From owner-chemistry@ccl.net Tue Feb 28 01:23:00 2006 From: "Eric Scerri scerri_+_chem.ucla.edu" To: CCL Subject: CCL: orbital observation article now published Message-Id: <-31030-060227221558-18983-UY7ZZXgMqAhxdQnCdcbmGg(-)server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-6--419345057 Date: Mon, 27 Feb 2006 19:16:52 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Eric Scerri [scerri^^^chem.ucla.edu] --Apple-Mail-6--419345057 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Essay Measuring Orbitals: Provocation or Reality? (p 1508-1517) W. H. Eugen Schwarz The article I mentioned about a week ago is now available on-line at http://www3.interscience.wiley.com/cgi-bin/jhome/26737 Any reaction from listmembers? Do textbooks claiming that orbitals are unobservable need to be modified or is this a very specific sense of 'observation', namely fitting data to models? regards, Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095-1569 E-mail scerri-x-chem.ucla.edu Tel: 310 206 7443 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-6--419345057 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Essay
Measuring Orbitals: Provocation or Reality? = (p=A01508-1517)=A0
W. H. Eugen Schwarz=A0


The article I mentioned = about a week ago is now available on-line at

http://www= 3.interscience.wiley.com/cgi-bin/jhome/26737


Any reaction from = listmembers?=A0=A0
Do textbooks claiming that orbitals are = unobservable need to be modified or is this a very specific sense of = 'observation', namely fitting data to models?


regards,




Dr. Eric = Scerri,
Department of Chemistry & = Biochemistry,
UCLA,
Los Angeles,
CA = 90095-1569

E-mail = scerri-x-chem.ucla.edu
Tel: 310 206 = 7443

UCLA faculty web = page:=A0=A0=A0http://www.chem.ucla.edu/dept/Faculty/scerri/

=
Editor of Foundations of = Chemistry,
http://www.springer.com/sgw/cda/frontpage/0,11855,4-4= 0399-70-35545882-detailsPage%253Djournal%257CmostViewedArticles%257CmostVi= ewedArticles,00.html

International Society for = the Philosophy of = Chemistry,
http://ispc.sas.upenn.edu/


