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Biotech Data Mining

Posted by Zonk on Sat Dec 31, 2005 10:37 PM
from the squirmy-thought-worms dept.
Biotech Databases Programming Software IT
Roland Piquepaille writes "In the last ten years, biotech companies have been busy accumulating mountains of data. And it's becoming more and more difficult to find useful information about interactions between genes and proteins for example. It's one of the reasons why the European Union has started the BioGrid project. In Mining biotech's data mother lode, IST Results describes this project. Among current results, the researchers involved in it have delivered a better search engine for PubMed by analyzing over-expressing genes and predicting the protein interactions that are likely occurring. And many of the tools developed by BioGrid are available for public use -- even by yourself. For more information, this overview contains additional details, pictures and references about this project."
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Maria Williams writes "KurzweilAI.net reported that: This year's recipients of the Lifeboat Foundation Guardian Award are Robert A. Freitas Jr.and Bill Joy, who have both been proposing solutions to the dangers of advanced technology since 2000. Robert A. Freitas, Jr. has pioneered nanomedicine and analysis of self-replicating nanotechnology. He advocates "an immediate international moratorium, if not outright ban, on all artificial life experiments implemented as nonbiological hardware. In this context, 'artificial life' is defined as autonomous foraging replicators, excluding purely biological implementations (already covered by NIH guidelines tacitly accepted worldwide) and also excluding software simulations which are essential preparatory work and should continue." Bill Joy wrote "Why the future doesn't need us" in Wired in 2000 and with Guardian 2005 Award winner Ray Kurzweil, he wrote the editorial "Recipe for Destruction" in the New York Times (reg. required) in which they argued against publishing the recipe for the 1918 influenza virus. In 2006, he helped launch a $200 million fund directed at developing defenses against biological viruses."
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  • ...I'd want to find the first biotech post ever. Now that would really be interesting!

  • Hopefully! (Score:3, Funny)

    by Anonymous Coward on Saturday December 31 2005, @10:51PM (#14372914)
    Hopefully this is the last Rololand Picapal article for the rest of the year.

    Lets celebrate by not clicking through to his poorly made blog!
      • Funny enough, the ZDNet blog link says "Posted by Roland Picklepail" right at the top... *ick*

        np: Lawrence - Two Minutes In August (Pingipung Plays: The Piano)

  • Roland the Plogger is Back! (Score:5, Interesting)

    by Animats (122034) on Saturday December 31 2005, @11:11PM (#14372958) Homepage
    He's Back! I thought we were rid of Roland the Plogger, still trying to drive traffic to his blog. But no. Must be some new editor on the night shift who let this one through.

  • Mod me Down or Mod me Funny... (Score:3, Funny)

    by NotQuiteReal (608241) on Saturday December 31 2005, @11:13PM (#14372965) Journal
    ... either way I don't win "karma".

    A lot of posts from here on out are implicit or explict observations that it is "New Years" at different times in different time zones all accross the globe. Just ignore them.

    Anyhow, for the on-topic part... the article describes what I think is reasonable follow-up to other research. E.g. Bio-tech is a science just like other, and needs to be confirmed and used as a starting point for further research.

    But that is boring to say.

  • I think these scientists deserve kudos, karma and lots of money. It's men and women that do boring jobs like this that will someday benifit humanity in ways we can't yet understand.
  • They have been accumualting lot of data. Well this is a forgone conclusion in any area of scientific research esepcially on of demand and has a direct relation to economic stability.

    The ability to search data for a highly pertinent area of research also a good idea. Perhaps the best ways to do this is not to establish one effective means of searching, but multiple.

    That being said just predicting results should be sufficient. It should be the means for basing an industry, and has proven to be succseful, in w
  • At first glance I thought it said Biatch Data Mining.. and subsequently had privacy concerns for ex-girlfriends.

  • I worked for a bioinformatics company ... (Score:4, Informative)

    by TallMatthew (919136) on Sunday January 01 2006, @07:26AM (#14373731)
    ... and I'm not sure this data is that useful.

    What they're hoping for is to find commonalities among individuals with certain traits, genetic diseases obviously, but also predisposition for certain drug therapies. Medications work for some people and not for others. It would be marvelous if you could do a genetic scan of someone and predict whether a certain drug therapy would work on them. It could also bring drugs to market that aren't already because they don't help some people and are in fact dangerous to others.

    Great idea, but there are serious obstacles. First, the dataset that comes off a DNA sample is enormous. You can currently sample DNA in about 500,000 places, each location represented by letters, those letters representing the type of molecule present in a certain position on the double helix. There are about a half-dozen of those, so what you end up with is half a million of these letters juxtaposed. And it's not as easy as "if there's an n at position 232.922, this drug won't work for you." It's more like "if there's a series of letters in one place, and there's a series of letters in another, then you can either have a series in this place or a series that one, etc.".

    Unfortunately, you don't know how long the series is and you don't know where, you don't know what depends on what. You just don't know. It's a statistical nightmare. You should see the algorithms they throw at those things.

    And of course, environment may play a role in such things, too, so you don't even know if what you're looking for means anything.

    Great idea, hope it works, not holding my breath.

    • Actually, you can 'sample DNA' (I think you mean genotype) at any one of the 3 billion bases in the genome, provided you can develop an assay.

      The 500K you refer to could be from one of the (now standard) affymetrix 500K chips that have a standardized set of variants to test. They exclude a number of other markers, but via indirect evidence (knowledge of haplotype structure in the population), you can test other areas as well, and increase your coverage of the whole genome.

      I'll agree that the statistics are
  • The DNA in the fist picture is LEFT handed instead of right. That's WRONG!
    http://www.lecb.ncifcrf.gov/~toms/LeftHanded.DNA.h tml [ncifcrf.gov]
  • There are a NUMBER of large scale efforts to perform the same in the US. I find it very weird that BioGrid, an European System is being tested on PubMed, a database maintained by the NIH/NCBI in the US. I am finding it weird that the author would choose to quote an obscure project in Europe. The integrated modeling of Biological systems is an extremely complicated problem, with data varying from sequence to microarray to literature to god knows what, and the author makes it look so simple. That is not the c
    • As the owner of a small Medical Device R&D company I can tell you that this is great news! It is vary hard to compete with the larger R&D companies out there and searchengins are from $1000 to $10,000 a month. There are engins that you can buy reports peice meal but they are $40 and up. So if it really is free I am all over that.
      • If you were a chemist, how would you have felt 150 years ago when the chemical table was being "discovered", that patents could have been applied for and recieved on elements?

        I guess that's my beef with Biotech and the patenting of genetic sequences in general. If you have a specific product developed off of one, then it should be patentable (i.e., genetic marker XYZ54 is a good target for identifying likely Slashdot trolls), but what if it also is a good marker for other traits? Should one group of researc
    • NEW FROM GOOGLE GoogleGenes Beta Search your own genetic code to discover any flaws or mistakes in your programming, and learn to debug yourself. Make yourself taller! Change your natural hair color! Change your eye color! Anything you dislike about yourself can now be changed with the help of Google!
    • The problem is not so much finding the relevant data, although that is very important. The "holy grail" is being able to exchange the data in a meaningful way - to be able to the mine the data that exists across disparate researchers and their systems. This is not in the search engine solution space. The EU and the US are making some slow progress on this, but it is remains a vexing problem. (I am not a Mirobiologist, but I do help them _try_ to design compatible systems -- NOT easy.)
    • Maybe Google could find my left sock for me too? I lost it somewhere in my aparment it must be easy for google, and I'd pay a few dollars too.

      "Google, the search company"

      and while we are at it, make it:

      "Google, the search and destroy company"

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