[Matplotlib-users] matplotlib at LIGO/GW observation

Tue Feb 16 15:59:39 EST 2016

Hi Ben,

Thanks for your input, I hope we can get quickly to the point where papers
with a smaller scope can cite the top-level software that enabled their
research (for methods papers, etc), but it might take a bit longer to get
the same for the full collaboration papers that have huge stacks underneath.

Thanks
D

On 16 February 2016 at 14:30, Benjamin Root <ben.v.root at gmail.com> wrote:

> Duncan,
>
> You do bring up a very good point. With large projects like yours, it does
> become difficult to explicitly cite every single piece of software that was
> used, and how far does that go? For example, do you cite BLAS/ATLAS if you
> were using numpy? A citation for Linux? For gcc?
>
> Probably the best way to deal with that is to treat it like a dependency
> problem. When a paper is published, cite the software that was immediately
> used for the paper and/or any papers that have already been put out for a
> particular portion of the software stack. So, ideally, several LIGO papers
> would have already been put out about particular portions of the technical
> stack that goes into great detail, and would have cited software more
> exhaustively there. Then, this particular paper would only need to cite
> those kinds of papers rather than redoing the entire citation stack again
> and again. The software packages get their impact factor, and the authors
> and reader maintain their sanity.
>
> Yes, this is a bit of a chicken-n-egg problem because many editors frown
> upon "software papers". I personally had a paper rejected once partly
> because the editor thought I was shirking my authorship duties of
> describing the procedures by footnoting a github link and citing
> NumPy/SciPy and such. I am hopeful that these attitudes are changing, even
> in the past few years since I submitted that paper. Your team's work is in
> a fantastic position to broadly change these attitudes due to your
> visibility across the sciences. Already, your efforts to make the source
> code and data easily accessible has stunned many scientists who are not
> used to this level of openness. I work in an atmospheric research shop, and
> long-time researchers are just amazed by how easy it was to "run the
> simulation" themselves via the jupyter notebooks! Being atmospheric
> scientists, they never thought that they could possibly study anything
> astrophysics related with just a click of a link.
>
> Rock on!
>
> Ben Root
>
>
> On Tue, Feb 16, 2016 at 3:02 PM, Duncan Macleod <duncan.macleod at ligo.org>
> wrote:
>
>> Hi Ben, all,
>>
>> You are correct, we haven't been very diligent in citing the software
>> used in our results, mainly from the problem of having a very large
>> software stack; everything from real-time interferometer operations and
>> low-latency data analysis through detection characterisation and myriad
>> offline analysis pipelines use hundreds of packages (C, C++, python,
>> matlab, ROOT, ... on multiple OSs) which becomes hard to cite.
>>
>> I will, however, bring the subject up in the collaboration to try and
>> collect citations from software so that we can get in the habit of
>> providing proper references. Thanks for bringing this to our attention.
>>
>>
>> Duncan
>>
>> On 16 February 2016 at 13:00, Benjamin Root <ben.v.root at gmail.com> wrote:
>>
>>> Speaking of citations, while we have your ear...
>>>
>>> Some of us have noticed that the paper did not include any citations to
>>> the scientific software that were utilized. This is somewhat of a new thing
>>> to cite software, but matplotlib, numpy and other projects all have
>>> suggested citations that we encourage researchers to use in their papers.
>>> Many of us are also researchers, and contributions to projects like numpy
>>> and matplotlib are often not treated as being on the same level as any
>>> other publication because researchers rarely cite the software projects
>>> they use.
>>>
>>> http://matplotlib.org/citing.html
>>>
>>> No hard feelings, we love what you guys have done. Just flagging it so
>>> that you guys might do so in future papers.
>>>
>>> Cheers!
>>> Ben Root
>>>
>>> On Tue, Feb 16, 2016 at 1:54 PM, Duncan Macleod <duncan.macleod at ligo.org
>>> > wrote:
>>>
>>>> Hi all,
>>>>
>>>> I'm a member of the LIGO Scientific Collaboration, and an author on the
>>>> PRL paper linked by Nils. Figure 1 did indeed use matplotlib, as did all of
>>>> the graphs in this paper (not the detector layout).
>>>>
>>>> The paper is 'open-access' with a Creative Commons Attribution 3.0
>>>> License attached, so I believe the figures can be freely included in other
>>>> documents as long as credits are given to the authors and the journal with
>>>> an appropriate citation. It would be very nice to see this included as an
>>>> example of using matplotlib for scientific analysis.
>>>>
>>>>
>>>> Thanks
>>>> D
>>>>
>>>> On 14 February 2016 at 07:52, Nils Becker <nilsc.becker at gmail.com>
>>>> wrote:
>>>>
>>>>> Hello everyone,
>>>>>
>>>>> as the direct observation of gravitational waves made its way round
>>>>> the world a few days ago, I was pleased to see that they (very probably)
>>>>> used matplotlib for their plots. They even used the new viridis colormap
>>>>> [1].
>>>>> I could not confirm this directly for the plots in the paper but at
>>>>> least the data analysis stack at LIGO seems to be built partly on python.
>>>>> They provide scripts to reproduce the data analysis in python and use
>>>>> matplotlib to plot it [2].
>>>>>
>>>>> In any case, maybe it's an idea to contact LIGO to confirm this and
>>>>> ask them if we could put the figure on the website gallery as a kind of
>>>>> "plot of honor" or something? I mean there is a chance that it's going to
>>>>> be the most famous plot done in matplotlib to this date.
>>>>>
>>>>> Cheers
>>>>> Nils
>>>>>
>>>>> [1]
>>>>> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102
>>>>> (page 2)
>>>>> [2] https://losc.ligo.org/software/
>>>>>
>>>>> _______________________________________________
>>>>> Matplotlib-users mailing list
>>>>> Matplotlib-users at python.org
>>>>> https://mail.python.org/mailman/listinfo/matplotlib-users
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Duncan Macleod
>>>> duncan.macleod at ligo.org
>>>> LIGO Data Grid systems development
>>>> Louisiana State University
>>>>
>>>> _______________________________________________
>>>> Matplotlib-users mailing list
>>>> Matplotlib-users at python.org
>>>> https://mail.python.org/mailman/listinfo/matplotlib-users
>>>>
>>>>
>>>
>>
>>
>> --
>> Duncan Macleod
>> duncan.macleod at ligo.org
>> LIGO Data Grid systems development
>> Louisiana State University
>>
>
>

-- 
Duncan Macleod
duncan.macleod at ligo.org
LIGO Data Grid systems development
Louisiana State University
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