=0A=0A

It is clear that the issue of the Science Code Manifesto=0Astirred= a lot of feelings. I must say that I found this topic almost as=0Aenjoyabl= e as the match between Fortran and C++. I learnt a couple of small=0Athings= with this discussion, but all in all I still subscribe to the same ideas= =0AI wrote some days ago:

=0A=0A

= =0A=0A

=E2=80=9CI like the idea of open software, a= nd in principle I=0Asupport the proposal of having access to the software c= ode=E2=80=A6 However, I feel=0Athat this is more wishful thinking than real= scientific life.=E2=80=9D

=0A=0A

=E2=80=9COpe= n or closed software (usually) doesn=E2=80=99t make me any=0Adifference, ex= cept from a philosophical perspective.=E2=80=9D

=0A=0A

I think of myself as a = pragmatic guy. That means that as=0Amuch as I like GPL and open software, I= am prepared to pay for a close program that=0Aworks better. And I dare to = say most of the computational chemists try not to=0Adive into the code anyw= ay, as we only want to obtain an energy value, and not=0Aunderstand how the= Roothaan=E2=80=99s equations were implemented.

=0A=0A

Let me rescue one thought that appeared (sorry I don=E2=80=99t=0Ar= emember the name of the author): =E2=80=9CReproducibility lies in the possi= bility of=0Aobtaining similar values, not necessarily with the same program= =E2=80=9D. So, if for=0Aexample I wrote down in the paper the functional an= d the basis set, that should=0Abe enough for reproducibility of the geometr= y (although a good=0Aresearcher should help his community by giving much mo= re information). If=0Aprograms X and Y give very different bond distances, = then clearly one of them=0Ais doing wrong its work. Who cares about the cod= e if it=E2=80=99s a crappy code anyway?=0AIt is not reproducible, and that = is death according to the scientific method.

=0A=0A

I still think that we must co= mpare ourselves with the=0Aexperimental chemistry world, and don=E2=80=99t = make a special epistemological rules for=0Acomputational science. If I use = a specific NMR, nobody will ask me to publish=0Athe designs of the equipmen= t including the Fourier transform algorithm and the=0Acrystal structure of = the superconductor (which I don=E2=80=99t have anyway); I must=0Aonly write= down the model and frequency of the machine. Should we ask more from=0Athe= theoreticians?

=0A=0A

Let me be repetitive:

=0A=0A

=E2=80=9CI like the idea of open software, and in principle I=0Asupport = the proposal of having access to the software code=E2=80=A6 However, I feel= =0Athat this is more wishful thinking than real scientific life.=E2=80=9D=0A=0A

=0A=0A

Now back to my calculations. From time to time we must stop=0Aarguing an= d make a bit of real work.

