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

Etienne Gaudrain et.gaudrain@free...
Sun Nov 4 09:57:29 CST 2007


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 .


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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