 =

= --Apple-Mail-6--419345057-- From owner-chemistry@ccl.net Tue Feb 28 03:06:00 2006 From: "Warren DeLano warren^^delsci.com" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31031-060228030154-24888-SeJ9tFt3NUkDlIwi70iy1Q[a]server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Feb 2006 00:04:37 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren|-|delsci.com] > The problem being that if you patent the algorithm you use other > researchers can't use that algorithm to reproduce and verify your work > and therefore such work does not belong in a peer reviewed journal. > If the algorithm itself is patented then nobody can verify your > results without paying you royalties. Nonsense -- if the above were true, vast areas of academic research simply wouldn't exist. In fact, there are many issued patents that cover procedures used everyday in research. Case in point: PCR Patents! In almost all cases, patent holders choose not to assert their rights to block research because there isn't any money in doing so. Patent lawsuits are very expensive, and it can even be in their interest to allow academics to infringe provided that they can preserve a claim to the proceeds of any subsequent commercialization. So in practice, patents do nothing to directly inhibit academic research -- they are largely irrelevant so long as you are not making money. In contrast, software copyrights greatly obstruct progress by making it necessary for every new developer to reimplement the same old tired algorithms from scratch instead of using good implementations which already exist. That is just not efficient, and it doesn't makes sense for enabling cumulative progress in research. Consequently, computer scientists have come to appreciate the shared benefits of open-source and copy-"lefted" approaches where royalty-free derivative usage is possible and even encoraged. We now see the fruits of that all around us in terms of the Internet, BSD-Unix, GCC, Perl/Python/Apache, Linux, etc. Though software copyrights in computational chemistry have historically prevented derivative reuse of existing publicly-funded implementations (e.g. TINKER, AMBER, DOCK, GAMESS, NAMD, VMD, etc.), many modern computational chemistry tools are now either open-source or copy-lefted (e.g. APBS, GROMACS, MMTK, Jmol, PyMOL, OpenBabel, CDK, JOElib, JChemPaint, etc.). That is no accident -- we developers are actively trying to avoid the mistakes of the past. Perhaps someday funding agencies will even make open-source licensing a requirement for publication of software? One can only hope! As for Jan's astute comments on Bayh Dole, that is one of the big reasons why "DeLano Scientific" is a private company and not simply the "DeLano Laboratory" at some local University of California. Mandatory software licensing policies in academia actively prevent the kind of collaborative software development that could best enable cumulative reseach progress. Change is needed! Cheers, Warren PS. For more discussion on open-source, see pro/con arguments in Drug Discovery Today: and , as well as our about page: -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren/./delsci.com > -----Original Message----- > From: owner-chemistry/./ccl.net [mailto:owner-chemistry/./ccl.net] > Sent: Monday, February 27, 2006 6:48 PM > To: Warren DeLano > Subject: CCL: software pattents in chemistry? > > Sent to CCL by: "Ross Walker" [ross]_[rosswalker.co.uk] > > > For what it's worth, the same figure appears to be included > in their > > publication of similar name, and is entirely legible in that format: > > > > J Chem Inf Comput Sci. 2003 Nov-Dec;43(6):1982-97. > > > > It appears they filed provisional patents, and then proceeded to > > publish the same material. > > And this is part of the problem with software patents I feel. > If you are going to patent an algorithm you can't then expect to > publish work that uses that algorithm in peer reviewed journals. The > problem being that if you patent the algorithm you use other > researchers can't use that algorithm to reproduce and verify your work > and therefore such work does not belong in a peer reviewed journal. > > Copyrighted code is a very different situation, however, since even if > you use a commercial implementation of an algorithm to do the research > other scientists can simply implement the algorithm described in your > paper to reproduce the results. If the algorithm itself is patented > then nobody can verify your results without paying you royalties. > > Thus perhaps the discussion should be whether publication of an > algorithm, by the authors of a patent, in scientific journals then > invalidates the scope of that patent. > > Just my 2c. > > All the best > Ross > > /\ > \/ > |\oss Walker > > | Department of Molecular Biology TPC15 | The Scripps > Research Institute > | | > | Tel: +1 858 784 8889 | EMail:- ross###rosswalker.co.uk | > | http://www.rosswalker.co.uk | PGP Key available on request | > > Note: Electronic Mail is not secure, has no guarantee of delivery, may > not be read every day, and should not be used for urgent or sensitive > issues. From owner-chemistry@ccl.net Tue Feb 28 03:40:01 2006 From: "Mikael Johansson mikael.johansson-,-helsinki.fi" To: CCL Subject: CCL: orbital observation article now published Message-Id: <-31032-060228032006-4918-KykjFGgRlvxPvBqImnOjaQ*server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 28 Feb 2006 10:19:55 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson+/-helsinki.fi] Hello Eric and All! On Tue, 28 Feb 2006, Eric Scerri scerri_+_chem.ucla.edu wrote: > Any reaction from listmembers? > Do textbooks claiming that orbitals are unobservable need to be > modified or is this a very specific sense of 'observation', namely > fitting data to models? I think textbooks claiming that orbitals are unobservable should at least provide an explanation to as _why_ this would be the case and not just state this as some obvious truth (which it isn't). I have the feeling that with this requirement, the statement would be much more infrequent :-) The article does bring up a few points that weren't explicitly discussed during the previous CCL orbital discussion about a year ago (at least as far as I remember, which might not be that long a distance): 1. Phase observation is not new to the 2004 Nature paper. See Weinacht, Ahn, Bucksbaum, "Measurement of the Amplitude and Phase of a Sculpted Rydberg Wave Packet", Phys. Rev. Lett. 80 (1998) 5508. 2. Observation of complex valued (classical) observables is not new. The article mentions the complex index of refraction. 3. To balance things, Schwarz also brings up the approximative nature of the orbital description via Cederbaum, Schirmer, Domcke, von Niessen, "Complete breakdown of the quasiparticle picture for inner valence electrons", J. Phys. B 10 (1977) L549. Otherwise, I feel the paper doesn't discuss much that hasn't been discussed here at CCL already. A big merit of the paper is of course that it brings this interesting topic of discussion to a "slightly" larger audience than CCL. Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From owner-chemistry@ccl.net Tue Feb 28 04:15:04 2006 From: "Marcel Swart m.swart]*[few.vu.nl" To: CCL Subject: CCL: orbital observation article now published Message-Id: <-31033-060228033114-9322-6FvkVR/wHLqeXOdVEXnL3w*_*server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Tue, 28 Feb 2006 09:29:54 +0100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Marcel Swart [m.swart]~[few.vu.nl] On Feb 28, 2006, at 7:34 AM, Eric Scerri scerri_+_chem.ucla.edu wrote: > Essay > Measuring Orbitals: Provocation or Reality? (p 1508-1517) > W. H. Eugen Schwarz > > The article I mentioned about a week ago is now available on-line at > > http://www3.interscience.wiley.com/cgi-bin/jhome/26737 The direct URL is: http://www3.interscience.wiley.com/cgi-bin/abstract/112404061/ABSTRACT > > Any reaction from listmembers? > Do textbooks claiming that orbitals are unobservable need to be > modified or is this a very specific sense of 'observation', namely > fitting data to models? > > regards, > > Dr. Eric Scerri, > Department of Chemistry & Biochemistry, > UCLA, > Los Angeles, > CA 90095-1569 > > E-mail scerri^chem.ucla.edu > Tel: 310 206 7443 > > UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ > > Editor of Foundations of Chemistry, > http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- > detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, > 00.html > > International Society for the Philosophy of Chemistry, > http://ispc.sas.upenn.edu/ From owner-chemistry@ccl.net Tue Feb 28 04:50:00 2006 From: "Igor Avilov avilovi*|*averell.umh.ac.be" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31034-060228041415-8538-tqD63KfbOd+OfIRRplXydg,+,server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 28 Feb 2006 10:14:00 +0100 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi++averell.umh.ac.be] Hello everybody, I thought that scientific methods and mathematical algorithms are not patentable... But probably this is true only for Europe... This particular invention looks just like a mathematical procedure. Igor. -----Original Message----- > From: owner-chemistry(_)ccl.net [mailto:owner-chemistry(_)ccl.net] Sent: lundi 27 février 2006 19:07 To: Igor Avilov Subject: CCL: software pattents in chemistry? Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl] Hi all, Today I learned that software pattents have hit chemistry, chemoinformatics in this case: http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO2005001743&F=0 I have no idea on the impact of this pattent, but was wondering if others saw more software pattents in chemistry, and wether software pattents in chemistry affected work in our field. Anyone who has experience with software pattents in cheminformatics, computational chemistry and the likes? Egon -- e.willighagen++science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen Blog: http://chem-bla-ics.blogspot.com/ http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6http://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 Tue Feb 28 05:26:01 2006 From: "Egon Willighagen egonw-.-sci.kun.nl" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31035-060228043718-21414-Bl9ALGYG3m+t8Zz/bUm/ng^^^server.ccl.net> X-Original-From: Egon Willighagen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Tue, 28 Feb 2006 10:36:45 +0100 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egonw=sci.kun.nl] On Tuesday 28 February 2006 09:52, Warren DeLano warren^^delsci.com wrote: > Sent to CCL by: "Warren DeLano" [warren|-|delsci.com] > > The problem being that if you patent the algorithm you use other > > researchers can't use that algorithm to reproduce and verify your work > > > > and therefore such work does not belong in a peer reviewed journal. > > > > If the algorithm itself is patented then nobody can verify your > > results without paying you royalties. > Nonsense -- if the above were true, vast areas of academic research > simply wouldn't exist. In fact, there are many issued patents that > cover procedures used everyday in research. Case in point: PCR > Patents! Verification would be no problem indeed. But this scientist would not be able to share his code that did this validation. See below. > In almost all cases, patent holders choose not to assert their rights to > block research because there isn't any money in doing so. Patent > lawsuits are very expensive, and it can even be in their interest to > allow academics to infringe provided that they can preserve a claim to > the proceeds of any subsequent commercialization. So in practice, > patents do nothing to directly inhibit academic research -- they are > largely irrelevant so long as you are not making money. Indeed, patents deal with the right to make money out of your idea. But how does this work for open source software? A competitor, e.g. an academic scientist, who releases his research as open source make it impossible to make money with your own commercial product (nuances skipped for brevity). While it holds that privately exploring ideas in patents is fine, bringing that to the market is not... open source does bring things to the market. So, I do think open source does infringe on software patents... > In contrast, software copyrights greatly obstruct progress by making it > necessary for every new developer to reimplement the same old tired > algorithms from scratch instead of using good implementations which > already exist. Do you mean that reimplementing the same algorithm (== same idea) as an open source product on the market does not infringe the patent? Egon -- e.willighagen%x%science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen Blog: http://chem-bla-ics.blogspot.com/ http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 From owner-chemistry@ccl.net Tue Feb 28 06:05:00 2006 From: "Jerome Pansanel j.pansanel[]pansanel.net" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31036-060228060323-20258-sGUO2sZgdih+gQ+9RbyHhg() server.ccl.net> X-Original-From: "Jerome Pansanel" Date: Tue, 28 Feb 2006 06:03:18 -0500 Sent to CCL by: "Jerome Pansanel" [j.pansanel%x%pansanel.net] Hi, Le Mardi 28 Fvrier 2006 11:02, Igor Avilov avilovi*|*averell.umh.ac.be a crit : > Sent to CCL by: "Igor Avilov" [avilovi++averell.umh.ac.be] > Hello everybody, > > I thought that scientific methods and mathematical algorithms are not > patentable... But probably this is true only for Europe... This particular > invention looks just like a mathematical procedure. Software patents are only granted in US and Japan. More informations are available on: http://en.wikipedia.org/wiki/Software_patent Another resources about software patents (applied to chemistry): http://www.alchem.org/article.php3?id_article=8 http://www.ccp14.ac.uk/maths/software-patents/software_patents_and_crystallography.html Jerome Pansanel > Igor. > > -----Original Message----- > > > From: owner-chemistry(-)ccl.net [mailto:owner-chemistry(-)ccl.net] > > Sent: lundi 27 fvrier 2006 19:07 > To: Igor Avilov > Subject: CCL: software pattents in chemistry? > > > Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl] > > Hi all, > > Today I learned that software pattents have hit chemistry, chemoinformatics > in this case: > > http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO2005001743&F=0 > > I have no idea on the impact of this pattent, but was wondering if others > saw more software pattents in chemistry, and wether software pattents in > chemistry affected work in our field. > > Anyone who has experience with software pattents in cheminformatics, > computational chemistry and the likes? > > Egon From owner-chemistry@ccl.net Tue Feb 28 06:39:00 2006 From: "may abdelghani may01dz%yahoo.fr" To: CCL Subject: CCL: Photodepletion,Photoelectron spectroscopy (PES) and excitation energy Message-Id: <-31037-060226091759-20862-m5i22Xh2GVhHmH1z/OPtnQ * server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-410951446-1140957072=:37801" Date: Sun, 26 Feb 2006 13:31:12 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz|*|yahoo.fr] --0-410951446-1140957072=:37801 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers What is a different between Photodepletion spectrum and UV-visible one? I.e. we can modeling it (Photodepletion spectrum) by TDDFT or CI methods, as like as we do with UV-visible spectrum? If there are any relationships between the Photoelectron spectroscopy (PES) and density of stats (DOS) spectrums; in order to interpret, theoretically, the experimental PES spectrum? What is the different between excitation energy and transition energy? We can calculate, for example, the excitation energy in terms of transition energy, and vice versa? What we mean by the density of excited states? Thanks a lot --------------------------------- Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.Téléchargez la version beta. --0-410951446-1140957072=:37801 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCLers
What is a different between Photodepletion spectrum and UV-visible one? I.e. we can modeling it (Photodepletion spectrum) by TDDFT or CI methods, as like as we do with UV-visible spectrum? 
 
