[IPython-dev] Concise citations for the Scipy stack

[Wes Turner]

On Mon, Feb 2, 2015 at 3:54 PM, Simon Cropper <
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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