=0A=0A
Best,
Sebastian

--270156429-1988330702-1319045960=:31035-- From owner-chemistry@ccl.net Wed Oct 19 17:05:00 2011 From: "Alexander Bagaturyants bagaturyants{=}gmail.com" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45702-111019142132-14714-9blRTthdKrhL5CmIgEtDLQ++server.ccl.net> X-Original-From: "Alexander Bagaturyants" Content-Language: ru Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 19 Oct 2011 22:21:23 +0400 MIME-Version: 1.0 Sent to CCL by: "Alexander Bagaturyants" [bagaturyants-#-gmail.com] Dear CCLers, I believe that the current discussion becomes counterproductive. Of course, the author may decide whether to give an access to one's code or not. It is the author's inherent right. Actually, the code itself is necessary if (when) somebody wants to use it somehow in his/her future work. > From the pure scientific point of view, we need only the results of calculations and their verification. However, some authors are so inadequate that they even protest against any comparison or benchmarking of their codes and the results obtained. I believe that the scientific community must strongly oppose such a position. It has nothing to do with an honest attitude to science at all. Any code must be open to any comparison, verification and benchmarking, and the results of such a comparison, verification or benchmarking must be fully available to scientific community. > -----Original Message----- > From: owner-chemistry+sasha==photonics.ru---ccl.net [mailto:owner- > chemistry+sasha==photonics.ru---ccl.net] On Behalf Of George Fitzgerald > George.Fitzgerald/./accelrys.com > Sent: Wednesday, October 19, 2011 6:50 PM > To: Ð‘Ð°Ð³Ð°Ñ‚ÑƒÑ€ÑŒÑÐ½Ñ† ÐÐ»ÐµÐºÑÐ°Ð½Ð´Ñ€ ÐÐ»ÐµÐºÑÐ°Ð½Ð´Ñ€Ð¾Ð²Ð¸Ñ‡ > Subject: CCL:G: Science code manifesto > > > 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 shouldnâ€™t have been > published without the reviewer reviewing the code? > > -george> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Wed Oct 19 17:41:00 2011 From: "Serdar Badoglu sbadoglu##gazi.edu.tr" To: CCL Subject: CCL:G: Macro or something for Gaussian 03 Message-Id: <-45703-111019145621-25935-m0zlEuFpBkvDHi426m//yA ~~ server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Wed, 19 Oct 2011 14:56:17 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu-$-gazi.edu.tr] Hi CCL'ers, Do any of you have / know an excel macro / a little program to extract calculated frequencies, infrared intensities, and Raman activities from Gaussian log file? I don't need the complete spectrum generated, I only need the mentioned data of vibrational modes. I'm really tired of switching between windows and reading and typing the data into spreadsheets. Regards. From owner-chemistry@ccl.net Wed Oct 19 18:27:00 2011 From: "Laurence Cuffe cuffe^_^mac.com" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45704-111019170051-2966-IdwwST7Z5mJR9wy+WDCrRQ^server.ccl.net> X-Original-From: Laurence Cuffe Content-type: multipart/alternative; boundary="Boundary_(ID_o2MbhioYPbvve8LNeVXD7w)" Date: Wed, 19 Oct 2011 21:00:36 +0000 (GMT) MIME-version: 1.0 Sent to CCL by: Laurence Cuffe [cuffe[-]mac.com] --Boundary_(ID_o2MbhioYPbvve8LNeVXD7w) Content-type: text/plain; charset=utf-8; format=flowed Content-transfer-encoding: quoted-printable On Oct 19, 2011, at 03:41 PM, "Jaroslav Kalinovski kofeinu:+:hotmail.com" = wrote: > > Sent to CCL by: Jaroslav Kalinovski [kofeinu-$-hotmail.com] > > Hi, > I really do not understand... for me, the source code I am writing is li= ke an equipment in the laboratory. Do you really need someone else equipme= nt 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 reviewin= g paper about experiment with one? > > If someone is having troubles with reproducing my results, one always ca= n write to me and simply ask for the code but I do not feel I HAVE TO publ= ish code explicitly. In the end it is my property, I can describe algorith= m, 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 re= sult. > > 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 tru= st in authors. > That is all for me. > > Best regards, > J.Kalinowski =20 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 rig= ht to run or license the code can be whatever you think the market can bea= r. 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 e= xtract the key data, who then asserts that they wont let us see how it wor= ks. I don't expect a reviewer to check the code implementation of every compu= tational development that apears, this would be a very onerous task, and w= ould not be realistic. However if a problem arises where a number of progr= ams claim to be calculating the same thing, but get different results, the= n 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 restricti= ons and limitations should be clearly flagged in any resulting scientific = papers. A very hypothetical example of this might be where a researcher w= as working for a pharmaceutical company which had developed proprietary so= ftware 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, wit= hout giving details of precisely how they had been developed then it=EF=BB= =BF 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 wh= at and how you have written it, but it also allows you to examine their co= de 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 conf= idence. > > > ---------------------------------------- > > 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 pro= bably have a different outlook on this than most CCLers. But I have one ve= ry practical question: as a reviewer, do you really have the time and expe= rtise to review 1000s of lines of source code? I find that properly review= ing a paper already takes several hours. From experience I know that revie= wing somebody's source code can take days. > > > > Can anybody give me an example of what you'd even look for in the sour= ce code? I'm thinking back to, for example, Peter Gill's 'PRISM' method fo= r Gaussian integration, or Benny Johnson and DFT analytic 2nd derivatives.= Are you claiming that those papers shouldn=E2=80=99t have been published = without the reviewer reviewing the code? > > > > -george> > > > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > --Boundary_(ID_o2MbhioYPbvve8LNeVXD7w) Content-type: multipart/related; boundary="Boundary_(ID_xjgkfyRBHDO5WrGT+yR05w)"; type="text/html" --Boundary_(ID_xjgkfyRBHDO5WrGT+yR05w) Content-type: text/html; charset=windows-1252 Content-transfer-encoding: quoted-printable

On Oct 19, 2011, at 03:41 PM, "Jaroslav Kalinovski= kofeinu:+:hotmail.com" <owner-chemistry_._ccl.net> wrote:

=0ASent to CCL by: Jaroslav Kalinovski [kofeinu-$-hotmail.com]
=0A=
=0AHi,
=0AI really do not understand... for me, the source code I a= m writing is like an equipment in the laboratory. Do you really need someo= ne else equipment to make a proper review? Maybe in this case it is easy t= o send the code but rules are the same. Do you ask for particle accelerato= r when reviewing paper about experiment with one?
=0A
=0AIf someone= is having troubles with reproducing my results, one always can write to m= e and simply ask for the code but I do not feel I HAVE TO publish code exp= licitly. 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.
=0A
=0AI think peopl= e are forgetting that code is just a tool not a research result.
=0A=0AIt 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 t= rust in authors.
=0AThat is all for me.
=0A
=0ABest regards,=0AJ.Kalinowski

And that's exactly it, you don't have to publish your source code, but yo= u 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 copyrigh= t, but people should be able to look over it and satisfy themselves that i= t 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.