If there are any relationships between the Photoelectron spectroscopy (PES) and density of stats (DOS) spectrums; in order to interpret, theoretically, the experimental PES spectrum?

What is the different between excitation energy and transition energy? We can calculate, for example, the excitation energy in terms of transition energy, and vice versa?
What we mean by the density of excited states?
Thanks a lot    

Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez la version beta. --0-410951446-1140957072=:37801-- From owner-chemistry@ccl.net Tue Feb 28 08:27:01 2006 From: "Pradipta Bandyopadhyay pradipta|iitg.ernet.in" To: CCL Subject: CCL: internal to cartesian code in CCL ! Message-Id: <-31038-060228082213-29027-u3mJlqaW0h+vwaGqKTlRPA]|[server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 28 Feb 2006 18:48:15 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta++iitg.ernet.in] Has anyone used any of the two codes present in CCL (i2c.f and COORD_XYZ.FOR) for conversion from Internal to cartesian coordinates? If so, can anyone share the input file for the code? thanks, Pradipta ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Tue Feb 28 09:02:01 2006 From: "Kai Hartmann Kai.Hartmann::uni-koeln.de" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31039-060228035838-30918-oi5U55ZMI6MpbsYRzXcN3w . server.ccl.net> X-Original-From: "Kai Hartmann" Date: Tue, 28 Feb 2006 03:58:37 -0500 Sent to CCL by: "Kai Hartmann" [Kai.Hartmann^_^uni-koeln.de] > And this is part of the problem with software patents I feel. If you are > going to patent an algorithm you can't then expect to publish work that uses > that algorithm in peer reviewed journals. The problem being that if you > patent the algorithm you use other researchers can't use that algorithm to > reproduce and verify your work and therefore such work does not belong in a > peer reviewed journal. At least for Germany this is not true. 11 PatG explicitly allows you to reproduce a patent for testing purposes as well as use the patent in the private, non-commercial areas (and allows usage in some other cases, too). I didn't cross-check with international laws, but I guess (and hope) that something similar holds true - in the sense of the Latin word patere (to lay open). And please don't misunderstand my statement as a defense of software patents - my thanks to the EU parliament and many OS developers ;) Kai From owner-chemistry@ccl.net Tue Feb 28 09:37:00 2006 From: "kefalidi]=[chem.auth.gr" To: CCL Subject: CCL: Antivirus software and VPN clients Message-Id: <-31040-060228022002-17461-o2DZuQcbvSpEAgwV5k6flQ!^!server.ccl.net> X-Original-From: kefalidi(!)chem.auth.gr Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-7; format="flowed" Date: Tue, 28 Feb 2006 08:44:49 +0200 MIME-Version: 1.0 Sent to CCL by: kefalidi:+:chem.auth.gr My suggestions is to install a Unix based system like Linux or to buy a Mac, because this OS does not have viruses. Quoting "John McKelvey jmmckel-$-attglobal.net" : > Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net] > > CClers, > > This may be off topic, Jan, but perhaps someone on the list can help. > > I currently am running 2005 Norton SystemWorks Premier, which of course > includes their antivirus package. At the same time I am using Nortel > VPN client to connect to a cluster. Now, I can not do both at the same > time as Norton antivirus thinks that the VPN client is a worm!!! I have > to disable the worm protection part of Norton inorder to get through. > Am running W2K which connects to the internet through a Netgear firewall > router. > > Interestingly enough, [;-), 3 weeks of wrangling with various support > groups got me nowhere in locating the above workaround. The solution > above was located in 3 minutes by a colleague using Google!!! > > Does anyone have a suggestion for a different approach where I would not > have to turn off worm protection? [Have queried Norton on this, but no > answer yet...] > > Best regards, and many thanks! > > John McKelvey> > > Christos E. Kefalidis PhD Student Laboratory of Applied Quantum Chemistry Department of Chemistry Aristotle University of Thessaloniki From owner-chemistry@ccl.net Tue Feb 28 10:58:00 2006 From: "=?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= jwegner#,#tibbe.JNJ.com" To: CCL Subject: CCL: internal to cartesian code in CCL ! Message-Id: <-31041-060228105028-21456-JGj5HfGv+yLniDk1Dz+23g^^^server.ccl.net> X-Original-From: =?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 28 Feb 2006 16:13:08 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= [jwegner-x-tibbe.JNJ.com] Hi, 1.a. as you might know the 'Blue Obelisk Movement' tries to collect such things. http://www.blueobelisk.org/ JCIM publication: http://dx.doi.org/10.1021/ci050400b 1.b. You can find related C++ and Java codes under the section: AlgorithmDictionary 2. BTW, this site is an OPEN Wiki, so any code contributions and link-outs are highly appreciated. 3. Any other algorithm, data and tutorial collections are also encouraged to create link-outs and cross-linking sections. Best regards, Joerg Kurt Wegner -----Original Message----- > From: owner-chemistry-.-ccl.net [mailto:owner-chemistry-.-ccl.net] Sent: Tuesday, February 28, 2006 2:56 PM To: Wegner, Joerg Kurt Subject: CCL: internal to cartesian code in CCL ! Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta++iitg.ernet.in] Has anyone used any of the two codes present in CCL (i2c.f and COORD_XYZ.FOR) for conversion from Internal to cartesian coordinates? If so, can anyone share the input file for the code? thanks, Pradipta ---------------------------------------------------------------------------- ------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.inhttp://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 Tue Feb 28 11:32:00 2006 From: "=?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= jwegner:tibbe.JNJ.com" To: CCL Subject: CCL: internal to cartesian code in CCL ! Message-Id: <-31042-060228104832-21059-u512Y/WY8aiW/DAwk9eLrg===server.ccl.net> X-Original-From: =?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 28 Feb 2006 16:20:08 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= [jwegner^^tibbe.JNJ.com] Hi, 1.a. as you might know the 'Blue Obelisk Movement' tries to collect such things. http://www.blueobelisk.org/ JCIM publication: http://dx.doi.org/10.1021/ci050400b 1.b. You can find related C++ and Java codes under the section: AlgorithmDictionary 2. BTW, this site is an OPEN Wiki, so any code contributions and link-outs are highly appreciated. 3. Any other algorithm, data and tutorial collections are also encouraged to create link-outs and cross-linking sections. Best regards, Joerg Kurt Wegner -----Original Message----- > From: owner-chemistry,ccl.net [mailto:owner-chemistry,ccl.net] Sent: Tuesday, February 28, 2006 2:56 PM To: Wegner, Joerg Kurt Subject: CCL: internal to cartesian code in CCL ! Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta++iitg.ernet.in] Has anyone used any of the two codes present in CCL (i2c.f and COORD_XYZ.FOR) for conversion from Internal to cartesian coordinates? If so, can anyone share the input file for the code? thanks, Pradipta ---------------------------------------------------------------------------- ------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.inhttp://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 Tue Feb 28 12:07:01 2006 From: "Konrad Hinsen konrad.hinsen/./cea.fr" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31043-060228112311-8363-1ReyKP1JgkHXeavq04YZ0w-.-server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Tue, 28 Feb 2006 11:23:05 -0500 Sent to CCL by: "Konrad Hinsen" [konrad.hinsen.