From owner-chemistry-!at!-ccl.net Mon Oct 17 12:37:01 2011 From: "=?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= jordi.villafreixa/a\gmail.com" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45662-111017115137-1836-ey6VUXEDFuv++f3z4s6diQ-,-server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= Content-Type: multipart/alternative; boundary=002215b02e325607ce04af8094c8 Date: Mon, 17 Oct 2011 17:51:26 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= [jordi.villafreixa\a/gmail.com] --002215b02e325607ce04af8094c8 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Allow me to be drastic here. In my opinion this is a quite absurd discussion. Having the ability to make code transparent for others to reuse and build on top of is obviously way better for science than having black boxes. It is not needed to provide the ability to the referee (who by definition is a busy guy) to rerun the calculations, but to the scientific community as a whole. It may be the tim= e already to reduce the often over-critic referee system and move to a more open science schema. Repositories for code have been extremely useful in th= e past and I think being concerned about the ability of the scientific community to improve our results is way more positive that believing that w= e and only we can run a code and understand its results. Having myself a foot in enterpreneourship in addition to academia, I think that closing/selling code is futurless in a world with tens of thousands of developers ready for better implementations for each new idea. What makes sense is understanding the possible use of each technology, not closing the= m in a useless effort of overprotection. So, the need for the manifesto is clear. Start opening our eyes to a wider conception of science, far from egoistic and closed minded uses of it. The system should follow this, one day or another. 2011/10/17 Pedro Silva pedros^ufp.edu.pt > > Sent to CCL by: Pedro Silva [pedros(_)ufp.edu.pt] > 2011/10/17 Jo=E3o Brand=E3o jbrandao+/-ualg.pt : > > Sorry, but I disagree. > > > > "but if there are real concerns about the work, it is necessary that th= e > > scientific > > community can look seriously at the code to see exactly what the progra= m > is > > doing." > > > > In my opinion: > > If anyone has real concerns about any work, the best way for science > > development is to write (or use) a different code and compare the > results. > > > > The problem is: if the results do not agree with each other, how can > you adjudicate between the competing claims without access to the > code? > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 -- Jordi Vill=E0 i Freixa Computational Biochemistry and Biophysics lab Research Program on Biomedical Informatics (GRIB) - IMIM/UPF Parc de Recerca Biom=E8dica de Barcelona C/ Doctor Aiguader, 88; 08003 Barcelona (Spain) Tel: +34 93 316 0504 // Fax: +34 93 316 0550 e-mail: jvilla|*|imim.es http://cbbl.imim.es --002215b02e325607ce04af8094c8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Allow me to be drastic here.

In my opinion this is a qui= te absurd discussion. Having the ability to make code transparent for other= s to reuse and build on top of is obviously way better for science than hav= ing black boxes. It is not needed to provide the ability to the referee (wh= o by definition is a busy guy) to rerun the calculations, but to the scient= ific community as a whole. It may be the time already to reduce the often o= ver-critic referee system and move to a more open science schema. Repositor= ies for code have been extremely useful in the past and I think being conce= rned about the ability of the scientific community to improve our results i= s way more positive that believing that we and only we can run a code and u= nderstand its results.

Having myself a foot in enterpreneourship in addition to aca= demia, I think that closing/selling code is futurless in a world with tens = of thousands of developers ready for better implementations for each new id= ea. What makes sense is understanding the possible use of each technology, = not closing them in a useless effort of overprotection.

So, the need for the manifesto is clear. Start opening = our eyes to a wider conception of science, far from egoistic and closed min= ded uses of it. The system should follow this, one day or another.



2011/10/17 Pedro Sil= va pedros^ufp.edu.pt &l= t;owner-chemistry|*|ccl.net>= ;

Sent to CCL by: Pedro Silva [pedros(_)ufp.edu.pt]
2011/10/17 Jo=E3o Brand=E3o jbrandao+/-ualg.pt <owner-chemistry^-^ccl.net>:
> Sorry, but I disagree.
>
> "but if there are real concerns about the work, it is necessary t= hat the
> scientific
> community can look seriously at the code to see exactly what the progr= am is
> doing."
>
> In my opinion:
> If anyone has real concerns about any work, the best way for science > development is to write (or use) a different code and compare the resu= lts.
>

The problem is: if the results do not agree with each other, how can
you adjudicate between the competing claims without access to the
code?



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--
--
Jordi = Vill=E0 i Freixa
Computational Biochemistry and Biophysics lab
Resear= ch Program on Biomedical Informatics (GRIB) - IMIM/UPF
Parc de Recerca B= iom=E8dica de Barcelona
C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
Tel: +34 93 316 0504 // = Fax: +34 93 316 0550
e-mail: jvilla|*|imim.es http://cbbl.imim.es
--002215b02e325607ce04af8094c8--