Matplotlib produced plots in academic journal articles

Community matplotlib-users
1

I think that is a great idea. I think it is worthwhile to put a highlighted spot, or whatever, that shows matplotlib plots in academic publications. Additionally, it is good for enlarging the matplotlib user base to ask people to acknowledge matplotlib in their papers if they use matplotlib to make plots, and share links of their publications. Of course, matplotlib.org should provide some sort of platform for people to share that kind of information, such as a public email address. Such acknowledgement is not a hard thing to do, and I think most people, if not all, that benefit from matplotlib would be more than happy to do so. :slight_smile:

Jianbao

···

Message: 4

Date: Thu, 4 Oct 2012 22:31:34 -0600

From: G?khan Sever <gokhansever@…287…>

Subject: [Matplotlib-users] Matplotlib produced plots in academic

    journal articles

To: matplotlib-users@lists.sourceforge.net

Message-ID:

    <CAE5kuyh17jsDcaejwx=XeKrYyYs9kF5Zw9Q7yigziAketiOmPg@...288...>

Content-Type: text/plain; charset=“utf-8”

Hello,

Is there any collection of articles that shows academic articles using

matplotlib produced plots? I have come across a few recent articles in my

field with plots produced by matplotlib. Though, the mpl page shows some

nice examples of publication quality plots, it would be nice to have a

discipline specific collection of academic paper citations/links (hopefully

mostly open-access titles) to raise awareness of mpl usage in academia by

attracting other language users.

What do you think?

–

G?khan

2

This is a great idea. Anything to raise the level of perceived "legitimacy" in the academic community would be great. We can definitely add content like this to the documentation and/or website.

Mike

···

On 10/05/2012 09:43 AM, Jianbao Tao wrote:

I think that is a great idea. I think it is worthwhile to put a highlighted spot, or whatever, that shows matplotlib plots in academic publications. Additionally, it is good for enlarging the matplotlib user base to ask people to acknowledge matplotlib in their papers if they use matplotlib to make plots, and share links of their publications. Of course, matplotlib.org <http://matplotlib.org> should provide some sort of platform for people to share that kind of information, such as a public email address. Such acknowledgement is not a hard thing to do, and I think most people, if not all, that benefit from matplotlib would be more than happy to do so. :slight_smile:

Jianbao

    Message: 4
    Date: Thu, 4 Oct 2012 22:31:34 -0600
    From: G?khan Sever <gokhansever@...287...
    <mailto:gokhansever@…287…>>
    Subject: [Matplotlib-users] Matplotlib produced plots in academic
            journal articles
    To: matplotlib-users@lists.sourceforge.net
    <mailto:matplotlib-users@lists.sourceforge.net>
    Message-ID:
               <CAE5kuyh17jsDcaejwx=XeKrYyYs9kF5Zw9Q7yigziAketiOmPg@...288... <mailto:XeKrYyYs9kF5Zw9Q7yigziAketiOmPg@…288…>>
    Content-Type: text/plain; charset="utf-8"

    Hello,

    Is there any collection of articles that shows academic articles using
    matplotlib produced plots? I have come across a few recent
    articles in my
    field with plots produced by matplotlib. Though, the mpl page
    shows some
    nice examples of publication quality plots, it would be nice to have a
    discipline specific collection of academic paper citations/links
    (hopefully
    mostly open-access titles) to raise awareness of mpl usage in
    academia by
    attracting other language users.

    What do you think?

    --
    G?khan

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3

Our strategy:

- Prominent display on the main page of a citation request, along with
links on our top nav-bar:
http://ipython.org/#citing-ipython

- A copy/paste ready citation entry: Citing IPython — IPython

Matplotlib has a 'canonical' paper back in the same CISE issue that
can be used, here's the bibtex entry for it (should probably be
trimmed only to the main fields):

@Article{Hunter:2007,
  Author = {Hunter, J. D.},
  Title = {Matplotlib: A 2D graphics environment},
  Journal = {Computing In Science \& Engineering},
  Volume = {9},
  Number = {3},
  Pages = {90--95},
  abstract = {Matplotlib is a 2D graphics package used for Python
                   for application development, interactive scripting, and
                   publication-quality image generation across user
                   interfaces and operating systems.},
  address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,
                   CA 90720-1314 USA},
  bdsk-url-1 =
{http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019\},
  date-added = {2010-09-23 12:22:10 -0700},
  date-modified = {2010-09-23 12:22:10 -0700},
  isi = {000245668100019},
  isi-recid = {155389429},
  month = may # "/" # jun,
  publisher = {IEEE COMPUTER SOC},
  year = 2007
}

Cheers,

f

···

On Fri, Oct 5, 2012 at 6:52 AM, Michael Droettboom <mdroe@...86...> wrote:

This is a great idea. Anything to raise the level of perceived "legitimacy"
in the academic community would be great. We can definitely add content like
this to the documentation and/or website.

