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Medicine Programming Science

Crowdsourced Coders Take On Immunology Big Data 31

Posted by Soulskill
from the still-no-cure-for-cancer-oh-wait dept.
ewenc writes "Mercenary computer coders are helping scientists cope with the deluge of data pouring out of research labs. A contest to write software to analyze immune-system genes garnered more than 100 entries, including many that vastly outperformed existing programs. The US$6,000 contest was launched by researchers at Harvard Medical School and Harvard Business School, both in Boston, Massachusetts. TopCoder.com, a community of more than 400,000 coders who compete in programming competitions, hosted the contest. The results are described in a letter published this week in Nature Biotechnology."
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Crowdsourced Coders Take On Immunology Big Data

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  • by K. S. Kyosuke (729550) on Friday February 08, 2013 @06:33PM (#42838153)

    With the help of employees at TopCoder.com, Guinan’s team created a contest that expressed the problem in generic, non-biological terms, such as strings and sub-strings instead of gene sequences and gene segments.

    That's funny, because I can't remember that any other approach than a stringological one has ever been used.

    • I agree!
    • by Anonymous Coward

      Next up on Stack Overflow:

      Can some1 pls post the codes for in generic, non-biological terms, such as strings and sub-strings instead of gene sequences and gene segments. full codes pls email me at topcodersplspostfullcodes@hotmail.com

      What a fuckin' scam...FTFA

      The US$6,000 contest was launched by researchers at Harvard Medical School and Harvard Business School, both in Boston, ....

      Their contest ran for two weeks and awarded weekly $500 prizes to top performers.

      In total, 122 people submitted computer programs to characterize the genes involved in immune responses. Half of the entrants were professional computer programmers, yet none worked as computational biologists. Contestants spent an average of 22 hours on the problem, accumulating a total of nearly 2,700 hours of development time.

      Who do you want to bet owns the copyright?

      How about open source instead of $6000 tossed at a starving pack of desperate coders to solve "Big Data" problems for them.

      • Exactly what I was thinking! In the world of the graphic artist, you see this shit a lot... It's called 'spec work' and it's the reason that there's fewer and fewer good-paying graphics positions out there. Hungry artists make logos, interfaces, and designs with the hope that their submission will be chosen. Who wins? The person on the receiving end. What a fucking joke. Seriously people, DO NOT do work for free! This is reminding me of the recent post where the submitter asks, "How much should I rev
      • as some kind of leet hacker haven. its full of the same horse shit you find all over those places

        "need powerpoint conversion ASAP!"

        "java lx2e zorbog buzzheavy lightyear lcick layer"

  • by v1 (525388)

    The results are described in a letter published this week in Nature Biotechnology [nature.com]

    looks to be paywalled, @ $32 for a single article?

  • not much return (Score:5, Insightful)

    by v1 (525388) on Friday February 08, 2013 @07:17PM (#42838713) Homepage Journal

    It's too bad the winning entry, at 970x the speed of the algo it replaced, only received $6k. Surely this was worth a lot more to the eggheads than that? You'd have difficulty contracting even simple, low grade code for that amount?

    • by Kozz (7764) on Friday February 08, 2013 @08:28PM (#42839339)

      It's too bad the winning entry, at 970x the speed of the algo it replaced, only received $6k. Surely this was worth a lot more to the eggheads than that? You'd have difficulty contracting even simple, low grade code for that amount?

      I think you're overlooking the fact that a coder who wins the contest gets something far more valuable: a demonstrable proof of one's mettle and a fairly admirable accomplishment that can only pay dividends for years to come when they're hired by a company who pays them what they're really worth.

      • by v1 (525388)

        I think you're overlooking the fact that a coder who wins the contest gets something far more valuable: a demonstrable proof of one's mettle and a fairly admirable accomplishment that can only pay dividends for years to come when they're hired by a company who pays them what they're really worth.

        true, but in the short-term, bragging rights and resume' bullet points don't pay the bills.

