Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Andreas Hilboll]

> 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?

I like that idea. Probably, a wiki page at github would be best for this?


--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan Sever]

On Fri, Oct 5, 2012 at 2:47 PM, Phil Austin  wrote:
>
> Nice to see our matplotlib acknowledgement generating ripples. We've also
got some
> mayavi animations and links to other matplotlib-plotted papers and posters
> at http://cafc.ubc.ca
>
> best, Phil
>

Nice visuals Phil. Thanks for making your articles easily accessible from
your page. In addition to your papers here are a couple more atmospheric
science related open-access articles that uses matplotlib for figures:


Mallet, V., Quélo, D., Sportisse, B., Ahmed de Biasi, M., Debry, É.,
Korsakissok, I., Wu, L., Roustan, Y., Sartelet, K., Tombette, M., and
Foudhil, H.: Technical Note: The air quality modeling system Polyphemus,
Atmos. Chem. Phys., 7, 5479-5487, doi:10.5194/acp-7-5479-2007, 2007.
http://www.atmos-chem-phys.net/7/5479/2007/acp-7-5479-2007.html


Batenburg, A. M., Walter, S., Pieterse, G., Levin, I., Schmidt, M., Jordan,
A., Hammer, S., Yver, C., and Röckmann, T.: Temporal and spatial
variability of the stable isotopic composition of atmospheric molecular
hydrogen: observations at six EUROHYDROS stations, Atmos. Chem. Phys., 11,
6985-6999, doi:10.5194/acp-11-6985-2011, 2011.
http://www.atmos-chem-phys.net/11/6985/2011/acp-11-6985-2011.html


Jones, C. R., Bretherton, C. S., and Leon, D.: Coupled vs. decoupled
boundary layers in VOCALS-REx, Atmos. Chem. Phys., 11, 7143-7153,
doi:10.5194/acp-11-7143-2011, 2011.
http://www.atmos-chem-phys.net/11/7143/2011/acp-11-7143-2011.html
(All except the first plot is produced by matplotlib)


Ungermann, J., Kalicinsky, C., Olschewski, F., Knieling, P., Hoffmann, L.,
Blank, J., Woiwode, W., Oelhaf, H., Hösen, E., Volk, C. M., Ulanovsky, A.,
Ravegnani, F., Weigel, K., Stroh, F., and Riese, M.: CRISTA-NF measurements
with unprecedented vertical resolution during the RECONCILE aircraft
campaign, Atmos. Meas. Tech., 5, 1173-1191, doi:10.5194/amt-5-1173-2012,
2012.
http://www.atmos-meas-tech.net/5/1173/2012/amt-5-1173-2012.html


Rautenhaus, M., Bauer, G., and Dörnbrack, A.: A web service based tool to
plan atmospheric research flights, Geosci. Model Dev., 5, 55-71,
doi:10.5194/gmd-5-55-2012, 2012.
http://www.geosci-model-dev.net/5/55/2012/gmd-5-55-2012.html
--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Damon McDougall]

On Fri, Oct 5, 2012 at 8:58 PM, Gökhan Sever  wrote:
>
>
> On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall 
> wrote:
>>
>> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
>> 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.
>>
>
> 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.

That's a good idea. Steven Boada's comment re: the arxiv is also a
good one. This looks workable :)

>> > 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?

Sounds good to me. Thanks for all the input.

-- 
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan Sever]

On Fri, Oct 5, 2012 at 2:02 PM, Francesco Montesano <
franz.berges...@gmail.com> wrote:
>
>
> I think that an official acknowledgment that people can copy and paste
> (and adapt) in their paper would be a great idea.
>
> Francesco
>
>

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
--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Francesco Montesano]

2012/10/5 Gökhan Sever 

>
>
> On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall  > wrote:
>
>> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
>> 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.
>>
>>
> 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


>
> --
> Gökhan
>
>
> --
> 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
>
>
--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan Sever]

On Fri, Oct 5, 2012 at 1:23 PM, Damon McDougall
wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
> 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.
>
>
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?


-- 
Gökhan
--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Steven Boada]

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  > wrote:
>
> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever
> mailto:gokhanse...@gmail.com>> 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
>
>
>
>
> --
> 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

--
Steven Boada
Dept. Physics and Astronomy
Texas A&M University
bo...@physics.tamu.edu

--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Nelle Varoquaux]

On 5 October 2012 21:23, Damon McDougall  wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
> 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
>
--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Floris van Breugel]

On Fri, Oct 5, 2012 at 12:23 PM, Damon McDougall
wrote:

> On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 
> 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.
>


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





>
> > 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
>
>
> --
> 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/
--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Damon McDougall]

On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever  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.

> 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

--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Fernando Perez]

On Fri, Oct 5, 2012 at 12:17 PM, Damon McDougall
 wrote:
> It's maybe a bit over the top,
> but it's certainly a good reference.

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

--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Damon McDougall]

On Fri, Oct 5, 2012 at 7:42 PM, Fernando Perez  wrote:
> On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux
>  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!

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

-- 
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan Sever]

On Fri, Oct 5, 2012 at 11:45 AM, 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: 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
>

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.


-- 
Gökhan
--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Fernando Perez]

On Fri, Oct 5, 2012 at 10:45 AM, Nelle Varoquaux
 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!

Cheers,

f

--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Floris van Breugel]

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
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.mcdoug...@gmail.com> wrote:
>>
>>> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever 
>>> wrote:
>>> >
>>> >
>>> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 
>>> > 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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Steven Boada]

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:
> 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
> mailto:damon.mcdoug...@gmail.com>> wrote:
>
> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever
> mailto:gokhanse...@gmail.com>> wrote:
> >
> >
> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez
> mailto:fperez@gmail.com>>
> > 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 

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Nelle Varoquaux]

>
> 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.mcdoug...@gmail.com> wrote:
>
>> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever 
>> wrote:
>> >
>> >
>> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 
>> > 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/
>
>

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Floris van Breugel]

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
wrote:

> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever 
> wrote:
> >
> >
> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 
> > 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/
--
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
Ma

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Damon McDougall]

On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever  wrote:
>
>
> On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 
> 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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan Sever]

On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 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
--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Fernando Perez]

On Fri, Oct 5, 2012 at 6:52 AM, Michael Droettboom  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.

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: http://ipython.org/citing.html

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

--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Michael Droettboom]

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. :-)


Jianbao

Message: 4
Date: Thu, 4 Oct 2012 22:31:34 -0600
From: G?khan Sever mailto:gokhanse...@gmail.com>>
    Subject: [Matplotlib-users] Matplotlib produced plots in academic
    journal articles
To: matplotlib-users@lists.sourceforge.net
<mailto:matplotlib-users@lists.sourceforge.net>
Message-ID:
   
mailto:xekryyys9kf5zw9q7yigziaketio...@mail.gmail.com>>

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



--
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


--
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

Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles

[Jianbao Tao]

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.orgshould 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. :-)

Jianbao

Message: 4
> Date: Thu, 4 Oct 2012 22:31:34 -0600
> From: G?khan Sever 
> Subject: [Matplotlib-users] Matplotlib produced plots in academic
> journal articles
> To: matplotlib-users@lists.sourceforge.net
> Message-ID:
>  xekryyys9kf5zw9q7yigziaketio...@mail.gmail.com>
> 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
>
--
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

[Matplotlib-users] Matplotlib produced plots in academic journal articles

[Gökhan Sever]

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?

-- 
Gökhan
--
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