4

That wos link is useful, however I see only a paper listed following the “Time Cited” link in the atmospheric science field. A few papers I have seen mentions mpl in acknowledgement section, but some not, though the plots in them are obviously produced by mpl.

Should we list some articles here, as a base for a section that would go to mpl website?

···

On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez <fperez.net@…287…> wrote:

@Article{Hunter:2007,

Author = {Hunter, J. D.},

Title = {Matplotlib: A 2D graphics environment},

Journal = {Computing In Science & Engineering},

Volume = {9},

Number = {3},

Pages = {90–95},

abstract = {Matplotlib is a 2D graphics package used for Python

               for application development, interactive scripting, and

               publication-quality image generation across user

               interfaces and operating systems.},

address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,

               CA 90720-1314 USA},

bdsk-url-1 =

{http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019},

date-added = {2010-09-23 12:22:10 -0700},

date-modified = {2010-09-23 12:22:10 -0700},

isi = {000245668100019},

isi-recid = {155389429},

month = may # “/” # jun,

publisher = {IEEE COMPUTER SOC},

year = 2007

}

–
Gökhan

5

Short version:
I think this is a good idea.

Long version:
I think a 'Who uses matplotlib?' section in the website would provide
good solid academic backing, too. I know the Met Office
(PHIL!!!!!!!!!!!!!!!!) and some of the guys in the PECOS group at ICES
use it.

Actual papers is great, but probably rather drab? I think if we want
to show it off, we should include sample images from citations, rather
than just citations. After all, how many people are going to chase a
citation to see sample output when we have a gallery section? Better
still would be to have an 'academic gallery' section. Perhaps this
could be part of the gallery re-work someone was going to do (was it
Tony? I forget).

I don't know. I think the idea is good, but I think there needs to be
some thought and consensus regarding the *best* way to get people to
*visually* judge matplotlib's capabilities in the academic realm.

This is just my two.

···

On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever <gokhansever@...287...> wrote:

On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez <fperez.net@...287...> > wrote:

@Article{Hunter:2007,
  Author = {Hunter, J. D.},
  Title = {Matplotlib: A 2D graphics environment},
  Journal = {Computing In Science \& Engineering},
  Volume = {9},
  Number = {3},
  Pages = {90--95},
  abstract = {Matplotlib is a 2D graphics package used for Python
                   for application development, interactive scripting, and
                   publication-quality image generation across user
                   interfaces and operating systems.},
  address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,
                   CA 90720-1314 USA},
  bdsk-url-1 =

{http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019\},
  date-added = {2010-09-23 12:22:10 -0700},
  date-modified = {2010-09-23 12:22:10 -0700},
  isi = {000245668100019},
  isi-recid = {155389429},
  month = may # "/" # jun,
  publisher = {IEEE COMPUTER SOC},
  year = 2007
}

That wos link is useful, however I see only a paper listed following the
"Time Cited" link in the atmospheric science field. A few papers I have seen
mentions mpl in acknowledgement section, but some not, though the plots in
them are obviously produced by mpl.

Should we list some articles here, as a base for a section that would go to
mpl website?

--
Gökhan

--
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

6

That citation should be much more prominent on the matplotlib homepage. I regret to say that I was unaware of that paper I should have cited in my last paper which made heavy use of matplotlib generated plots with lots of customizations. Next time I’ll be sure to include the proper citation!

