[SciPy-user] Subject: Re: Scientific Python publications

Matthieu Brucher matthieu.brucher@gmail....
Sun Nov 4 10:54:50 CST 2007

Well, and in some communities, if your work is done in Matlab and not in C
or C++, your work is not even looked at... (not even talking about the fact
that generally you don't even say if your code is in X or Y)


2007/11/4, Etienne Gaudrain <et.gaudrain@free.fr>:
>  Hi,
> I understand you consider this is absurd. In a way, it is. And I agree
> that it is not pleasant to have to go back to Matlab when you moved up to
> Python.
> However, scientific publication have to meet a few standards and beside
> the infightings and abuse of power of some editors, we have to consider that
> scientific publication:
> - must be archived and archives must be reachable
> - must be readable/understandable by the community
> - must describe things that one could reproduce
> The two last points are, for now, not good for Python. Most of the
> community still don't know that Python exists. Then they consider themselves
> as unable to understand Python code (even if anybody who read in Matlab can
> actually read in Python). Worth, they don't have Python installed on their
> computer, so they can't run the .py. Ok, this no big deal, since Python can
> be freely downloaded. But, publications don't come along with a tutorial on
> how to install Python... (and Numpy.... and Scipy... and Pylab... and...)
> Finally, what is the most important in choosing between Python and Matlab
> is that Matlab is far more broadly used is the community than Python. For
> now. In scientific publication, the most common language must be used, even
> if it is not optimal. Look, we (try to) write papers in English, while
> French is far more elegant :-P .
> So, since Matlab is the standard, editors will require source codes in
> Matlab. But The Mathworks has recently done some mistakes in Matlab
> distributions (broke some backward compatibility for example), and a part of
> the community is moving to Python. So we can hope that since Scipy
> developement look stable, and since the documentation of Python/Numpy/Scipy
> is reliableenough, the community will largely move to Python. And will make
> substantial economies of money and time :-D .
> Regards,
> -Etienne
> Stef Mientki a écrit :
> Matthieu Brucher wrote:
>      As I said - the use of Matlab was necessary to include the code
>     for the
>     various descriptors introduced in the paper - unfortunately Scipy
>     code
>     would not have been accepted (I know this for a fact). The Python
>     software
>     used in this paper was much more complex than the Matlab
>     one-liners - I had
>     to process the recordings and do the calculations. Also, I had to
>     write a
>     speparate program to produce the animation. Of course this
>     software was not
>     converted to Matlab - just the mathematical expressions.
> In my field, the same problem arises with a Matlab toolbox, SPM. You
> can't write an article without using this toolbox, especially if you
> want to publish it in NeuroImage (the editor in chief is one of the
> writter of the toolbox).
>  This is really SAD:
> you're doing medical research, investigating and describing some
> physiological phenomena,
> well I can assume they are interested what algorithm you used,
> to verify your conclusions,
> but it's absolutely absurd, they make it obligatory that you write your
> manuscript with a pen of a certain brand !!
> It's even more absurd, if you realize
> that in MatLab the algorithms are unknown,
> so you can't verify them in case of weird results.
> ( I had a few a couple of years ago,
> and the answer of MathWorks was "try to get a job at MathWorks" ;-)
> But rethinking this attitude, maybe it's not absurd at all:
> because there are unknown errors in MatLab,
> they are unable to verify your results if you did the analysis in SciPy
> ;-) ;-)
> cheers,
> Stef Mientki
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> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Etienne Gaudrain
> Universite Claude Bernard LYON 1
> CNRS - UMR5020, Neurosciences Sensorielles, Comportement, Cognition
> 50, avenue Tony Garnier
> 69366 LYON Cedex 07
> Tél : 04 37 28 74 85
> Fax : 04 37 28 76 01
> Page web equipe : http://olfac.univ-lyon1.fr/unite/equipe-02/equipe-2-f.html
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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French PhD student
Website : http://miles.developpez.com/
Blogs : http://matt.eifelle.com and http://blog.developpez.com/?blog=92
LinkedIn : http://www.linkedin.com/in/matthieubrucher
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