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

Matthew Brett matthew.brett@gmail....
Sun Nov 4 09:39:49 CST 2007


> > 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 !!

Hmm - I'm in the same field, and trying to work out a way to fix this with:


The problem is not as silly as it seems.  Neuroimaging is moderately
complex, and it's difficult for reviewers to understand what has been
done if you have used a variety of software packages.  The advantage
of SPM, in this case, is that the code for the neuroimaging part is
open source (GPL), it covers the whole range of processing (more or
less), and it's fairly easy to extend.  The disadvantage is that - you
need matlab - and that matlab is so clunky as a programming language
that it deals very badly with the increasing need for complexity,
meaning it is harder and harder to develop in SPM as time goes by.
Our thought was that the only way out of this was to develop a system
that would allow you to call the core algorithms of SPM within python,
and develop new ones that you could validate against SPM (and other
tools) as the standard.  But it's hard work getting that right,
because our community is so fragmented.




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