I think including a gallery of published examples would be great, however, there will be some serious challenges with regards to copyright. It would be great to show MPL being used in high impact journals (which it is), but getting permission from them to show the plots on the MPL website may require some paperwork. So, a list of citations might be a good place to start. Here’s mine: http://jeb.biologists.org/content/215/11/1783.full

  • Floris
···

On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall <damon.mcdougall@…287…> wrote:

On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever <gokhansever@…287…> wrote:

On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez <fperez.net@…287…> > > > wrote:

@Article{Hunter:2007,

Author = {Hunter, J. D.},

Title = {Matplotlib: A 2D graphics environment},

Journal = {Computing In Science & Engineering},

Volume = {9},

Number = {3},

Pages = {90–95},

abstract = {Matplotlib is a 2D graphics package used for Python

               for application development, interactive scripting, and

               publication-quality image generation across user

               interfaces and operating systems.},

address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,

               CA 90720-1314 USA},

bdsk-url-1 =

{http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019},

date-added = {2010-09-23 12:22:10 -0700},

date-modified = {2010-09-23 12:22:10 -0700},

isi = {000245668100019},

isi-recid = {155389429},

month = may # “/” # jun,

publisher = {IEEE COMPUTER SOC},

year = 2007

}

That wos link is useful, however I see only a paper listed following the

“Time Cited” link in the atmospheric science field. A few papers I have seen

mentions mpl in acknowledgement section, but some not, though the plots in

them are obviously produced by mpl.

Should we list some articles here, as a base for a section that would go to

mpl website?

–

Gökhan

Short version:

I think this is a good idea.

Long version:

I think a ‘Who uses matplotlib?’ section in the website would provide

good solid academic backing, too. I know the Met Office

(PHIL!!!) and some of the guys in the PECOS group at ICES

use it.

Actual papers is great, but probably rather drab? I think if we want

to show it off, we should include sample images from citations, rather

than just citations. After all, how many people are going to chase a

citation to see sample output when we have a gallery section? Better

still would be to have an ‘academic gallery’ section. Perhaps this

could be part of the gallery re-work someone was going to do (was it

Tony? I forget).

I don’t know. I think the idea is good, but I think there needs to be

some thought and consensus regarding the best way to get people to

visually judge matplotlib’s capabilities in the academic realm.

This is just my two.

–

Damon McDougall

http://www.damon-is-a-geek.com

B2.39

Mathematics Institute

University of Warwick

Coventry

West Midlands

CV4 7AL

United Kingdom

Don’t let slow site performance ruin your business. Deploy New Relic APM

Deploy New Relic app performance management and know exactly

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Try New Relic at no cost today and get our sweet Data Nerd shirt too!

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Matplotlib-users mailing list

Matplotlib-users@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/matplotlib-users

–
Floris van Breugel
PhD Candidate at Caltech
Control and Dynamical Systems
(925) 963 8280

Wildlife and Landscape Photographer
Galleries: http://www.ArtInNaturePhotography.com/

Blog: http://www.ArtInNaturePhotography.com/wordpress/

7

I think including a gallery of published examples would be great, however, there will be some serious challenges with regards to copyright. It would be great to show MPL being used in high impact journals (which it is), but getting permission from them to show the plots on the MPL website may require some paperwork. So, a list of citations might be a good place to start. Here’s mine: http://jeb.biologists.org/content/215/11/1783.full

I just came back from a bioinformatics workshop: I was suprised by the amound of people using matplotlib to display results.

I think it wouldn’t be too hard to gather images and published them on matplotlib’s website if the authors are OK with it. Also, in cancer research, publications and/or plots are often available publicly.

I don’t think citations would be as efficient: I personnally wouldn’t bother looking at those.

Here is an example on circos’ website of how they advertise the use of their plotting library in research: http://circos.ca/intro/published_images/

Cheers,

N

···
  • Floris

On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall <damon.mcdougall@…287…> wrote:

On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever <gokhansever@…287…> wrote:

On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez <fperez.net@…287…> > > > > > wrote:

@Article{Hunter:2007,

Author = {Hunter, J. D.},

Title = {Matplotlib: A 2D graphics environment},

Journal = {Computing In Science & Engineering},

Volume = {9},

Number = {3},

Pages = {90–95},

abstract = {Matplotlib is a 2D graphics package used for Python

               for application development, interactive scripting, and

               publication-quality image generation across user

               interfaces and operating systems.},

address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,

               CA 90720-1314 USA},

bdsk-url-1 =

{http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019},

date-added = {2010-09-23 12:22:10 -0700},

date-modified = {2010-09-23 12:22:10 -0700},

isi = {000245668100019},

isi-recid = {155389429},

month = may # “/” # jun,

publisher = {IEEE COMPUTER SOC},

year = 2007

}

That wos link is useful, however I see only a paper listed following the

“Time Cited” link in the atmospheric science field. A few papers I have seen

mentions mpl in acknowledgement section, but some not, though the plots in

them are obviously produced by mpl.

