From owner-chemistry@ccl.net Thu Oct 20 04:09:00 2011 From: "Vasile Chis vasile.chis__phys.ubbcluj.ro" To: CCL Subject: CCL:G: Macro or something for Gaussian 03 Message-Id: <-45709-111020025952-23282-VUMb844ovaCW3nzN6lq6qg],[server.ccl.net> X-Original-From: "Vasile Chis" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 20 Oct 2011 10:00:01 +0300 MIME-Version: 1.0 Sent to CCL by: "Vasile Chis" [vasile.chis[*]phys.ubbcluj.ro] Dear Serdar, You can find such a program at: www.phys.ubbcluj.ro/~vasile.chis/group It is written in Python and runs under Linux or Windows. In the last case you need to have Python installed on your computer. The program will extract the symmetry, wavenumbers, IR intensities and Raman activities, as well as the redundant internal coordinates contributing to each normal mode. In order to have the contribution to normal modes you need to include Freq(intmodes) in the route section of your job. When running the program you will be prompted for a scaling factor, the exciting laser wavenumber and a threshold for the contribution of internal coordinates to normal modes. This threshold will be subsequently reduced until at least one redundant coordinate is printed. Thus, the output file you will contain both the unscaled and scaled wavenumbers, Raman activities and intensities. Raman intensities are obtained according to: [1] P.L. Polavaru, J. Phys. Chem. 94 (1990) 8106. [2] V. Krishnakumar, G. Keresztury, T. Sundius, R. Ramasamy, J. Mol. Struct. 702 (2004) 9. [3] S.D. Williams, T.J. Johnson, T.P. Gibbons, C.L. Kitchens, Theor. Chem. Acc. 117 (2007) 283. A non-uniform scaling is performed according to Scott and Radom: A.P. Scott, L. Radom, J. Phys. Chem. 100 (1996) 16502. Run the program using the following commands: Windows: python vibrational_modes.py gaussian_log_file Linux : vibrational_modes.py gaussian_log_file The output will be written in a text file that, subsequently, can be imported in a spreadsheet. An example of output is given bellow: # Nr Sym Freq[cm-1] Freq_scaled[cm-1] IR_int Raman_Act Raman_Int internal coordinates description (> 80 %) 95 A 1604.6052 1546.8394 942.8991 15.4054 1.3349 (C6-C13)[5.9%] (C8-C15)[5.9%] 96 A 1648.8879 1589.5279 59.3426 97.4519 8.1193 (C20-O31)[7.3%] (C23-O32)[7.3%] 97 A 1651.8142 1592.3489 401.4215 191.6471 15.9263 (C20-O31)[9.1%] (C23-O32)[9.1%] 99 A 1789.4568 1725.0364 380.4338 95.9056 7.0859 (C17-O28)[20.8%] 100 A 3212.3860 3096.7401 0.5753 0.1183 0.0032 (C8-H35)[38.4%] (C6-H34)[37.7%] 101 A 3212.8063 3097.1453 5.3733 63.3501 1.7295 (C6-H34)[38.3%] (C8-H35)[37.6%] 102 A 3757.3178 3622.0544 96.2644 86.7792 1.7111 (O29-H36)[83.0%] Please do not hesitate to contact me for any question you may have. Hope it helps! Yours, Vasile =========================== Prof.dr. Vasile Chis Babes-Bolyai University Faculty of Physics Kogalniceanu 1 400084 Cluj-Napoca Romania Tel: +40264405300 ext. 5153 Fax: +40264591906 Email: vasile.chis[a]phys.ubbcluj.ro =========================== -----Original Message----- > From: owner-chemistry+vchis==phys.ubbcluj.ro[a]ccl.net [mailto:owner-chemistry+vchis==phys.ubbcluj.ro[a]ccl.net] On Behalf Of Serdar Badoglu sbadoglu##gazi.edu.tr Sent: Wednesday, October 19, 2011 9:56 PM To: Chis, Vasile Subject: CCL:G: Macro or something for Gaussian 03 Sent to CCL by: "Serdar Badoglu" [sbadoglu-$-gazi.edu.tr] Hi CCL'ers, Do any of you have / know an excel macro / a little program to extract calculated frequencies, infrared intensities, and Raman activities from Gaussian log file? I don't need the complete spectrum generated, I only need the mentioned data of vibrational modes. I'm really tired of switching between windows and reading and typing the data into spreadsheets. Regards.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Oct 20 08:51:00 2011 From: "David A Mannock dmannock.,.ualberta.ca" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45710-111020010109-14222-+0+zdxx0K8deVJ+wpDogQQ,server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=00248c0eee4ec3d1b704afb3d770 Date: Wed, 19 Oct 2011 23:01:00 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock\a/ualberta.ca] --00248c0eee4ec3d1b704afb3d770 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi! A couple of people have suggested that explaining and providing details of software code is like providing details of the design of a piece of equipment used to perform a measurement. I don't think this is accurate. Experimentalists have to justify and validate the experimental approach, no= t the design of the equipment. The same practice should be part of manuscript= s using specific QC code for the first time. Dave On Wed, Oct 19, 2011 at 3:00 PM, Laurence Cuffe cuffe^_^mac.com < owner-chemistry*ccl.net> wrote: > > > On Oct 19, 2011, at 03:41 PM, "Jaroslav Kalinovski kofeinu:+:hotmail.com" > wrote: > > > Sent to CCL by: Jaroslav Kalinovski [kofeinu-$-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>
>