^.cea.fr] On Feb 28, 2006, at 9:17, Warren DeLano warren^^delsci.com wrote: >the proceeds of any subsequent commercialization. So in practice, >patents do nothing to directly inhibit academic research -- they are >largely irrelevant so long as you are not making money. What about collaboration with industrial research? And what about using patented algorithms in published open-source software? The latter does not generate any money, but could easily be in competition with commercial activities of the patent holder. Personally, I prefer to have no software patents at all. For the moment this is the case in Europe - let's hope it remains so. >"DeLano Laboratory" at some local University of California. Mandatory >software licensing policies in academia actively prevent the kind of >collaborative software development that could best enable cumulative >reseach progress. Change is needed! The French research organizations have recognized this and have worked out their own Open Source license that they recommend French scientists to adopt for their code: http://www.cecill.info/index.en.html This differs from the GPL mostly by being based on French rather than US law. -- --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: konrad.hinsen^cea.fr --------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Feb 28 12:42:00 2006 From: "Warren DeLano warren^delsci.com" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31044-060228113849-12759-RXas2LdUfOhuJ7NBQRbQog(-)server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Feb 2006 08:41:34 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren~!~delsci.com] > But how does this work for open source software? A competitor, e.g. an > academic scientist, who releases his research as open source make it > impossible to make money with your own commercial product (nuances > skipped for brevity). That isn't strictly true. Open source only addresses licensing costs -- all of the other costs are still present (support, maintenance, integration, & training), and they may even be higher in some cases. Availability of an open-source product does not make it impossible to make money, it just increases the competitive pressure on the proprietary alternatives to lower their upfront costs. Open-source competition is one reason for the industry-wide shift to subscription licensing, and for the increased prevalence of increasingly capable free-but-still-proprietary products. (Egon, consider the new DSVisualizer vs. Jmol or PyMOL, as a personal example relevant to both of us!) > While it holds that privately exploring ideas in patents is fine, > bringing that to the market is not... open source does bring things to > the market. > So, I do think open source does infringe on software patents... Patents cover "make, use, or sell", so patents do very much apply to open source, and large open-source code projects like Linux are almost certainly in violation of numerous patents. The question is, who do patent holders sue when a piece of open-source software is "made" by a large segment of the community and "used" by everyone? My experience is that open-source projects tend to get away with infringement because it just isn't practical for patent holders to sue each individual user or participant for lost revenue or royalties. It is somewhat analagous to the RIAA suing music downloaders, but most patent holders don't have the deep pockets of the RIAA, and patents are much harder to enforce than copyrights. That being said, it makes sense to avoid infringement in open-source whenever possible, since there is always the potential of being liable for damages. Proving equivalence for complex algorithmic computer code can be expensive and difficult, but it is not impossible. However, in the grand scheme of things, patents expire rather quickly, and they are entirely consistent with the open-source idea that everyone eventually gets access to everything for free. Patents have served society well as a means of both rewarding innovation and sharing the fruits of such innovation by eliminating royalties after 20 years. Copyrights, on the other hand, can last a human lifetime or more, and it is very easy to determine (under discovery) whether or not copyrights have been infringed. As compared to patents, software copyrights excessively reward innovation, and they provide no reasonable mechanism through which such innovation could eventually become available to the community as a whole in a royalty-free fashion. Thus, copyrights are the real problem we need to focus on. They involve applying an extremely strong form of legal protection intended for books and unique works of art to an important modern class of productive tool. Prior to the invention of computers, analogous tools could only be protected by short-lived patents and trade secrets. Software is mis-treated as a work of art because centuries-old intellectual property laws weren't written with software in mind. Open-source and copyleft/GPL are merely work-arounds for this serious defect (or bug!) in our legal system. Ultimately, copyright law needs to softened for software works in order to bring their protections more in line with patented inventions. Cheers, Warren PS. The usual disclaimers apply. I am not a lawyer -- I just spend inordinate amounts of time with them discussing many of these same issues. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren a delsci.com From owner-chemistry@ccl.net Tue Feb 28 13:18:01 2006 From: "Thomas H Dr Pierce TPierce()rohmhaas.com" To: CCL Subject: CCL: Antivirus software and VPN clients Message-Id: <-31045-060228110825-477-XxtGrG9GFALF4lDiHRxmcg,,server.ccl.net> X-Original-From: Thomas H Dr Pierce Content-Type: multipart/alternative; boundary="=_alternative 00547CAE85257123_=" Date: Tue, 28 Feb 2006 10:22:50 -0500 MIME-Version: 1.0 Sent to CCL by: Thomas H Dr Pierce [TPierce-,-rohmhaas.com] This is a multipart message in MIME format. --=_alternative 00547CAE85257123_= Content-Type: text/plain; charset="US-ASCII" Too funny. John, I do not have the Antivirus system you have. However, one often can tell the software firewall that a particular application is "authorized and safe". Can you do that with your VPN application inside the 2005 Norton SystemWorks Premier? You may have to allow it to both communicate to and > from your computer as well. ------ Sincerely, Tom Pierce Bldg 7/ Rm 207D - Spring House, PA 215-641-7475 - Office "kefalidi]=[chem.auth.gr" Sent by: owner-chemistry::ccl.net 02/28/2006 09:48 AM Please respond to "CCL Subscribers" To "Pierce, Tom " cc Subject CCL: Antivirus software and VPN clients Sent to CCL by: kefalidi:+:chem.auth.gr My suggestions is to install a Unix based system like Linux or to buy a Mac, because this OS does not have viruses. Quoting "John McKelvey jmmckel-$-attglobal.net" : > Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net] > > CClers, > > This may be off topic, Jan, but perhaps someone on the list can help. > > I currently am running 2005 Norton SystemWorks Premier, which of course > includes their antivirus package. At the same time I am using Nortel > VPN client to connect to a cluster. Now, I can not do both at the same > time as Norton antivirus thinks that the VPN client is a worm!!! I have > to disable the worm protection part of Norton inorder to get through. > Am running W2K which connects to the internet through a Netgear firewall > > Does anyone have a suggestion for a different approach where I would not > have to turn off worm protection? [Have queried Norton on this, but no > answer yet...] > > John McKelvey> Christos E. Kefalidis PhD Student Laboratory of Applied Quantum Chemistry Department of Chemistry Aristotle University of Thessalonikihttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 00547CAE85257123_= Content-Type: text/html; charset="US-ASCII"
Too funny.