Should we list some articles here, as a base for a section that would go to

mpl website?

–

Gökhan

Short version:

I think this is a good idea.

Long version:

I think a ‘Who uses matplotlib?’ section in the website would provide

good solid academic backing, too. I know the Met Office

(PHIL!!!) and some of the guys in the PECOS group at ICES

use it.

Actual papers is great, but probably rather drab? I think if we want

to show it off, we should include sample images from citations, rather

than just citations. After all, how many people are going to chase a

citation to see sample output when we have a gallery section? Better

still would be to have an ‘academic gallery’ section. Perhaps this

could be part of the gallery re-work someone was going to do (was it

Tony? I forget).

I don’t know. I think the idea is good, but I think there needs to be

some thought and consensus regarding the best way to get people to

visually judge matplotlib’s capabilities in the academic realm.

This is just my two.

–

Damon McDougall

http://www.damon-is-a-geek.com

B2.39

Mathematics Institute

University of Warwick

Coventry

West Midlands

CV4 7AL

United Kingdom

Don’t let slow site performance ruin your business. Deploy New Relic APM

Deploy New Relic app performance management and know exactly

what is happening inside your Ruby, Python, PHP, Java, and .NET app

Try New Relic at no cost today and get our sweet Data Nerd shirt too!

http://p.sf.net/sfu/newrelic-dev2dev

Matplotlib-users mailing list

Matplotlib-users@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/matplotlib-users

–
Floris van Breugel
PhD Candidate at Caltech
Control and Dynamical Systems
(925) 963 8280

Wildlife and Landscape Photographer
Galleries: http://www.ArtInNaturePhotography.com/

Blog: http://www.ArtInNaturePhotography.com/wordpress/

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Matplotlib-users mailing list

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8

The idea of pulling key (and sexy) figures from papers is an awesome idea. I know when I am trying to make figures, I often search around looking at the different styles that people use to present similar data. There is also something different about publication level plots than the simple examples that MPL has on the gallery page now. Sure some of them are neat, but more importantly, they show you how to do something. Pulling figures from papers show you how to convey information and look good doing it.

I'll certainly cite MPL and ipython as I have used those a lot to both develop and present my results. Sadly, most of us in astronomy are still using IDL for all of the figure making.

Steven

···

On Fri 05 Oct 2012 12:45:30 PM CDT, Nelle Varoquaux wrote:

    I think including a gallery of published examples would be great,
    however, there will be some serious challenges with regards to
    copyright. It would be great to show MPL being used in high impact
    journals (which it is), but getting permission from them to show
    the plots on the MPL website may require some paperwork. So, a
    list of citations might be a good place to start. Here's mine:
    The visual control of landing and obstacle avoidance in the fruit fly Drosophila melanogaster | Journal of Experimental Biology | The Company of Biologists

I just came back from a bioinformatics workshop: I was suprised by the
amound of people using matplotlib to display results.
I think it wouldn't be too hard to gather images and published them on
matplotlib's website if the authors are OK with it. Also, in cancer
research, publications and/or plots are often available publicly.

I don't think citations would be as efficient: I personnally wouldn't
bother looking at those.
Here is an example on circos' website of how they advertise the use of
their plotting library in research:
http://circos.ca/intro/published_images/

Cheers,
N

    - Floris

    On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall > <damon.mcdougall@...287... <mailto:damon.mcdougall@…287…>> wrote:

        On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever > <gokhansever@...287... <mailto:gokhansever@…287…>> wrote:
        >
        > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez > <fperez.net@...287... <mailto:fperez.net@…287…>> > > wrote:
        >>
        >> @Article{Hunter:2007,
        >> Author = {Hunter, J. D.},
        >> Title = {Matplotlib: A 2D graphics environment},
        >> Journal = {Computing In Science \& Engineering},
        >> Volume = {9},
        >> Number = {3},
        >> Pages = {90--95},
        >> abstract = {Matplotlib is a 2D graphics package
        used for Python
        >> for application development, interactive
        scripting, and
        >> publication-quality image generation
        across user
        >> interfaces and operating systems.},
        >> address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014
        <tel:3014>, LOS ALAMITOS,
        >> CA 90720-1314 USA},
        >> bdsk-url-1 =
        >>
        {Clarivate},
        >> date-added = {2010-09-23 12:22:10 -0700},
        >> date-modified = {2010-09-23 12:22:10 -0700},
        >> isi = {000245668100019},
        >> isi-recid = {155389429},
        >> month = may # "/" # jun,
        >> publisher = {IEEE COMPUTER SOC},
        >> year = 2007
        >> }
        >
        > That wos link is useful, however I see only a paper listed
        following the
        > "Time Cited" link in the atmospheric science field. A few
        papers I have seen
        > mentions mpl in acknowledgement section, but some not,
        though the plots in
        > them are obviously produced by mpl.
        >
        > Should we list some articles here, as a base for a section
        that would go to
        > mpl website?
        >
        > --
        > Gökhan

