[IPython-dev] Concise citations for the Scipy stack

Simon Cropper simoncropper at fossworkflowguides.com
Mon Feb 2 17:36:33 EST 2015

PLOS is just one journal and one specifically marketing the open source 
community. That said, liberal as it might be the author guidelines for 
referencing don't include any information on software (e.g.)...



On 03/02/15 09:20, Wes Turner wrote:
> On Mon, Feb 2, 2015 at 3:54 PM, Simon Cropper
> <simoncropper at fossworkflowguides.com
> <mailto:simoncropper at fossworkflowguides.com>> wrote:
>     Hi Mark
>     My personal view when publishing work done with any software is...
>     1. Each bit of software used, its version and who released/sold it and
>          if it is readily available on the Internet, a URL to the release
>          should be cited. All foss software have specific attribution
>          requirements so care should be made to ensure these are met.
>     2. In the methodology you need to outline the specific configuration
>          or setup for any program that is able to vary the output of an
>          algorithm based on different settings; and any work/papers that
>     help
>          justify these settings.
>     3. Where appropriate, as you are publishing in the academic arena,
>          cite vanilla background papers -- like you suggested in your
>          original post -- supporting the framework/library methodology.
>     4. Finally, to avoid problems with varying definitions of what actually
>          constitutes the Scipy stack, outline only those software
>     packages or
>          libraries used. As pointed out by Aron the objective is to give
>          enough information to the reader that your analysis can be
>          reproduced.
> http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285#s4
> "Rule 3: Archive the Exact Versions of All External Programs Used"
>     The problem is however that journals don't like gray literature or web
>     references, let alone software or data sinks references.
> http://www.plos.org/policies/#sharing
> "7. Sharing of Data, Materials, and Software"
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> IPython-dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/ipython-dev

Cheers Simon

    Simon Cropper - Open Content Creator

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