In any case, does Nature Methods actually publish any papers that fall
into the category (quote) "custom-designed software necessary for the
method's implementation" where "a software program is the focus of the
report", at least in the area of macromolecular structure determination?
Come to that, are its sister journals Nature or even Nature Structural &
Molecular Biology well-known for publishing such papers, and is this the
reason that there is not the same requirement for them?

Recently we were looking for a journal to publish precisely such a paper
and on looking at the "Aims and scope of journal"
(http://www.nature.com/nmeth/authors/index.html) we saw "Biomolecular
structural analysis technologies, including NMR and crystallography",
but then looking through the past issues we couldn't find any papers
remotely similar to ours so it was way down the list of options.

There is actually no absolute requirement by Nature Methods that the
software be Open Source, quote "The guiding principle is that enough
information must be provided so that users can reproduce the procedure
and use the method in their own research at reasonable cost." and that
closed-source software "may be acceptable if the operations performed by
the software are sufficiently clear.".  
If however "the software is only an ancillary part of the method, and
the focus is on the methodological approach or an insight gained from
it" then "releasing the code may not be a requirement for publication".

Actually I would be rather more concerned with the statement: "a
condition of publication in a Nature journal is that authors are
required to make materials, data and associated protocols available to
readers promptly on request".  "Materials" would appear to include
purified and crystallised protein, at least they aren't specifically
excluded, so does this really mean I'm obliged to give the 10mg of pure
protein that has taken me 6 months to isolate to anyone that asks for
it, even though I'm apparently allowed to charge "reasonable" costs
(presumably in this case 6 months salary + overheads + all materials
used).  Even so, losing all my protein in this way would be a major
set-back to my research program!  I concede this is an extreme example
but where does one draw the line?

Cheers

-- Ian

> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On 
> Behalf Of Nadir T. Mrabet
> Sent: 23 March 2007 18:57
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Nature policy update regarding source code
> 
> Hi,
> 
> I believe such requirements concern only "Nature Methods" rather than 
> "Nature" by and large.
> Regards,
> 
> Nadir Mrabet
> 
> Pr. Nadir T. Mrabet
>     Cellular & Molecular Biochemistry
>     INSERM U-724
>     UHP - Nancy 1, School of Medicine
>     Avenue de la Foret de Haye, BP 184
>     54505 Vandoeuvre-les-Nancy Cedex
>     France
>     Phone: +33 (0)3.83.68.32.73
>     Fax:   +33 (0)3.83.68.32.79
>     E-mail: [log in to unmask]
>     
> 
> 
> [log in to unmask] wrote:
> > I thought that some of you might be interested that the 
> journal Nature
> > has clarified the publication requirements regarding source code
> > accessibility.  It is likely that some of you deserve congrats
> > for this.  Cheers!
> >
> > http://www.nature.com/nmeth/journal/v4/n3/full/nmeth0307-189.html
> >
> > Although there are still some small problems, I think that this is a
> > big step forward, and certainly an interesting read, if you are
> > interested in FOSS and science.
> >
> > Regards,
> > Michael L. Love Ph.D
> > Department of Biophysics and Biophysical Chemistry
> > School of Medicine
> > Johns Hopkins University
> > 725 N. Wolfe Street
> > Room 608B WBSB
> > Baltimore MD 21205-2185
> >
> > Interoffice Mail: 608B WBSB, SoM
> >
> > office: 410-614-2267
> > lab:    410-614-3179
> > fax:    410-502-6910
> > cell:   443-824-3451
> > http://www.gnu-darwin.org/
> >
> >
> >
> >   
> 
> 

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