-=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


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--00248c0eee4ec3d1b704afb3d770-- From owner-chemistry@ccl.net Thu Oct 20 09:26:00 2011 From: "Georg Lefkidis lefkidis * physik.uni-kl.de" To: CCL Subject: CCL:G: AW: Science code manifesto Message-Id: <-45711-111020052617-956-pYhTgfGoItD5b5LZiOwvhQ/a\server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 20 Oct 2011 11:25:57 +0200 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis=physik.uni-kl.de] Hello everyone, I don't know if this was brought to the list's attention already, but there is an additional component as well (much as most of us would not like to admit it). Writing a source code often is the most time consuming part of one's results, even if the mathematical analysis per se might be done relatively quickly. This means, that once a code is there, the author(s) would like to use it over and over again (perhaps for different but similar systems) and of course *publish* more. The algorithmic implementation of a mathematical formula is part of the process. So I believe that most scientists-programmers would not feel very comfortable with sharing the codes with *anonymous* referees, which at the end might even reject the paper, and see that work appear elsewhere for other systems. Let's not forget it is not only the systems, the analysis and the results, but also the programming itself that is worth a publication. Everyone who ever programmed a data-mining algorithm for Gaussian or Gamess output knows that only too well. Perhaps this is not of concern to great professors with huge groups and meanwhile bug-free codes that have been around for decades but to a common mortal (like myself) it is (since I've seen that happen, although luckily not to me yet). Another issue is the quality of different third-party programs used. I read a couple of posts below, that it is (or might be) that the group's reputation is decisive. In fact there is more to that: being able to evaluate the quality of the results (by comparing to experiment or assessing the quality of derived properties, selection rules, symmetries etc.) plays also a very big role. For me a paper interpreting the importance of scaling a parameter done with not the best code is at least equally important as the best uncommented results produces out of the code only. So I see a potential danger there if the code itself becomes more and more important. Besides, good results will always get reproduced by other groups even with other codes or methods (for instance theory vs. experiment etc.). I am not saying I am for or against those two arguments, I just want to mention them as possible issues which need thinking. Best regards Georg -----Ursprüngliche Nachricht----- Von: owner-chemistry+lefkidis==physik.uni-kl.de|,|ccl.net [mailto:owner-chemistry+lefkidis==physik.uni-kl.de|,|ccl.net] Im Auftrag von Andrew Dalke dalke a dalkescientific.com Gesendet: Mittwoch, 19. Oktober 2011 11:39 An: Lefkidis, Georg Betreff: CCL: Science code manifesto Sent to CCL by: Andrew Dalke [dalke^^^dalkescientific.com] On Oct 18, 2011, at 4:17 PM, Adrià Cereto Massagué adrian.cereto,+,gmail.com wrote: > I don't think the manifesto is at odds with FSF. GPL'd software can be sold at any price, but its source code must be available for those who own the software at no further cost. And someone who has bought some GPL software is allowed to redistribute it for free, so researchers using it for a paper would be able to provide the software to reviewers and readers of the paper at no cost. Abstract: How much can the paper authors ask for access to the source code? How much can the curators charge? What should the curator do if the curated software contains a license violation? If I write a paper which depends on software for its analysis, and others should have access to the software as part of effective peer review, then how much can I charge others to get access to the software? US $1 billion? The FSF says I can charge as much as you want, and that freedom is one of the core freedoms of free software. The philosophy that others need access to my source code to provide good peer review has the implicit assumption that I will