Begin forwarded message:
From what I have read on Nature Methods decision then if the
journals of J.
Applied Cryst and Acta Cryst were to go down the same path then
2000 plus
users of TOPAS and TOPAS-Academic would be without a means of
reading peer
reviewed articles on the algorithms used by those programs. This
would be a
tragedy...
I think that people are misreading the intent of the editorial. From
the abstract:
Software that is custom-developed as part of novel methods is as
important for the method's implementation as reagents and protocols.
Such software, or the underlying algorithms, must be made available
to readers upon publication.
Note that TOPAS is available to Nature Method readers... one only has
to buy it, so no problem here. The problem is really when a
scientific result is obtained with software that is both unique and
not distributed. How could cold-fusion, polywater etc be debunked if
one has to know the secret handshake to know enough details to
duplicate the work.
I personally feel that open source software is usually in the best
interests of scientific methods development. I would be uncomfortable
if the only method available to me to check that a structural model
matches data were a single undisclosed code (such as GSAS or TOPAS).
However one has a wealth of programs that can be used to verify that
a model matches the observed data. In worst case, I could pull out a
calculator and grind out some structure factors. There may be some
improvements in the algorithms, but the fundamental equations are all
well understood here.
Access to code improves science, IMHO. When people can read through
code, errors are spotted. Access to code allows a motivated scientist
to develop a new method by building on an existing one rather than
starting from scratch, where the latter can be a huge hurdle. Perhaps
the argument is less acute, as few scientists are prepared to code or
even modify programs. However, I don't see the intent of the
editorial to force that model on anyone.
Brian
