matplotlib at LIGO/GW observation

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/
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Hi,

There is a Reddit Ask us Anything concerning the LIGO Scientific
Collaboration, with a dedicated discussion on the use of Python (and
Matplotlib):

https://www.reddit.com/r/IAmA/comments/45g8qu/we_are_the_ligo_scientific_collaboration_and_we/czxnlux

Regards,

Julien

2016-02-14 14:52 GMT+01:00 Nils Becker <nilsc.becker at gmail.com>:

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

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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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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

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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
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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

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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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Hi Ben,

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

···

On 16 Feb 2016, at 12:30 PM, Benjamin Root <ben.v.root at gmail.com> wrote:

Rock on!

Ben Root

On Tue, Feb 16, 2016 at 3:02 PM, Duncan Macleod <duncan.macleod at ligo.org <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:Matplotlib-users at python.org>
https://mail.python.org/mailman/listinfo/matplotlib-users

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

_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org <mailto:Matplotlib-users at python.org>
https://mail.python.org/mailman/listinfo/matplotlib-users

--
Duncan Macleod
duncan.macleod at ligo.org <mailto: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

--
Jody Klymak
http://web.uvic.ca/~jklymak/

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Hi

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.

How about acknowledgements section? Perhaps listing how each figure was
made is too verbose but maybe something like: I/we thank the
contributors of matplotlib [ref N] for making the software freely available.

Ilja

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/

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

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--
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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I think that if they are paying attention, the copy editors for our
journals would strip those out.

Eric

···

On 2016/02/16 11:47 AM, Benjamin Root wrote:

Including references without corresponding citations is generally a bad
idea, but it may be warranted in special situations.

Most journals I?m familiar with will not let you put uncited references into the reference section, for sadly obvious reasons :wink:

The acknowledgements section is fine, the only issue being where does one draw the line? I guess in the methods section simply saying, plots were rendered using matplotlib \cite{hunter} isn?t a terrible solution. Not usually done, but if it helps matplotlib stay funded, then its probably worth it. Apologies in advance for my recent paper where I didn?t do this, but its probably less well publicized than the LIGO paper, so maybe I?ll get away w/ it.

Cheers, Jody

···

On 16 Feb 2016, at 13:47 PM, Benjamin Root <ben.v.root at gmail.com> wrote:

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.

--
Jody Klymak
http://web.uvic.ca/~jklymak/

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