        Short version:
        I think this is a good idea.

        Long version:
        I think a 'Who uses matplotlib?' section in the website would
        provide
        good solid academic backing, too. I know the Met Office
        (PHIL!!!!!!!!!!!!!!!!) and some of the guys in the PECOS group
        at ICES
        use it.

        Actual papers is great, but probably rather drab? I think if
        we want
        to show it off, we should include sample images from
        citations, rather
        than just citations. After all, how many people are going to
        chase a
        citation to see sample output when we have a gallery section?
        Better
        still would be to have an 'academic gallery' section. Perhaps this
        could be part of the gallery re-work someone was going to do
        (was it
        Tony? I forget).

        I don't know. I think the idea is good, but I think there
        needs to be
        some thought and consensus regarding the *best* way to get
        people to
        *visually* judge matplotlib's capabilities in the academic realm.

        This is just my two.

        --
        Damon McDougall
        http://www.damon-is-a-geek.com
        B2.39
        Mathematics Institute
        University of Warwick
        Coventry
        West Midlands
        CV4 7AL
        United Kingdom

        ------------------------------------------------------------------------------
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        Relic APM
        Deploy New Relic app performance management and know exactly
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        .NET app
        Try New Relic at no cost today and get our sweet Data Nerd
        shirt too!
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        <mailto:Matplotlib-users@lists.sourceforge.net>
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    --
    Floris van Breugel
    PhD Candidate at Caltech
    Control and Dynamical Systems
    (925) 963 8280

    Wildlife and Landscape Photographer
    Galleries: http://www.ArtInNaturePhotography.com/
    Blog: Art In Nature : Floris van Breugels Wilderness Photography and Adventure Blog

    ------------------------------------------------------------------------------
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--
Steven Boada
Dept. Physics and Astronomy
Texas A&M University
boada@...3847...

9

The problem is with many journals the content (including figures) is copyright by the journal, not the author. But I imagine most journals would grant permission, it’s just an additional step that should be taken where required.

The circos layout looks nice!

  • Floris
···

On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux <nelle.varoquaux@…287…> wrote:

I think including a gallery of published examples would be great, however, there will be some serious challenges with regards to copyright. It would be great to show MPL being used in high impact journals (which it is), but getting permission from them to show the plots on the MPL website may require some paperwork. So, a list of citations might be a good place to start. Here’s mine: http://jeb.biologists.org/content/215/11/1783.full

I just came back from a bioinformatics workshop: I was suprised by the amound of people using matplotlib to display results.

I think it wouldn’t be too hard to gather images and published them on matplotlib’s website if the authors are OK with it. Also, in cancer research, publications and/or plots are often available publicly.

I don’t think citations would be as efficient: I personnally wouldn’t bother looking at those.

Here is an example on circos’ website of how they advertise the use of their plotting library in research: http://circos.ca/intro/published_images/

Cheers,

N

  • Floris

On Fri, Oct 5, 2012 at 10:12 AM, Damon McDougall <damon.mcdougall@…287…> wrote:

On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever <gokhansever@…287…> wrote:

On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez <fperez.net@…287…> > > > > > > > wrote:

@Article{Hunter:2007,

Author = {Hunter, J. D.},

Title = {Matplotlib: A 2D graphics environment},

Journal = {Computing In Science & Engineering},

Volume = {9},

Number = {3},

Pages = {90–95},

abstract = {Matplotlib is a 2D graphics package used for Python

               for application development, interactive scripting, and

               publication-quality image generation across user

               interfaces and operating systems.},

address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS,

               CA 90720-1314 USA},

bdsk-url-1 =

{http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245668100019},

date-added = {2010-09-23 12:22:10 -0700},

date-modified = {2010-09-23 12:22:10 -0700},

isi = {000245668100019},

isi-recid = {155389429},

month = may # “/” # jun,

publisher = {IEEE COMPUTER SOC},

year = 2007

}

That wos link is useful, however I see only a paper listed following the

“Time Cited” link in the atmospheric science field. A few papers I have seen

mentions mpl in acknowledgement section, but some not, though the plots in

them are obviously produced by mpl.

