Beyond Open Access: Open Source Scientific Software

from the sauce-for-the-goose,-sauce-for-the-gander dept

Although the traditional image of a science laboratory typically consists of a room full of test tubes or microscopes, the reality is that computers now play a central role there, just as they do for business and life in general.

Computers need software, and some of that software will be specially written or adapted from existing code to meet the particular needs of the scientists' work. This makes computer software a vital component of the scientific process. It also means that being able to check that code for errors is as important as being able to check the rest of the experiment's methodology. And yet very rarely can other scientists do that, because the code employed is not made available.

A new paper in Science points out that this needs to change:

The publication and open exchange of knowledge and material form the backbone of scientific progress and reproducibility and are obligatory for publicly funded research. Despite increasing reliance on computing in every domain of scientific endeavor, the computer source code critical to understanding and evaluating computer programs is commonly withheld, effectively rendering these programs "black boxes" in the research work flow. Exempting from basic publication and disclosure standards such a ubiquitous category of research tool carries substantial negative consequences. Eliminating this disparity will require concerted policy action by funding agencies and journal publishers, as well as changes in the way research institutions receiving public funds manage their intellectual property (IP).
As that notes, the open exchange of knowledge and materials are obligatory for publicly-funded research, and there's no reason why it should be any different for software that is written in order to conduct the experiment. After all, this, too, has been funded by the tax-payers, who therefore have a right to enjoy the results. There may not be much they can do with it directly, but they can still benefit when other scientists are able to build on the code of others, instead of needing to re-invent the digital wheel for their own experiments.

The paper makes an important point that deserves a wide audience, because it's about a public policy issue. So it's a huge pity that, ironically, it is not published under an open access licence, and can only be read by Science's subscribers.

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Reader Comments (rss)

(Flattened / Threaded)

  1.  
    identicon
    Rich Kulawiec, Jun 5th, 2012 @ 3:01am

    Full text is available elsewhere

    I found it as a PDF here.

     

    reply to this | link to this | view in thread ]

  2.  
    identicon
    Glyn Moody, Jun 5th, 2012 @ 4:32am

    Re: Full text is available elsewhere

    thanks

     

    reply to this | link to this | view in thread ]

  3.  
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    BentFranklin (profile), Jun 5th, 2012 @ 6:09am

    It's great that scientists are waking up to this problem with the accountability of their software. Now perhaps they will wake up to the exact same problem when using proprietary election machines.

     

    reply to this | link to this | view in thread ]

  4.  
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    Jesse (profile), Jun 5th, 2012 @ 7:22am

    I think we need to take open access one step further, with a viral license like the GPL. "If you base future research upon this paper/study, then your research must also be open access."

    Businesses should not get to benefit from public research, directly or indirectly, if they aren't going to give back just as much.

     

    reply to this | link to this | view in thread ]

  5.  
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    Brent (profile), Jun 5th, 2012 @ 9:03am

    Re:

    I doubt scientists have overlooked that possibility but in any case, it's the problem of 'scientists' to fix.

     

    reply to this | link to this | view in thread ]

  6.  
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    Brent (profile), Jun 5th, 2012 @ 9:13am

    I recently learned about Cosmoquest.org which is a project of the scientists in charge of the New Horizons spacecraft that will go past Pluto and on to the Kuiper Belt. They are crowd sourcing amateur fans of astronomy to look thru tons of photos to spot actual objects in the Kuiper Belt that could be the target of the spacecraft after Pluto. The images users go thru are grainy and confusing to look at b/c of the technology behind the image meshing software. They explain right on the site that they have to use very specific standards to ensure all of the vast quantity of images are produced in a verifiable way. This got me thinking about scientific software and how useless any software written by a private company would be if they would not share the source code. Its sad but also understandable b/c there could never be an 'agreement' with the scientists that they wouldn't share the code, they would have to if they want their results to be verified and that would essentially make the code open source meaning it would retain little value comparatively. I don't know of a solution other than scientists developing their own code, relying on their universities to develop code for them or some generous group of programmers creating the code for them for free. It is good that scientists aren't just assuming all software is created correctly though, there has to remain some semblance of intelligence in our global community.

     

    reply to this | link to this | view in thread ]


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