On Oct 19,
2011, at 03:41 PM, "Jaroslav Kalinovski kofeinu:+:
http://hotmail.com"
target="_blank">hotmail.com" <owner-chemistry- -
ccl.net> wrote:
Sent to CCL by: Jaroslav Kalinovski [kofeinu-$-
hotmail.com]
Hi,
I really do not understand... for me, the source code I am writing is like an
equipment in the laboratory. Do you really need someone else equipment to make a
proper review? Maybe in this case it is easy to send the code but rules are the
same. Do you ask for particle accelerator when reviewing paper about experiment
with one?
If someone is having troubles with reproducing my results, one always can write
to me and simply ask for the code but I do not feel I HAVE TO publish code
explicitly. In the end it is my property, I can describe algorithm, points of
theory but why should I give the code? No one is watching at the hands of
experimentalists while reviewing their papers.
I think people are forgetting that code is just a tool not a research
result.
It is true that relying only on reputation is not the perfect way but it works
for other disciplines. In the end we always have to put on some trust in
authors.
That is all for me.
Best regards,
J.Kalinowski
And
that's exactly it, you don't have to publish your source code, but you
should be prepared to let someone look over it if they ask.
Also you don't have to let them use it, you can protect that by
copyright, but people should be able to look over it and satisfy themselves that
it should do what you say it will. The right to look should be free, the
right to run or license the code can be whatever you think the market can
bear.
The call for openness is in the context of devising
code to analyze large data sets in the context of climate change. In this
context we should not be comfortable with a researcher telling us that they
wrote a program to extract the key data, who then asserts that they wont let us
see how it works.
I don't expect a reviewer to check the code
implementation of every computational development that apears, this would be a
very onerous task, and would not be realistic. However if a problem arises where
a number of programs claim to be calculating the same thing, but get different
results, then I think the scientific community would be best served if they knew
that the source code was available for their perusal.
There may be a case for certain restrictions to apply,
but these restrictions and limitations should be clearly flagged in any
resulting scientific papers. A very hypothetical example of this might be
where a researcher was working for a pharmaceutical company which had developed
proprietary software for developing leads in drug discovery. If the researcher
wished to pubish details of research in which a number of potential drug
candidates had been developed by applying the software to orphan drug discovery,
without giving details of precisely how they had been developed then it might be
appropriate to flag this and publish the leads as a matter of public
interest.
One final point, open access to your code does allow
ones rivals to see what and how you have written it, but it also allows you to
examine their code and identify cases where they have stolen your IP.
All the best
Laurence
Cuffe
---
Laboratory of Physical Chemistry
University of Helsinki
---
Logic is a systematic method of coming to the wrong conclusion with
confidence.
----------------------------------------
> From: owner-chemistry- -
ccl.net
> To: kofeinu- -
hotmail.com
> Subject: CCL:G: Science code manifesto
> Date: Wed, 19 Oct 2011 07:50:08 -0700
>
>
> Sent to CCL by: George Fitzgerald [George.Fitzgerald[A]
accelrys.com]
> As a member of a company that makes money from selling software, I probably
have a different outlook on this than most CCLers. But I have one very practical
question: as a reviewer, do you really have the time and expertise to review
1000s of lines of source code? I find that properly reviewing a paper already
takes several hours. From experience I know that reviewing somebody's source
code can take days.
>
> Can anybody give me an example of what you'd even look for in the
source code? I'm thinking back to, for example, Peter Gill's
'PRISM' method for Gaussian integration, or Benny Johnson and DFT
analytic 2nd derivatives. Are you claiming that those papers shouldn’t
have been published without the reviewer reviewing the code?
>
> -george>
>
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