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Bringing Open Source To Biomedicine 60

waderoush writes "'Facebook and Twitter may have proven that humans have a deep-seated desire for sharing, [but] this impulse is still widely suppressed in biomedicine,' biotech reporter Luke Timmerman observes in this column on Sage Bionetworks founder Stephen Friend. Friend is working to convince drugmakers and academic researchers to pool their experimental genomic data in a shared database called the Sage Commons. The database could be used to track adverse drug events, or to 'visually display network models of disease that connect the dots between genes, proteins, and clinical manifestations of disease in ways that [scientific] journals are not equipped to handle,' Timmerman says. Researchers from Stanford, Columbia, UCSF, and UCSD are already contributing to the Sage Commons, and Friend is now calling for a community effort by drugmakers, academic scientists, doctors, regulators, insurers, and patients to 'grab this platform and run with it on their own."
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Bringing Open Source To Biomedicine

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  • there will no be any "openness" of any kind. There is just too much financial gain at stake (not that it is a good thing).
    • We can fight to have pockets of open. Hopefully about 1000 academic articles and 1000 drugs and 1000 genomes to study.
      (Starting small)

    • You mean "no openness of any kind...besides the ones listed in TFA who are already sharing" right?

      • I think it was apparent what I mean. But, I'll spell it out. Big companies will not be willing to open source everything while they are raking in profits. The comment was meant in disregard to those mentioned
        • by rtb61 ( 674572 )

          They will also not open up anything that remotely hints of greed driven culpability. In fact that will be the driving factor for not only not loading up data by the pharmaceuticals but to also attack Sage Commons with claims that any negative data is false and it will sue to cripple the data base.

          The only counter will be foreign governments with universal health who are directly financially affected by poorly performing drugs and who will fight to protect the billions at stake.

    • I can tell you didn't RTFA, or even RTFS.
      TFH is fucking misleading.

      There is very little to do with open source, or openness in general.

      Some guy is simply trying to get various players to buy into his system, with money and data, so he can then go back and run a few queries, maybe make a little graph, etc., and sell that data to others (for the price of money and more data).

      It's basically stone soup [], but he demands money as well as all the work. (And if he's not demanding money now, just wait until the date

  • Thing is, there is a lot of money involved Biomedicine. Research Institutes can hope to gain a lot of funding by selling their results to pharmaceutical companies. It would be the equivalent of Microsoft open sourcing the datasets used for their multibillion dollar speech and language technologies.

    I can see this happening at universities though with a "GPLv2 equivalent" license on the database.

    • The mixture of medicine with so much moneyed interest produces noxious stench like no other. And no other fields are propped up with so much pubic fund - look up NIH funding vs. any other research funding.

      Soon enough, it will also implode our finance, both public and private.

  • I'd say it's more than sharing - it's about exposing ones thoughts in the desire for acknowledgement or acceptance .. I am not alone.

    Also, useful for slagging others to prop up own self esteem and plugging ones own site/service/content or film one has participated in.

    As for medicine .. I think it would be great to get more people on-line with folk remedies, to see if any actually have merit, i.e. chewing willow bark helped relieve my headache (this is the origin of Aspirin as salicylic acid.) The only worr

  • Drugmakers are already required to keep track of adverse drug events that arise during clinical testing. Much of this information is reported to regulatory agencies on almost a daily basis and there's a lot of work going behind the scenes to make sure the information is reliable, consistent and keeps patient privacy.

    I can understand to some extent why drugmakers aren't too keen to jump into this. There is little use in adding yet another database into an already busy workflow. This new database is guarante

    • Adverse event reporting covers only a tiny fraction of the data gathered in any clinical trial. There's an enormous amount of information that would be useful for future research locked up in clinical trials databases, and as we move into the "genomic medicine" era, this will be ever more the case. Having gone back and forth between bioinformatics and clinical research, and being persistently annoyed at how difficult it is to access data in the latter field, I say that anything that can bring bioinformati

  • TFT&TFS are as misleading as others have noted; this is about "open-data", not really "open-source".

    I am skeptical and have two questions:

    (1) In terms of research, isn't this what peer review and publication are supposed to accomplish?

    (2) How is "biomedicine" different from "medicine"?
    • (1) Peer review is a lot more powerful when you can review the data itself, not just what the paper says about the data. In bioinformatics, we've known this for years, which is why you absolutely can't publish a paper concerning a microarray experiment without making the raw data available in GEO [] or a similar repository.

      (1.5) Any high-throughput experiment generates enormous amounts of data (that's pretty much the definition of "high-throughput") and that data is very often useful for answering questions

    • Marketing.
  • by Anonymous Coward

    Sage is a spinoff of Merck as Rosetta Inpharmatics. Rosetta died and Sage emerged from it. The spin was that Merck has deposited thousands of clinical mouse strains that supposedly worth tens of millions USD. I don't buy it.

    I know Stephen Friend has been "promoting" his idea of pooling genetic data. The pitch is that by pooling, his company can offer "better" analysis. However, by "pooling" means for his company's (Sage) use and NOT for public good. This article is absolutely misleading! I'm speaking as som

  • Facebook and Twitter may have proven that humans have a deep-seated desire for sharing

    If anything, sharing is merely a byproduct of the actual desires that drive those sites. Desires and tendencies such as showing off, egoism, seeking acceptance, seeking affirmation, or gathering information. And more so in the case of Facebook than Twitter, given the studies that repeatedly indicate that Twitter's graph is structured as a news graph rather than as a social graph (what was the last statistic? That the top 1% of Twitter users produce 98% of the tweets that get retweeted?).

    To suggest that shar

  • Easy, this is why: $

    Except for the companies providing the publishing service, nobody makes money with your tweets. On the other hand, complex drug interaction and related biomedical info is a potential source of great return which is gathered at great risk for the company (they can spend millions on R&D and get nothing currently usable out of it). Biomed companies will not share info that a competitor could use.

  • ...soon to usher in the "lawsuit era for the bio-med hack" I can see it now...somewhere some how some yo-yo is going to state open source lead to a hack into some company's personal bottom line. (i.e. personel info, pay scale, profits info, secret formula for some new ED med...etc)

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