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

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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
<nel...@gm...>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 <
>> dam...@gm...> wrote:
>>
>>> On Fri, Oct 5, 2012 at 5:55 PM, Gökhan Sever <gok...@gm...>
>>> wrote:
>>> >
>>> >
>>> > On Fri, Oct 5, 2012 at 10:26 AM, Fernando Perez <fpe...@gm...>
>>> > 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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>>
>>
>>
>> --
>> 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
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>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
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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/