Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles
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.mcdoug...@gmail.comwrote:
On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever gokhanse...@gmail.com
wrote:
On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 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=2SrcAuth=AlertingSrcApp=AlertingDestApp=WOSDestLinkType=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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Control and Dynamical Systems
(925) 963 8280
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Galleries: http://www.ArtInNaturePhotography.com/
Blog: http://www.ArtInNaturePhotography.com/wordpress/
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Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles
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.varoqu...@gmail.comwrote:
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 gokhanse...@gmail.com
wrote:
On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez 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=2SrcAuth=AlertingSrcApp=AlertingDestApp=WOSDestLinkType=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
Re: [Matplotlib-users] Matplotlib produced plots in academic journal articles
On Fri, Oct 5, 2012 at 12:23 PM, Damon McDougall damon.mcdoug...@gmail.comwrote: On Fri, Oct 5, 2012 at 8:11 PM, Gökhan Sever 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. 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