Should we list some articles here, as a base for a section that would go to

mpl website?

–

Gökhan

Short version:

I think this is a good idea.

Long version:

I think a ‘Who uses matplotlib?’ section in the website would provide

good solid academic backing, too. I know the Met Office

(PHIL!!!) and some of the guys in the PECOS group at ICES

use it.

Actual papers is great, but probably rather drab? I think if we want

to show it off, we should include sample images from citations, rather

than just citations. After all, how many people are going to chase a

citation to see sample output when we have a gallery section? Better

still would be to have an ‘academic gallery’ section. Perhaps this

could be part of the gallery re-work someone was going to do (was it

Tony? I forget).

I don’t know. I think the idea is good, but I think there needs to be

some thought and consensus regarding the best way to get people to

visually judge matplotlib’s capabilities in the academic realm.

This is just my two.

–

Damon McDougall

http://www.damon-is-a-geek.com

B2.39

Mathematics Institute

University of Warwick

Coventry

West Midlands

CV4 7AL

United Kingdom

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10

Wow, that is one hell of a visually spiffy site. Can't find any links
to development repositories, but in terms of targeting end users, the
author (because it looks like a single-person job, given the many "I"
references) has done a solid job.

Sites like this remind me that we really should put a bit more effort
into the 'marketing' aspect of our sites. From what I can tell,
circos is very nice but has nowhere the technical depth, complexity
and flexibility of matplotlib. It's a fairly narrowly targeted tool.
But a site like that makes it really appealing to people.

Thanks for that link, Nelle!

Cheers,

f

···

On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux <nelle.varoquaux@...287...> wrote:

Here is an example on circos' website of how they advertise the use of their
plotting library in research: http://circos.ca/intro/published_images/

11

I think citation based discipline specific listing would make a good simple start. For instance:

Atmospheric Science:

Article 1 citation [link1]

Article 2 citation [link2]

Bioinformatics:

Article 1 citation [link1]

Article 2 citation [link2]

etc…

Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would provide context to the use of plots rather that extracting figures and putting them separately (dealing with copyright issues and such) on an alternative gallery page. The figures you linked look shinny but not much practical use in my field. Later, we can work on a more specific academic gallery page, once citation gallery grows to a critical limit.

···

On Fri, Oct 5, 2012 at 11:45 AM, Nelle Varoquaux <nelle.varoquaux@…287…> wrote:

I think including a gallery of published examples would be great, however, there will be some serious challenges with regards to copyright. It would be great to show MPL being used in high impact journals (which it is), but getting permission from them to show the plots on the MPL website may require some paperwork. So, a list of citations might be a good place to start. Here’s mine: http://jeb.biologists.org/content/215/11/1783.full

I just came back from a bioinformatics workshop: I was suprised by the amound of people using matplotlib to display results.

I think it wouldn’t be too hard to gather images and published them on matplotlib’s website if the authors are OK with it. Also, in cancer research, publications and/or plots are often available publicly.

I don’t think citations would be as efficient: I personnally wouldn’t bother looking at those.

Here is an example on circos’ website of how they advertise the use of their plotting library in research: http://circos.ca/intro/published_images/

Cheers,

N

–
Gökhan

12

Yes, that site was *full* of eye-candy. It's maybe a bit over the top,
but it's certainly a good reference.

···

On Fri, Oct 5, 2012 at 7:42 PM, Fernando Perez <fperez.net@...287...> wrote:

On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux > <nelle.varoquaux@...287...> wrote:

Here is an example on circos' website of how they advertise the use of their
plotting library in research: http://circos.ca/intro/published_images/

Wow, that is one hell of a visually spiffy site. Can't find any links
to development repositories, but in terms of targeting end users, the
author (because it looks like a single-person job, given the many "I"
references) has done a solid job.

Sites like this remind me that we really should put a bit more effort
into the 'marketing' aspect of our sites. From what I can tell,
circos is very nice but has nowhere the technical depth, complexity
and flexibility of matplotlib. It's a fairly narrowly targeted tool.
But a site like that makes it really appealing to people.

