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Re: [science-iwg] Scientific papers - scientific software
On 4/16/2015 8:32 AM, Peter A wrote:
Hi,

I would be interested in joining that Hangout.  The situation is a little bit of a mess right now.  Besides authors not getting acknowledgement there is the reproducibility issue.  Different implementations of the same algorithm can have very different results.  When I review a paper I try to remind people to cite the software and the specific version.  I know of at least a couple of cases where performance claims were invalid because they used software with a known "bug" in it.

I've been lazy and haven't bothered to publish papers for most of my software.  Used to get e-mails from people asking how to cite it since there was no paper.  I now think people have learned how to cite webpages better.

For everyone's info:  There is a 2014 book from CRC Press called Implementing Reproducible Research [1].  There two chapters that discuss the use of OS practices in the conduction of science research, and they make points wrt reproducibility similar to those Peter has made above.  One of those chapters is by Millman and Perez, and in keeping with many of their points they've made the chapter available via github [2].  :)  

My point with this reference is to support what Peter is saying WRT reproducibility, but also to point out the other ways that open source...both in the creation of scientific software and in research practice/process...can/could/will/is benefiting the conduction of scientific research.

My $0.03:  I perceive that there is a great hunger in research communities for the now clear benefits of using open source practices:  collaboration, transparency and the resulting improvements in communication and education, technical innovation, cross-org and cross-discipline information sharing, as well as the rigor and scalability that comes from 'good practice/process' (e.g. releng) and associated tooling...to mention but a few ;).

In other words:  +1

Scott

[1] http://www.crcpress.com/product/isbn/9781466561595
[2] https://github.com/fperez/repro-chapter-oss


- Peter

On Thu, Apr 16, 2015 at 7:36 AM, Martin Hammitzsch <martin.hammitzsch@xxxxxxxxx> wrote:

Hi Everyone,

Philip, thanks for raising this issue and thanks to all for sharing.

If you are interested we may arrange a Hangout to share and discuss ideas. We may present approaches and activities already implemented as well as ideas and eventually next steps how to overcome related issues.

If this would be fine with you we could consider end of April or beginning of May for a Hangout.

Best,
Martin

On 16 Apr 2015 15:51, "Philip Wenig" <philip.wenig@xxxxxxxxxxxxx> wrote:
I like the blogpost about the reasons to be a research software engineer :-).

Thanks also Jay for adding your comment. As far as I understood Martin, the DOIed "software" package could contain also a paper describing it. The difference to a sole paper is, that the reviewers and/or readers can have a better understanding of it by using the software with test or real world data.


Best,
Philip


Am 16.04.2015 um 14:46 schrieb Jay Jay Billings:
I concur, although I will add one point.

We recognize these problems at ORNL and are working on it. However, one thing that we have started doing to kind of have our cake and eat it too is to publish papers on the software itself from a software engineering perspective and to work with users to jointly author papers on the science. Most of both papers can be constructed from documentation in the source.

Jay

On Thu, Apr 16, 2015 at 8:14 AM, <Matt.Gerring@xxxxxxxxxxxxx> wrote:
Hi Philip,

This could be a great step for Research Software Engineers to get their work recognised to the community. One of our staff here, Mark Basham, has recently been involved with how to recognise the software contribution to science including creating an industry recognised term for the role, see http://www.rse.ac.uk/who.html and http://www.software.ac.uk/blog/2013-08-23-ten-reasons-be-research-software-engineer.

I think your proposal is in synergy with the idea and would help greatly.

Sincerely,

Matt Gerring
Diamond Light Source Ltd.

-----Original Message-----
From: science-iwg-bounces@xxxxxxxxxxx [mailto:science-iwg-bounces@xxxxxxxxxxx] On Behalf Of Philip Wenig
Sent: 16 April 2015 13:04
To: science-iwg@xxxxxxxxxxx; location-iwg@xxxxxxxxxxxxxxxx; Martin Hammitzsch
Subject: [science-iwg] Scientific papers - scientific software

Hi folks,

Martin gave an excellent talk about the publication of software at the EGU meeting yesterday. Scientists get reward for papers but not for software. Papers are cited, software not. That's a drawback for a scientific career. As we know, software has become crucial in scientific research nowadays. Hence, I'd like to share some of Martin's ideas with you:

* Certain Science/LocationTech WG releases/packages get a DOI
* The DOI points to a landing page with appropriate metadata to cite the release/package
* The release/package can be cited and will be ranked on Google Scholar and other systems

= This could be an incentive for more scientists to publish their software under the umbrella of the Science and LocationTech WG.

What's your opinion?


Best,
Philip

PDF of Martin's presentation:
https://docs.google.com/presentation/d/1tulhwtEK9l1yGaAX1YWsMR7OrQAwWDee4N2M1Yy7bIo/edit?pli=1#slide=id.gada00e2fc_0_866

--
~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx » http://www.openchrom.net ~~~~~~~~~~~~~~~~~~~~~~~~

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Jay Jay Billings
Oak Ridge National Laboratory
Twitter Handle: @jayjaybillings


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-- 
~~~~~~~~~~~~~~~~~~~~~~~~
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~~~~~~~~~~~~~~~~~~~~~~~~

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