provide the software at a non-prohibitive cost. There is clearly a tension between these two viewpoints. This manifesto says nothing of what that cost might be, nor even that it might be an issue. What should be the cost to get access to source code from the author, or > from the curator? Does the curator get no-cost access to it as a condition of publication? Doesn't any limit on cost curtail what the FSF says is my freedom to charge as much as I want? Remember, the FSF encourages software freedom. I argue that scientific communication has overlapping but different goals. Science communications needs to have a low cost so that many people can get access to it. The FSF is only concerned about what happens *after* someone gets access to software. This is of course similar to (most) scientific papers. There the author gives the curator the right to redistribute the paper without paying royalties, and the curator can charge effectively any price for it. Most paper publishers want to maximize revenue, and therefore set high but not prohibitive prices. The software author may have other concerns. Interestingly, the software curator takes on a more difficult challenge than a paper curator. The authors of a paper (with a few exceptions usually well-covered by fair use exceptions) are the only copyright holders of a paper. More often though, the accompanying software has many more copyright holders. That can lead to problems. Consider the CDK chemistry toolkit. The package contains many copyright holders, including those from third-party libraries which it incorporates. A few years ago the CDK was in minor violation of the LGPL requirement of some of those libraries. (It omitted the credit required by those licenses.) This was quickly fixed once pointed out. I can easily imagine cases where it can't be easily fixed. The curator takes on the risk that someone else, who is a copyright holder to the software in question but not a paper author, may challenge the right of the curator to distribute the software. How does the curator resolve the violation, especially if the original author doesn't want to be involved? Does the curator remove the software in question? If so, and if you insist that the software must be available in order to do correct peer review, then should the corresponding paper also be withdrawn? As I said before, these are solvable. I bring them up because I encourage people to distribute their source code along with the paper, and to be aware that it's not a simple, clear issue. Andrew dalke:+:dalkescientific.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Oct 20 10:16:00 2011 From: "Sergio Manzetti sergio.manzetti(0)gmail.com" To: CCL Subject: CCL: Nitrenium ion on the Guanosine base Message-Id: <-45712-111020101231-10119-xiFyMKCToXs3CUpOIXFcjg[-]server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=bcaec51b1803cc0bff04afbb8a07 Date: Thu, 20 Oct 2011 16:12:09 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti#,#gmail.com] --bcaec51b1803cc0bff04afbb8a07 Content-Type: text/plain; charset=ISO-8859-1 Dear CCLrs, I am running some calculations on benzo[a]pyrene and its qualities, but they do not seem to be familiar with other carcinogens, although this is one of the most potent carcinogens. The mechanism of adduct formation is delineated in the literature as a amine-epoxy mechanism, but some issues do not compare well to this theory. Has anyone one this list seen a reference or thought about that the guanosine base may undergo ceonversion to a nitrenium-guanosine upon interaction with the epoxide or a radical of the PAH? Best wishes Sergio --bcaec51b1803cc0bff04afbb8a07 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLrs, I am running some calculations on benzo[a]pyrene and its qualit= ies, but they do not seem to be familiar with other carcinogens, although t= his is one of the most potent carcinogens. The mechanism of adduct formatio= n is delineated in the literature as a amine-epoxy mechanism, but some issu= es do not compare well to this theory. Has anyone one this list seen a refe= rence or thought about that the guanosine base may undergo ceonversion to a= nitrenium-guanosine upon interaction with the epoxide or a radical of the = PAH?

