claimed, in quotes, that it was your "job"... who said it was your job? are you a registered sex worker? did you have a pimp? either you consented, and stated your desire to engage in wanted sexual contact, and later lied about it; or you were raped. are you a liar?

    cower in my shadow some more, feeb.

    did jay little regret you claiming that he libeled you? you said that he would too, but it seems his website is still up after many years, and no action was ever taken..., as well as many other individuals who you've threatened with libel suits that resulted in no action. you're a demonstrated liar. you're a moronic buffoon. you are completely worthless.

    searching for "Alexander Peter Kowalski" on google responds with the top result "How to Respond When People Threaten to Sue You on the Web"... full of people mocking your pathetic attempts to invoke legal action where none is warranted. why do you think that is?

    cower in my shadow some more, feeb.

    you're completely pathetic.

  54. ur mum's face're history by MichaelKristopeit483 · · Score: 1
    oh noes... are you going to type some more?

    you're an ignorant hypocrite.

    having sex without consent is being a party to rape. you claimed, in quotes, that it was your "job"... who said it was your job? are you a registered sex worker? did you have a pimp? either you consented, and stated your desire to engage in wanted sexual contact, and later lied about it; or you were raped. are you a liar?

    cower in my shadow some more, feeb.

    did jay little regret you claiming that he libeled you? you said that he would too, but it seems his website is still up after many years, and no action was ever taken..., as well as many other individuals who you've threatened with libel suits that resulted in no action. you're a demonstrated liar. you're a moronic buffoon. you are completely worthless.

    searching for "Alexander Peter Kowalski" on google responds with the top result "How to Respond When People Threaten to Sue You on the Web"... full of people mocking your pathetic attempts to invoke legal action where none is warranted. why do you think that is?

    cower in my shadow some more, feeb.

    you're completely pathetic.

  55. Plenty of nothing was done to Jay Little by MichaelKristopeit484 · · Score: 1
    having sex without consent is being a party to rape. you claimed, in quotes, that it was your "job"... who said it was your job? are you a registered sex worker? did you have a pimp? either you consented, and stated your desire to engage in wanted sexual contact, and later lied about it; or you were raped. are you a liar?

    cower in my shadow some more, feeb.

    did jay little regret you claiming that he libeled you? you said that he would too, but it seems his website is still up after many years, and no action was ever taken..., as well as many other individuals who you've threatened with libel suits that resulted in no action. you're a demonstrated liar. you're a moronic buffoon. you are completely worthless.

    searching for "Alexander Peter Kowalski" on google responds with the top result "How to Respond When People Threaten to Sue You on the Web"... full of people mocking your pathetic attempts to invoke legal action where none is warranted. why do you think that is?

    cower in my shadow some more, feeb.

    you're completely pathetic.

  56. Re:clone53421=clone52431 lol by clone53421 · · Score: 1

    Oh geez. For some reason that was posted anonymously. Old habits die hard...

    By the way, sedans aren't sports cars.

    --
    Alexander Peter Kristopeit bought his basement from his mommy for one dollar.
  57. Re:clone53421=clone52431 lol by clone52431 · · Score: 1

    trolllolllollloll.

    Wanna see the .40? Okay sure.

    --
    Distributed Denial of APK: It takes 15 seconds to reply to him anonymously, but wastes tons of his time if we all do it.
  58. Re:You don't READ, do you? See the wiki I posted by squiggleslash · · Score: 1

    Ping of death was corrected in most OS around 2000, but there are NT boxes & even 9x boxes out there still - so, ping CAN still issue a "ping of death" - fact!

    No, it can't. No mainstream operating system has ever shipped with a version of ping that outputs malformed ping packets, let alone ping packets malformed in a way that would cause a PoD. Ever. Exploiting the PoD requires a specially written tool to output a malformed ping packet. You cannot use the ping command to do that.

    If I'm wrong, it's fairly easy to prove. Show me the bug report that reports to Microsoft, Canonical, or Apple, that the ping command shipped with their system outputs malformed ping packets. And in the mean time, demonstrate for me how a Windows 7 machine can crash an unpatched Windows 95 machine using the ping command. Don't just handwave and claim it's "fact", put up or shut up. Tell me the exact command line to issue from a Windows 7 Administrator cmd.exe window to crash a Windows 95 machine whose IP address is 10.0.0.1.

    You won't because you can't. You can't because you don't know what you're talking about. You've never known what you're talking about. The same thing goes for the "Spybot SAD" hosts file modification thing. You don't understand why CA was asking about modifying HOSTS, which interestingly enough probably means you unintentionally fed false information to them about the operation of your application.

    You claim your app isn't scriptable, yet also claim it's "two lines of code" which means it cannot possibly verify that the application its hiding is what you intended it to be. So it is scriptable, and it is usable by a malware writer. Which is probably why most malware organizations still report the software as malware.

    Meanwhile you post here over and over again with increasingly ridiculous assertions about your work and knowledge, and cannot understand it when a bunch of us find it hilarious and needle you over it.

    If you know of a way to use the ping command to exploit the PoD please post it here. More importantly, make sure Microsoft, Canonical/GNU, the various *BSD groups, and Apple are made aware of it immediately. If their ping utilities, as shipped, are outputting malformed packets, then they have major bugs in them. You would be utterly irresponsible not to let them know.

    --
    You are not alone. This is not normal. None of this is normal.