John,

I do not have the Antivirus system you have. However, one often can tell the software firewall that a particular application is "authorized and safe". Can you do that with your VPN application inside the 2005 Norton SystemWorks Premier? You may have to allow it to both communicate to and from your computer as well.

------
Sincerely,

  Tom Pierce
   Bldg 7/ Rm 207D - Spring House, PA
   215-641-7475 - Office


"kefalidi]=[chem.auth.gr" <owner-chemistry::ccl.net>
Sent by: owner-chemistry::ccl.net

02/28/2006 09:48 AM
Please respond to
"CCL Subscribers" <chemistry::ccl.net>
To
"Pierce, Tom " <tpierce::rohmhaas.com>
cc
Subject
CCL: Antivirus software and VPN clients





Sent to CCL by: kefalidi:+:chem.auth.gr
My suggestions is to install a Unix based system like Linux or to buy a Mac,
because this OS does not have viruses.


Quoting "John McKelvey jmmckel-$-attglobal.net" <owner-chemistry-*-ccl.net>:

> Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net]
>
> CClers,
>
> This may be off topic, Jan, but perhaps someone on the list can help.
>
> I currently am running 2005 Norton SystemWorks Premier, which of course
> includes their antivirus package.  At the same time I am using  Nortel
> VPN client to connect to a cluster.  Now, I can not do both at the same
> time as Norton antivirus thinks that the VPN client is a worm!!!  I have
> to disable the worm protection part of Norton inorder to get through.
> Am running W2K which connects to the internet through a Netgear firewall

>
> Does anyone have a suggestion for a different approach where I would not
> have to turn off worm protection?  [Have queried Norton on this, but no
> answer yet...]
>
> John McKelvey>




        Christos E. Kefalidis
            PhD Student
Laboratory of Applied Quantum Chemistry
      Department of Chemistry
Aristotle University of Thessaloniki


