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UNC Scientists Open Source Their Genomic Research

Posted by timothy on from the awesome-pickup-line dept.

ectoman writes: The human genome specifies more than 500 "kinases," enzymes that spur protein synthesis. Four hundred of them are still mysteries to us, even though knowledge about them could spark serious medical innovations. But scientists at the University of North Carolina, Chapel Hill, have initiated an open source effort to map them all—research they think could pioneer a new generation of drug discovery. As members of the Structural Genomics Consortium, the chemical biologists are spearheading a worldwide community project. "We need a community to build a map of what kinases do in biology," one said. "It has to be a community-generated map to get the richness and detail we need to be able to move some of these kinases into drug facilities. But we're just doing the source code. Until someone puts the source code out there and makes it available to everybody, people won't have anything to modify."

10 comments

  1. Spur protein synthesis? by Alopex · · Score: 5, Informative

    Kinases do much more than just spur protein synthesis. They are among the primary signaling enzymes in the body, involved in turning on and off a multitude of cellular processes by attaching phosphate groups to various targets. Some enzymes simply don't function without being triggered by a kinase. The summary just irks me when it's misleading or wrong

    1. Re:Spur protein synthesis? by Anonymous Coward · · Score: 1

      They are important for life. It's pretty much impossible for life to exist without them.

    2. Re:Spur protein synthesis? by Anonymous Coward · · Score: 0

      Not only turning on and off things but also carrying out analog computations at the cellular level. They form complex networks of circuitry that problably implement both digitial and probably a lot of analog computation.

  2. Open source isn't the exception, it's the norm by avarus · · Score: 4, Informative

    I work in this field, and outside of the commercial pharma companies, the general rule is that all the data goes public and that all the code written is open source. All the big publicly funded agencies, and certainly all the research councils here in the UK, follow this principle. Admittedly some people do sit on the data a bit longer than they should before releasing it, but in principle it all goes public and freely available.

    Want to find open, public data in genomic science, or contribute to an open database? - fill your boots: http://www.oxfordjournals.org/...
    Want to find new open-source algorithms for genome analysis? There are so many it's hard to keep up - http://blends.debian.org/med/t...

    In the EU, there is so much data in public databases they had to start a pan-European effort called ELIXIR just to try and work out how they were going to handle all the data curation work.

    So, not to take anything away from this fine project, the idea that it's special because it's open source or because scientists are collaborating widely is just plain silly.

    TIM

    1. Re:Open source isn't the exception, it's the norm by the+gnat · · Score: 1

      I agree that this isn't an extraordinary example, but I have to take issue with this:

      the general rule is that all the data goes public and that all the code written is open source

      The first part is correct in the literal sense (this is an absolute requirement of public funding agencies and journals), but that doesn't mean they're unencumbered by patents. The second part, unfortunately, is incorrect: open source is getting more common and scientists are slowly coming around to the idea that this shouldn't be optional, but there are plenty of examples of closed-source software being developed by academic groups, and many more examples where the code is available but not redistributable. Only in the last few years did the NIH start to explicitly state that openness of source code would be a consideration in evaluating grant applications for computational (biomedical) R&D.

    2. Re:Open source isn't the exception, it's the norm by Anonymous Coward · · Score: 0

      The first part is correct in the literal sense (this is an absolute requirement of public funding agencies and journals), but that doesn't mean they're unencumbered by patents.

      Indeed, the patent issue is probably one of the major hurdles they'll have to clear to get the community involved in this, I think. From TFA the Structural Genomics Consortium (SGC) of which UNC is a member has "[decided] not to patent discoveries," but it's unclear how strictly they're bound by that or what effect their decision not to patent might have on potential future discoveries based on their non-patented ones. It seems to me that fewer people may want to contribute to the effort if they think their freely-contributed work could be subsumed by a patent fence that (e.g.) GlaxoSmithKline might decide to slap around a derivative discovery.

    3. Re:Open source isn't the exception, it's the norm by the+gnat · · Score: 1

      It seems to me that fewer people may want to contribute to the effort if they think their freely-contributed work could be subsumed by a patent fence that (e.g.) GlaxoSmithKline might decide to slap around a derivative discovery.

      In practice, you are almost certainly incorrect. Scientists working in basic research - the ones I've met, anyway - are almost universally thrilled if their research leads to improvements in human health, regardless of whether or not they or someone else profits from it. (In fact, I was unhappy working as a developer on an academic project that was partly funded by charging companies for access to our software - I thought we should just give it away, because I wanted as many people as possible to use my work.) I have no fondness for GSK or any other big pharma company - quite frankly, they're a pain in the ass to deal with - but the extent to which they leech off public discoveries is vastly overstated, and they perform a huge amount of very expensive and very boring work to bring drugs to market. This combination of publicly-funded basic research and privately-funded development is one of the primary justifications for the existence of the NIH and on the whole it works relatively smoothly, although the perverse incentives of the Bayh-Dole act are problematic.

  3. It will not spur anything other than greed. by deviated_prevert · · Score: 1
    Most medical research that is publicly funded winds up being used by the drug corporations to line the pockets of a few very rich people. Take for example the recent cures for hep c. Much of the primary research into the HCV rna structure and thus the secondary chemical binding processes was done on the public purse. The result is medicines that can cure the disease at over 1000 dollars a pill that in reality cost the company very small amounts of money to actually produce. One company even paid 11 billion for a drug chemical patent and even though the process used by the new chemical is not something which can be patented they now have to recoup huge amounts of dollars to pay for so called "Intellectual Property Rights".

    No wonder why the Indians just said screw you we will bring out a generic of this chemical and you can eat your stupid IP patent. The attitude toward research being a magic box that will line the pockets of the already rich because they can afford to buy a monopoly on something is not new! In fact Queen Elizabeth 1 had the foresight to stop much of the practice and her change to so called "property right monopolies upon commerce" which is the same thing as "intellectual property" made a huge difference and spurred on the Renaissance. We are heading backwards by creating a ruling class of rich people again that insists upon owning the "rights" to enterprise and it is killing our economy and will lead to financial and social upheaval and revolutions! Elizabeth was one smart cookie she saw that the rich had not learned how to do anything other than use their gold to dominate others and this was and is destructive to an advanced society, always was and always will be!

    Enough of my rant, but the current economic trend in the US is very scary because we have lost our way as a people and have begun to create a class war that we cannot stop because of the acceptance of greed on a social level.

    --
    This message was not sent from an iPhone because Peter Sellers really was a deviated prevert without a dime for the call
    1. Re:It will not spur anything other than greed. by the+gnat · · Score: 1

      Much of the primary research into the HCV rna structure and thus the secondary chemical binding processes was done on the public purse

      A huge fraction of it was done privately as well, but that's still just one tiny piece in a much larger project. Solving a structure isn't that difficult or expensive for a well-validated experimental system, and the end result helps you guess at what chemical syntheses to try, but actually putting something on the market takes the better part of a decade and hundreds of millions of dollars - and a huge fraction of the time it will fail anyway. It is almost guaranteed that Gilead spent at least $100 million developing their new HCV drug, and you have to add to that an even larger amount of money spent trying stuff that didn't work, which they still need to recoup somehow. I have no idea whether this justifies their selling price or not, but the claim that it cost the company "very small amounts of money" is complete nonsense.