CCL: RE: Where can you publish articles on software?
- From: "Warren DeLano" <warren-x-delsci.com>
- Subject: CCL: RE: Where can you publish articles on software?
- Date: Wed, 12 Oct 2005 12:23:06 -0700
Sent to CCL by: "Warren DeLano" [warren(~)delsci.com]
> Sent to CCL by: "Andy Holder" [holdera%umkc.edu]
Ironically, JMGM editor Andy Holder offers compelling reasons for why
developer-scientists should shift their attention away from
closed-access journals like JMGM and toward peer-reviewed
open-access/open-source venues that better serve the overall needs of
the field.
> I am the editor of the Journal of Molecular Graphics and Modelling,
> and we specifically EXCLUDE program announcements/descriptions from
> our pages. Programs are not original research, but may be
> implementations of original research.
This fails to acknowledge the critical enabling role of software in
computational chemistry and conveys a shockingly dismissive view of the
original research aspects of computer programs! To put it as politely
as I can, I most vehemently disagree. Such comments insult and demean
the creative efforts of those who might have otherwise considered
publishing papers in JMGM.
> The data from JMGM indicate that our IF went DOWN
> when we included these item and has been steadily increasing since we
> eliminated them.
Effective running software is at least as impactful as algorithmic
descriptions, if not more so. (We live in real buildings, not
architectural plans; we travel by plane, not via designs of planes).
"Impact Factor" (I.F.) in terms of follow-on citations has little
relevance as a measure of impact for scientific software and especially
so once usage becomes widespread (e.g. ChemDraw, RasMol, Excel, etc.).
Speaking from personal experience, recognizable PyMOL images are now
routinely found in Science, Nature, C&EN, and many other journals, but
such usage is rarely cited. So what is PyMOL's impact factor? Zero! It
has never been officially "published" per se, even though its source
code has been published continuously on the internet since early 2000.
> The algorithm is perhaps worthy of
> publication, and the program can certainly be mentioned, but is not in
> and of itself worthy of the valuable space in a research journal.
Such comments reflect little "editorial" sympathy for the
publish-or-perish plight faced by academic scientists who develop
practical algorithms in the form of working software programs instead of
abstract algorithms in the form of non-working descriptive publications.
Without such publications, the impact of developer-scientists is
invisible to tenure review committees and funding agencies. That is
unfair to many scientists and damaging to the field as a whole since
better research software is very much needed. Developer-scientists need
to be appropriately recognized and rewarded through career advancement,
and thus it is not by accident that so many talented scientific software
developers have chosen the private sector over the academic world. The
system of academic credit is largely broken with respect to creation of
quality research software.
While JMCM may indeed have a fine "editorial" policy on this matter,
it
is justified for the wrong reasons.
Programs cannot truly be "published" in traditional journals because
they are too complex to describe precisely in such venues. A standalone
print article does not deliver reproducibility and verifiability with
respect to research software. Thus, journal articles describing
software do not meet fundamental requirements of the scientific method.
The only way to publish software in a scientifically robust manner is to
share source code, and that means publishing via the internet in an
open-access/open-source fashion. Anything short of that amounts to
issuing unproven claims based on limited empirical tests regarding what
a given program allegedly does. What is that called outside of science?
Advertising! And as such, I agree that it does not belong in a
scientific journal. Either you publish software with source code and
stand behind it, or you are blowing smoke and quite *literally* hiding
something -- no matter how noble your intent.
> Being a former member of the Dewar group, they certainly published a
> large number of papers on semiempirical methods, but never published
> any article on AMPAC itself.
Such comments confirm the notion that research software developers are
not recognized for the critical enabling contributions they make, and
reveal just how incapable the old closed-access, print-journal
publication system is of meeting current needs.
So, go live fellow research software developers, go live! Bypass an
inadequate and obsolete system, and instead pursue internet-based
open-access/open-source publishing of your work. If you lead, the world
will follow.
http://www.plos.org , http://www.doaj.org ,
http://pubchem.ncbi.nlm.nih.gov , http://www.blueobelisk.org
,
http://www.chmoogle.com ,
http://www.sf.net , etc.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:warren-,-delsci.com
> -----Original Message-----
> From: owner-chemistry-,-ccl.net [mailto:owner-chemistry-,-ccl.net]
> Sent: Tuesday, October 11, 2005 4:46 PM
> To: Warren DeLano
> Subject: CCL: W:CCL: Where can you publish articles on software?
>
>
> Sent to CCL by: "Andy Holder" [holdera%umkc.edu] In reply to:
>
> > This programme is surely useful, but the editors of
> research journals
> > would probably not accept it for publication. If this kind
> of article
> > is acceptable, I guess that many people would produce tons of
> > technical programmes
> >>This is exactly what I think *should* be encouraged! If we look at
> >>bioinformatics, the latest issue of "BMC Bioinformatics"
has 7
> >>software articles (this journal has an impact factor of 5.42); the
> >>latest issue of "Bioinformatics" has 9 'Application
Notes' (this
> >>journal has an impact factor of 5.74). There is a real interest in
> >>useful software that can make it easier to do science.
>
> I am the editor of the Journal of Molecular Graphics and Modelling,
> and we specifically EXCLUDE program announcements/descriptions from
> our pages. Programs are not original research, but may be
> implementations of original research.
>
> Being a former member of the Dewar group, they certainly published a
> large number of papers on semiempirical methods, but never published
> any article on AMPAC itself. These programs were even run on just a
> few examples of "suitable data of interest"! The algorithm is
perhaos
> worthy of publication, and the program can certainly be mentioned, but
> is not in and of itself worthy of the valuable space in a research
> journal.
>
> Comparison to various other journals with high impact factors is
> anecdotal at best. The data from JMGM indicate that our IF went DOWN
> when we included these item and has been steadily increasing since we
> eliminated them. But that could also have been for a number of other
> reasons.
>
> My 0.02.
>
> Regards, Andy Holder
>
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> JJJJJJJJ MMM MMM GGG MMM MMM | ANDREW J. HOLDER
> JJ MM MM GG GG MM MM | Editor
> JJ MMM MMM GG MMM MMM |J. of Molclr Grphcs & Modelling
> JJ MM M MM GG GGGG MM M MM | Dept. of Chemistry
> JJ JJ MM M MM GG GG MM M MM | Univ. of Missouri-Kansas City
> JJ GGG | Kansas City, MO 64110
> | holdera-$-umkc.edu
> Published by Elsevier Science | (816)235-2293 * (816)235-6543F
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