Thanks for that link, Nelle!

--
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

13

I agree, a bit too rich for my taste too. But our sites tend to be
the opposite extreme, so it's a good data point to keep in mind.

Cheers,

f

···

On Fri, Oct 5, 2012 at 12:17 PM, Damon McDougall <damon.mcdougall@...287...> wrote:

It's maybe a bit over the top,
but it's certainly a good reference.

14

Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would

This is not true. A lot of articles are unavailable to certain
institutions due to a lack of subscription. A major sticking point.

Am I wrong in thinking that journals copyright the final product?
Thus, it would be up to the author(s) to decide whether or not to
'donate' a figure for a gallery.

provide context to the use of plots rather that extracting figures and
putting them separately (dealing with copyright issues and such) on an
alternative gallery page. The figures you linked look shinny but not much
practical use in my field.

Point taken on the context argument. I'll take that. To resolve it,
make the figure/html image link to the underlying publication?

···

On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gokhansever@...287...> wrote:

--
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

15

Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would

This is not true. A lot of articles are unavailable to certain

institutions due to a lack of subscription. A major sticking point.

Yes… this is indeed a problem… perhaps there could be a list of citations specifically to open journal articles (many journals make papers public after some period of time), in addition to ones that are only available with a subscription. After all, many of those looking to use matplotlib in a scientific publication are usually at an institution with access. That way people who don’t have access don’t have to waste time finding links that work for them.

Am I wrong in thinking that journals copyright the final product?

Thus, it would be up to the author(s) to decide whether or not to

‘donate’ a figure for a gallery.

Many journals copyright the final product, so an author could only ‘donate’ a figure to the gallery if they had written permission from the journal that published their paper. Lame, I know.

Similarly, if someone wishes to reproduce a figure for news coverage or a review article, they need permission from the journal, not the author.

  • Floris
···

On Fri, Oct 5, 2012 at 12:23 PM, Damon McDougall <damon.mcdougall@…287…> wrote:

On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gokhansever@…287…> wrote:

provide context to the use of plots rather that extracting figures and

putting them separately (dealing with copyright issues and such) on an

alternative gallery page. The figures you linked look shinny but not much

practical use in my field.

Point taken on the context argument. I’ll take that. To resolve it,

make the figure/html image link to the underlying publication?

–

Damon McDougall

http://www.damon-is-a-geek.com

B2.39

Mathematics Institute

University of Warwick

Coventry

West Midlands

CV4 7AL

United Kingdom

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–
Floris van Breugel
PhD Candidate at Caltech
Control and Dynamical Systems
(925) 963 8280

Wildlife and Landscape Photographer
Galleries: http://www.ArtInNaturePhotography.com/

Blog: http://www.ArtInNaturePhotography.com/wordpress/

16

Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would

This is not true. A lot of articles are unavailable to certain

institutions due to a lack of subscription. A major sticking point.

Am I wrong in thinking that journals copyright the final product?

Thus, it would be up to the author(s) to decide whether or not to

‘donate’ a figure for a gallery.

I think it depends on the journal, and on the agreement. I think in most journals you/your institute can pay to have your paper publicly available.

I wouldn’t be shocked if a requirement to be in the gallery would be to donate a figure.

provide context to the use of plots rather that extracting figures and

putting them separately (dealing with copyright issues and such) on an

alternative gallery page. The figures you linked look shinny but not much

practical use in my field.

I was just showing an example of a gallery of published figures. It is much easier to go through a gallery, to quickly see what a library is capable of, than clicking on links to articles, that may often be of closed access.

···

On 5 October 2012 21:23, Damon McDougall <damon.mcdougall@…287…> wrote:

On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gokhansever@…287…> wrote:

Point taken on the context argument. I’ll take that. To resolve it,

make the figure/html image link to the underlying publication?

–

Damon McDougall

http://www.damon-is-a-geek.com

B2.39

Mathematics Institute

University of Warwick

Coventry

West Midlands

CV4 7AL

United Kingdom

17

For example, in astronomy, a lot of people will 'publish' their paper to Arxiv before it is accepted into a journal. Arxiv is accessible by the general public and a little digging around will reveal that you can download the actual Latex source for the paper. This includes all of the figures. I have never heard of anyone getting sued by a journal for posting their stuff on the arxiv.