Best wishes

Sergio
--bcaec51b1803cc0bff04afbb8a07-- From owner-chemistry@ccl.net Thu Oct 20 12:56:00 2011 From: "Mihaly Mezei Mihaly.Mezei ~~ mssm.edu" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45713-111020125449-21753-zNYixfYX+kSpa3irxhVIAQ+/-server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Thu, 20 Oct 2011 12:54:40 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei(-)mssm.edu] > 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, not the design of the equipment. So, why do we have to justify the design of our equipment (i.e., the source code)? Or, conversely, why don't they have to to justify the design of their equipment? Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Thu Oct 20 21:30:01 2011 From: "Bruce Palfey brupalf:+:umich.edu" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45714-111020211625-30539-/dTV3o2+EyubDzykNYkCzw#server.ccl.net> X-Original-From: Bruce Palfey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 20 Oct 2011 21:16:13 -0400 Mime-Version: 1.0 (1.0) Sent to CCL by: Bruce Palfey [brupalf{}umich.edu] Actually, the design of experimental equipment *is* usually justified by publications. There are many many papers describing - take your pick. NMR and infrared and ultraviolet spectrometers. Simple chromatography and HPLC technology. Stopped-flow spectrophotometers and fluorimeters. Isothermal titration and differential scanning calorimeters. Organic and inorganic synthesis has publications describing fancy glassware. Theory being put into practice with new devices needs to be described, if the answers the devices deliver are to be believed. Some of these publications are old and maybe forgotten, but new stuff generally gets explained in a paper when it's introduced. Maybe beakers and test-tubes didn't need publications... ciao, Bruce On Oct 20, 2011, at 12:54 PM, "Mihaly Mezei Mihaly.Mezei ~~ mssm.edu" wrote: > > Sent to CCL by: Mihaly Mezei [Mihaly.Mezei(-)mssm.edu] >> 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, not the design of the equipment. > > So, why do we have to justify the design of our equipment (i.e., the source code)? > > Or, conversely, why don't they have to to justify the design of their equipment? > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of Medicine > Voice: (212) 659-5475 Fax: (212) 849-2456 > WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu> > > > From owner-chemistry@ccl.net Thu Oct 20 22:04:01 2011 From: "David A Mannock dmannock#ualberta.ca" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45715-111020214759-8387-rFdwrv37CCmUMecNbYd9AQ[A]server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=0022158df36fb4fff904afc54294 Date: Thu, 20 Oct 2011 19:47:49 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock|ualberta.ca] --0022158df36fb4fff904afc54294 Content-Type: text/plain; charset=ISO-8859-1 The computer is your equipment, whereas the code is the analytic tool used to calculate the result and is thus part of the experiment.. On Thu, Oct 20, 2011 at 10:54 AM, Mihaly Mezei Mihaly.Mezei ~~ mssm.edu < owner-chemistry,ccl.net> wrote: > > Sent to CCL by: Mihaly Mezei [Mihaly.Mezei(-)mssm.edu] > > 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, not the design of the equipment. > > So, why do we have to justify the design of our equipment (i.e., the source > code)? > > Or, conversely, why don't they have to to justify the design of their > equipment? > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of > Medicine > Voice: (212) 659-5475 Fax: (212) 849-2456 > WWW (MSSM home): > http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu> > > --0022158df36fb4fff904afc54294 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable The computer is your equipment, whereas the code is the analytic tool used = to calculate the result and is thus part of the experiment..

On Thu, Oct 20, 2011 at 10:54 AM, Mihaly Mezei Mihaly.M= ezei ~~ mssm.edu <owner-chemistry,ccl.net> wrote:

Sent to CCL by: Mihaly Mezei [Mihaly.Mezei(-)mssm.edu]
> Hi! A couple of people have suggested that explaining and providing > details of software code is like providing details of the design of = =A0a piece of
> equipment used to perform a measurement. I don't think this is
> accurate.Experimentalists have to justify and validate the
> experimental approach, not the design of the equipment.

So, why do we have to justify the design of our equipment (i.e., the source= code)?

Or, conversely, why don't they have to to justify the design of their e= quipment?

Mihaly Mezei

Department of Structural and Chemical Biology, Mount Sinai School of Medici= ne
Voice: =A0(212)= 659-5475 =A0 Fax: (212) 849-2456
WWW (MSSM home): http://www.mountsin= ai.org/Find%20A%20Faculty/profile.do?id=3D0000072500001497192632
WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
WWW (Department): http://atlas.physbio.mssm.edu



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