        • by Kozz (7764)

          If you're conquering the challenge for the short-term, you're doing it for all the wrong reasons.

          • by v1 (525388)

            It's a matter of priorities. If you're lost in the wilderness, you work on obtaining (1) shelter, (2) water, and (3) food. in that order. It doesn't do you any good to have a good food and water supply if you freeze to death.

            If you want a resume bullet or experience, that's what workstudy and unpaid apprenticeships are for. This was supposed to be offering financial reward. And I'm sure it also factored in the bullets, but I think they assigned the bullets too much value.

            I think if I was on a big proje

            • by easyTree (1042254)

              The whole premise of contests is a scam. Everyone works their ass off for some 'prize'. Only one wins yet the contest hosts get to benefit from all entries.

              • by Morpf (2683099)

                That is why I only take part in contests, where my work is not usable in any production environment. Contests for the contest sake. Google CodeJam, Project Euler, ACM ICPC, you name it.

            • by Jmc23 (2353706)
              Whine, whine, whine. Why such a whiner if you couldn't even win the prize? $6k for 2 weeks of work is nothing to sneeze at. Some strange people aren't even greedy self-important pricks and actually feel that the advancement of science is payment enough.
        • when they're hired by a company who pays them what they're really worth.

          Same kid of shit my old boss would say like "when our ship comes in". The bigger boss pulled him aside and told him not to say things about when the important people got rewarded, and that we didn't belong to that group. My job and yours is to weigh anchor and row vigorously while they water ski.

          I got the last laugh, the company barely exists now, that ship was really a trap, our captain gave away the company jewels without verifiable data metrics.

      • by Morpf (2683099)

        But what if the company supposed to hire this winner just starts a TopCoder Contest, too? This example shows quite clearly that there are people out there selling their souls for bragging rights. Why do you think, this will not be exploited? Remember: That contest yielded 2,684 hours of development time with an overwhelming result for just 6k USD, there is no way to get cheaper. You can brag, that's it. I think those competitions ruin the income of software developers in the long run. Not to mention that so

    • by eulernet (1132389)

      The source codes of the winners are here:
      http://apps.topcoder.com/wiki/display/OpenSource/SequenceAlignment [topcoder.com]

      Frankly, $6k is a lot of money for the amount of effort (less than 22 hours of work in average).

  • Very timely piece, following on from the Slate bio of Aron Swartz and O'Reilly's decision to make 'Open government' free for download.

    I've just finished reading the first few chapters of that book and i have to say it really blew my mind. I work in a quasi-IT role in a public sector health organisation; it's really amazing to me how difficult everyone makes it all out to be. Our IT systems are cobbled together from a range of hugely expensive 3rd party solutions - none of which inter-operate and all of wh

    • in the public sector, your dick is measured by how big your budget is. why the fuck would you want to spend LESS money than you did last year? then your budget gets cut - not only do you have to fire some people, you destroy any chance of advancing up the hierarchy. not only that, you dont have anyone to sue if the 'solution' is behind schedule or doesnt work or, in healthcare, kills someone (Therac 25 anyone?).

      Also, you typically get kickbacks from vendors for 'implementing' their 'solution' after a 'caref

      • by Jmc23 (2353706)
        Some rare people have this thing called a conscience. You might want to research it.
    • by sorisos (2702365)
      Perhaps the lack of out-of-the-box thinking in public sector is because it's not a wide spread practice and you have to fight a lot of bureaucracy for these kind of projects. Also it might be hard to fund a project without any guarantees of success, as compared to buying proprietary sofware x with a huge spec list.
  • Crowd sourcing is a great concept, but this sounds like an abuse of it. It's like someone thought: "Hey, let's throw some bread crumbs and watch these suckers do the work for us."
  • Coders work for free? Looks like they've taken a tip from gaming companies, which do Q&A and product testing by outsourcing it to gamers who do it for free - or even pay for the privilege, as has been seen in various betas requiring payment.

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