Steven

···

On Fri 05 Oct 2012 02:42:06 PM CDT, Nelle Varoquaux wrote:

On 5 October 2012 21:23, Damon McDougall <damon.mcdougall@...287... > <mailto:damon.mcdougall@…287…>> wrote:

    On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever > <gokhansever@...287... <mailto:gokhansever@…287…>> wrote:
    > Seeing mpl produced plots would be only 1 or 2 clicks away, plus
    this would

    This is not true. A lot of articles are unavailable to certain
    institutions due to a lack of subscription. A major sticking point.

    Am I wrong in thinking that journals copyright the final product?
    Thus, it would be up to the author(s) to decide whether or not to
    'donate' a figure for a gallery.

I think it depends on the journal, and on the agreement. I think in
most journals you/your institute can pay to have your paper publicly
available.

I wouldn't be shocked if a requirement to be in the gallery would be
to donate a figure.

    > provide context to the use of plots rather that extracting
    figures and
    > putting them separately (dealing with copyright issues and such)
    on an
    > alternative gallery page. The figures you linked look shinny but
    not much
    > practical use in my field.

I was just showing an example of a gallery of published figures. It is
much easier to go through a gallery, to quickly see what a library is
capable of, than clicking on links to articles, that may often be of
closed access.

    Point taken on the context argument. I'll take that. To resolve it,
    make the figure/html image link to the underlying publication?

    --
    Damon McDougall
    http://www.damon-is-a-geek.com
    B2.39
    Mathematics Institute
    University of Warwick
    Coventry
    West Midlands
    CV4 7AL
    United Kingdom

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--
Steven Boada
Dept. Physics and Astronomy
Texas A&M University
boada@...3847...

18

Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would

This is not true. A lot of articles are unavailable to certain

institutions due to a lack of subscription. A major sticking point.

I was only thinking open-access journals, which open-source users (i.e. users of python tools) tend to publish their articles in open-journals. Of course, there are subscription required articles but those are secondary concerns. Sometimes authors make their articles publicly available even the article is on a paid journal.

provide context to the use of plots rather that extracting figures and

putting them separately (dealing with copyright issues and such) on an

alternative gallery page. The figures you linked look shinny but not much

practical use in my field.

Point taken on the context argument. I’ll take that. To resolve it,

make the figure/html image link to the underlying publication?

Citation listing is easier for me, we can go both ways, a page listing only citations, another one a more experimental figure/citation if copyright issues can be resolved easily. In anyways, we will have to gather citations. Let’s start doing that?

···

On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall <damon.mcdougall@…287…> wrote:

On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gokhansever@…287…> wrote:

–
Gökhan

19

2012/10/5 Gökhan Sever <gokhansever@…287…>

Seeing mpl produced plots would be only 1 or 2 clicks away, plus this would

This is not true. A lot of articles are unavailable to certain

institutions due to a lack of subscription. A major sticking point.

I was only thinking open-access journals, which open-source users (i.e. users of python tools) tend to publish their articles in open-journals. Of course, there are subscription required articles but those are secondary concerns. Sometimes authors make their articles publicly available even the article is on a paid journal.

provide context to the use of plots rather that extracting figures and

putting them separately (dealing with copyright issues and such) on an

alternative gallery page. The figures you linked look shinny but not much

practical use in my field.

Point taken on the context argument. I’ll take that. To resolve it,

make the figure/html image link to the underlying publication?

Citation listing is easier for me, we can go both ways, a page listing only citations, another one a more experimental figure/citation if copyright issues can be resolved easily. In anyways, we will have to gather citations. Let’s start doing that?

I think that an official acknowledgment that people can copy and paste (and adapt) in their paper would be a great idea.

Francesco

···

On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall <damon.mcdougall@…287…> wrote:

On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever <gokhansever@…287…> wrote:

–
Gökhan

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20

Some open-access journals permit this:

See for instance (also an example of a title that has all mpl produced figures):

Dawe, J. T. and Austin, P. H.: Statistical analysis of an LES shallow cumulus cloud ensemble using a cloud tracking algorithm, Atmos. Chem. Phys., 12, 1101-1119, doi:10.5194/acp-12-1101-2012, 2012, http://www.atmos-chem-phys.net/12/1101/2012/acp-12-1101-2012.html

···

On Fri, Oct 5, 2012 at 2:02 PM, Francesco Montesano <franz.bergesund@…287…> wrote:

I think that an official acknowledgment that people can copy and paste (and adapt) in their paper would be a great idea.

Francesco