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.

The call for openness is in the con= text 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 te= lling us that they wrote a program to extract the key data, who then asser= ts that they wont let us see how it works.

&n= bsp;I don't expect a reviewer to check the code implementation of every co= mputational development that apears, this would be a very onerous task, an= d would not be realistic. However if a problem arises where a number of pr= ograms claim to be calculating the same thing, but get different results, = then I think the scientific community would be best served if they knew th= at the source code was available for their perusal.

There may be a case for certain restrictions to apply, but these re= strictions and limitations should be clearly flagged in any resulting scie= ntific papers.  A very hypothetical example of this might be where a = researcher was working for a pharmaceutical company which had developed pr= oprietary software for developing leads in drug discovery. If the research= er wished to pubish details of research in which a number of potential dru= g candidates had been developed by applying the software to orphan drug di= scovery, without giving details of precisely how they had been developed t= hen it might be appropriate to flag this and publish the leads as a matter= of public interest.

One final point, open ac= cess to your code does allow ones rivals to see what and how you have writ= ten it, but it also allows you to examine their code and identify cases wh= ere they have stolen your IP.

All the best

Laurence Cuffe

=0A---
=0ALaboratory = of Physical Chemistry
=0AUniversity of Helsinki
=0A---
=0ALogic i= s a systematic method of coming to the wrong conclusion with confidence.=0A
=0A
=0A----------------------------------------
=0A> F= rom: owner-chemistry- -ccl.net
=0A> To: kofeinu- -hotmail.com
=0A= > Subject: CCL:G: Science code manifesto
=0A> Date: Wed, 19 Oct 2= 011 07:50:08 -0700
=0A>
=0A>
=0A> Sent to CCL by: George= Fitzgerald [George.Fitzgerald[A]accelrys.com]
=0A> As a member of a= company that makes money from selling software, I probably have a differe= nt outlook on this than most CCLers. But I have one very practical questio= n: as a reviewer, do you really have the time and expertise to review 1000= s of lines of source code? I find that properly reviewing a paper already = takes several hours. From experience I know that reviewing somebody's sour= ce code can take days.
=0A>
=0A> Can anybody give me an exampl= e of what you'd even look for in the source code? I'm thinking back to, fo= r example, Peter Gill's 'PRISM' method for Gaussian integration, or Benny = Johnson and DFT analytic 2nd derivatives. Are you claiming that those pape= rs shouldn=92t have been published without the reviewer reviewing the code= ?
=0A>
=0A> -george>
=0A>
=0A
=0A
=0A
=0A= -=3D This is automatically added to each message by the mailing script =3D= -
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