From owner-chemistry -8 at 8- ccl.net Thu Oct 20 08:51:00 2011 From: "David A Mannock dmannock.,.ualberta.ca" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45710-111020010109-14222-+0+zdxx0K8deVJ+wpDogQQ,server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=00248c0eee4ec3d1b704afb3d770 Date: Wed, 19 Oct 2011 23:01:00 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock\a/ualberta.ca] --00248c0eee4ec3d1b704afb3d770 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi! A couple of people have suggested that explaining and providing details of software code is like providing details of the design of a piece of equipment used to perform a measurement. I don't think this is accurate. Experimentalists have to justify and validate the experimental approach, no= t the design of the equipment. The same practice should be part of manuscript= s using specific QC code for the first time. Dave On Wed, Oct 19, 2011 at 3:00 PM, Laurence Cuffe cuffe^_^mac.com < owner-chemistry*ccl.net> wrote: > > > 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 lik= e > 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 pa= per > 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 publi= sh > 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 th= e > 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 tru= st > 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 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 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 ri= ght > 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 result= s, > then I think the scientific community would be best served if they knew t= hat > 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 b= een > 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 on= e > 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 tha= t > reviewing somebody's source code can take days. > > > > Can anybody give me an example of what you'd even look for in the sourc= e > 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=92t have been published without th= e > reviewer reviewing the code? > > > > -george> > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> the strange characters on the top line to the - - sign. You can also > > > E-mail to subscribers: CHEMISTRY- -ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST- -ccl.net or use > > --00248c0eee4ec3d1b704afb3d770 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi! A couple of people have suggested that explaining and providing details= of software code is like providing details of the design of a piece of equ= ipment used to perform a measurement. I don't think this is accurate. E= xperimentalists have to justify and validate the experimental approach, not= the design of the equipment. The same practice should be part of manuscrip= ts using specific QC code for the first time. Dave

On Wed, Oct 19, 2011 at 3:00 PM, Laurence Cu= ffe cuffe^_^mac.com <owner-chemistry*ccl.net> wrote:

=
On Oct 19, 2011, at 03:41 PM, "Jaroslav Kalinovski kofeinu:+:hotmail.com" <owner= -chemistry- -ccl.net> w= rote:


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 t= o 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 pape= r about experiment with one?

If someone is having troubles with reproducing my results, one always can w= rite 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, po= ints of theory but why should I give the code? No one is watching at the ha= nds of experimentalists while reviewing their papers.

I think people are forgetting that code is just a tool not a research resul= t.

It is true that relying only on reputation is not the perfect way but it wo= rks for other disciplines. In the end we always have to put on some trust i= n authors.
That is all for me.

Best regards,
J.Kalinowski
=A0
A= nd that's exactly it, you don't have to publish your source code, b= ut 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 co= pyright, but people should be able to look over it and satisfy themselves t= hat it should do what you say it will.=A0 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 devisi= ng code to analyze large data sets in the context of climate change. In thi= s context we should not be comfortable with a researcher telling us that th= ey wrote a program to extract the key data, who then asserts that they wont= let us see how it works.

=A0I don't expect a reviewer to check the cod= e implementation of every computational development that apears, this would= be a very onerous task, and would not be realistic. However if a problem a= rises where a number of programs claim to be calculating the same thing, bu= t get different results, then I think the scientific community would be bes= t served if they knew that the source code was available for their perusal.=

There may be a case for certain restrictions to a= pply, but these restrictions and limitations should be clearly flagged in a= ny resulting scientific papers.=A0 A very hypothetical example of this migh= t be where a researcher was working for a pharmaceutical company which had = developed proprietary software for developing leads in drug discovery. If t= he researcher wished to pubish details of research in which a number of pot= ential drug candidates had been developed by applying the software to orpha= n drug discovery, without giving details of precisely how they had been dev= eloped 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 al= low 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 I= P.

All the best

Laurenc= e Cuffe

---
Laboratory of Physical Chemistry
University of Helsinki
---
Logic is a systematic method of coming to the wrong conclusion with confide= nce.


----------------------------------------
> From: owner-chemistry- -c= cl.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 ver= y practical question: as a reviewer, do you really have the time and expert= ise 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 'P= RISM' method for Gaussian integration, or Benny Johnson and DFT analyti= c 2nd derivatives. Are you claiming that those papers shouldn=92t have been= published without the reviewer reviewing the code?
>
> -george>
>



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