[Matplotlib-users] matplotlib at LIGO/GW observation

Benjamin Root ben.v.root at gmail.com
Tue Feb 16 16:47:41 EST 2016


In latex, you could utilize the \nocite{} feature. I've done this on
certain occasions.

*Including references that are not cited in the paper.* Bibtex builds the
bibliography from the references that are actually cited in the paper.
Including references without corresponding citations is generally a bad
idea, but it may be warranted in special situations. To include a reference
that is not cited in the paper, but which has a record in the bibtex
database, add the command \nocite{xxx} at the end of the paper, just before
the bibliography; here "xxx" is the key for the paper to be cited. The
command \nocite{*} causes all items in the database to be included in the
references, regardless of whether or not they are cited in the paper.

http://www.math.uiuc.edu/~hildebr/tex/bibliographies0.html



On Tue, Feb 16, 2016 at 4:26 PM, Jody Klymak <jklymak at uvic.ca> wrote:

>
> Hi Ben,
>
> On 16 Feb 2016, at  12:30 PM, 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?
>
>
> OK, so I have a data paper, where does a citation go?  the software stack
> is *rarely* cited at all, unless the software author has made available a
> paper that uses a specialized technique that a reader would have trouble
> finding themselves.  i.e. "the data was filtered with the Smith filter
> [Smith ’89]".
>
> There is rarely a statement in a paper that says “Figure X was plotted
> with Matlab”, “Figure y was plotted with GMT” and "Figure z was plotted
> with matplotlib”.
>
> Suggestions welcome - I value matplotlib, and don’t want to take
> advantage, but the request is a bit awkward to fulfill.
>
> Cheers,   Jody
>
>
>
> 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
>>>>
>>>> _______________________________________________
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>>>> 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
>>
>
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> --
> Jody Klymak
> http://web.uvic.ca/~jklymak/
>
>
>
>
>
>
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