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Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
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--=_alternative 00547CAE85257123_=-- From owner-chemistry@ccl.net Tue Feb 28 13:52:00 2006 From: "Ross Walker ross _ rosswalker.co.uk" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31046-060228115805-20144-BiL21x1fDol12XcdN5tYxQ() server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Feb 2006 08:57:53 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross-*-rosswalker.co.uk] Dear Warren I believe you have misinterpreted the intent of my previous message. I was referring to whether software (algorithm) patent applications should also be publishable not arguing the virtues of software copyrights. The point I was trying to make is that someone can, at least in the US, patent an algorithm and then publish work based on that algorithm in a peer reviewed journal. Now, as you rightly point out, the vast majority of such patent holders choose not to assert their patent and thus reproduction of their results by other researchers is possible. However, they still reserve the right to assert that patent at a later date and should they choose to do that the reproduction of their published work will only be possible by negotiating with the patent holder. I am not a lawyer but as a reviewer I would not look favourably on publications where I am prevented from testing the hypothesises discussed in that paper or indeed from extending the work discussed in the paper. Such issues I feel require a clear and precise definition of what is acceptable and what isn't with regards to published scientific research. With regards to the issue of software copyright the point I am trying to raise is not how easily the results of a published paper can be reproduced but the fact that they can be reproduced. Copyrighted software does not in any way block somebody from implementing algorithms discussed in a scientific journal it simply involves more work on their part. The point I am trying to hammer home is that anything published in a peer reviewed journal must be able to be subjected, independently, to careful scrutiny. The best way to test the results is to re-implement the algorithms from scratch. Simply re-using the same software the authors of the paper did does nothing to address any errors that they may have made in their implementation. Independent verification is an important foundation of our scientific research infrastructure and something we should not disregard lightly. All the best Ross /\ \/ |\oss Walker | Department of Molecular Biology TPC15 | | The Scripps Research Institute | | Tel: +1 858 784 8889 | EMail:- ross%a%rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. > -----Original Message----- > From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net] > Sent: Tuesday, February 28, 2006 00:54 > To: Walker, Ross > Subject: CCL: software pattents in chemistry? > > Sent to CCL by: "Warren DeLano" [warren|-|delsci.com] > > > The problem being that if you patent the algorithm you use other > > researchers can't use that algorithm to reproduce and > verify your work > > > and therefore such work does not belong in a peer reviewed journal. > > > If the algorithm itself is patented then nobody can verify your > > results without paying you royalties. > > Nonsense -- if the above were true, vast areas of academic research > simply wouldn't exist. In fact, there are many issued patents that > cover procedures used everyday in research. Case in point: PCR > Patents! > > In almost all cases, patent holders choose not to assert > their rights to > block research because there isn't any money in doing so. Patent > lawsuits are very expensive, and it can even be in their interest to > allow academics to infringe provided that they can preserve a claim to > the proceeds of any subsequent commercialization. So in practice, > patents do nothing to directly inhibit academic research -- they are > largely irrelevant so long as you are not making money. > > In contrast, software copyrights greatly obstruct progress by > making it > necessary for every new developer to reimplement the same old tired > algorithms from scratch instead of using good implementations which > already exist. That is just not efficient, and it doesn't makes sense > for enabling cumulative progress in research. Consequently, computer > scientists have come to appreciate the shared benefits of open-source > and copy-"lefted" approaches where royalty-free derivative usage is > possible and even encoraged. We now see the fruits of that all around > us in terms of the Internet, BSD-Unix, GCC, Perl/Python/Apache, Linux, > etc. > > Though software copyrights in computational chemistry have > historically > prevented derivative reuse of existing publicly-funded implementations > (e.g. TINKER, AMBER, DOCK, GAMESS, NAMD, VMD, etc.), many modern > computational chemistry tools are now either open-source or > copy-lefted > (e.g. APBS, GROMACS, MMTK, Jmol, PyMOL, OpenBabel, CDK, JOElib, > JChemPaint, etc.). That is no accident -- we developers are actively > trying to avoid the mistakes of the past. Perhaps someday funding > agencies will even make open-source licensing a requirement for > publication of software? One can only hope! > > As for Jan's astute comments on Bayh Dole, that is one of the big > reasons why "DeLano Scientific" is a private company and not > simply the > "DeLano Laboratory" at some local University of California. Mandatory > software licensing policies in academia actively prevent the kind of > collaborative software development that could best enable cumulative > reseach progress. Change is needed! > > Cheers, > Warren > > PS. For more discussion on open-source, see pro/con arguments in Drug > Discovery Today: and > , as well as > our about > page: > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:warren!A!delsci.com > > > > -----Original Message----- > > From: owner-chemistry!A!ccl.net [mailto:owner-chemistry!A!ccl.net] > > Sent: Monday, February 27, 2006 6:48 PM > > To: Warren DeLano > > Subject: CCL: software pattents in chemistry? > > > > Sent to CCL by: "Ross Walker" [ross]_[rosswalker.co.uk] > > > > > For what it's worth, the same figure appears to be included > > in their > > > publication of similar name, and is entirely legible in > that format: > > > > > > J Chem Inf Comput Sci. 2003 Nov-Dec;43(6):1982-97. > > > > > > It appears they filed provisional patents, and then proceeded to > > > publish the same material. > > > > And this is part of the problem with software patents I feel. > > If you are going to patent an algorithm you can't then expect to > > publish work that uses that algorithm in peer reviewed > journals. The > > problem being that if you patent the algorithm you use other > > researchers can't use that algorithm to reproduce and > verify your work > > > and therefore such work does not belong in a peer reviewed journal. > > > > Copyrighted code is a very different situation, however, > since even if > > > you use a commercial implementation of an algorithm to do > the research > > > other scientists can simply implement the algorithm > described in your > > paper to reproduce the results. If the algorithm itself is patented > > then nobody can verify your results without paying you royalties. > > > > Thus perhaps the discussion should be whether publication of an > > algorithm, by the authors of a patent, in scientific journals then > > invalidates the scope of that patent. > > > > Just my 2c. > > > > All the best > > Ross > > > > /\ > > \/ > > |\oss Walker > > > > | Department of Molecular Biology TPC15 | The Scripps > > Research Institute > > | | > > | Tel: +1 858 784 8889 | EMail:- ross###rosswalker.co.uk | > > | http://www.rosswalker.co.uk | PGP Key available on request | > > > > Note: Electronic Mail is not secure, has no guarantee of > delivery, may > > > not be read every day, and should not be used for urgent or > sensitive > > issues. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > From owner-chemistry@ccl.net Tue Feb 28 14:27:06 2006 From: "Dave Young dave.young^-^springmail.com" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31047-060228114706-15693-ui+blySKpQ3Q1biC0HaDcQ%server.ccl.net> X-Original-From: Dave Young Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 28 Feb 2006 09:42:44 -0600 (GMT-06:00) Mime-Version: 1.0 Sent to CCL by: Dave Young [dave.young.^^^.springmail.com] Hi, Here are a few comments to mull over. Tenants of US patent law, as it pertains to chemistry software. 1) You can't patent a law of nature, so you can't patent the exact solution to the Schrodinger equation, but you can patent a useful approximation method. 2) You can't patent things that were known publicly previously, the "prior art" clause. Many people try and some succeed, but hardly ever will they try to defend such patents if you threaten a court case to get the patent thrown out. 3) The patent must contain enough information for someone "skilled in the art" to reproduce what they did. This is because the information becomes public domain when the patent expires. One of the founding principles of patent law is to gurantee that things will become public domain eventually. 4) A limited time monopoly on the idea patented. Who would invest time and money into making a nice commercial piece of software when someone could legally clone it and undercut your price (because they didn't pay the high R&D costs). The users of the software benefit from having good quality commercial software, just as much as the people who make money creating that software. I've installed and used a large percentage of the chemistry and drug design packages on the market. There are some really good free codes, and there are some dogs that cost money. However, on average my observations have been Commercial software packages are easier to install. Commercial software packages have fewer bugs. Bugs get fixed faster in commercial packages. Commercial software incorporates more new features, more innovative features, and does so much more quickly. Commercial software packages have better documentation. Commercial software has better tech support. Commercial software has been more throughly tested on a wider variety hardware platforms. There are exceptions to all of these, but on average it is what I see. I have to admire the nobility of someone who gives away the fruits of their labor for free, while risking starving their own children. However, I'm not that noble. I like working in commercial software development environments, which are much more professional. Most of the public domain software I see has been written by students, who haven't got a clue what Hungarian naming is, what design patterns are, or unit testing, or many of the other tentants of good commercial software development. There are a number of public domain codes that I can't get to compile and run correctly, and I've been doing that over 20 years with some of the most complex codes in the world on a wide variety of operating systems. How can you expect to get state of the art public domain code, when many are still using 1960s coding practices? There are places in the world for both public domain software and commercial software. But keep in mind that our society needs the commercial software, which fills needs that no public domain software has ever come close to filling. I don't begrudge anyone their right to patent codes and make what money they can from it. As for public domain code repositories. There are and have been quite a few... Oak, Simtel20, CCL, QCPE, Sourceforge... All the authors have to do is pick one, include their favorite public domain license, upload the source, and let everyone else work on it. That's not as easy to do as it sounds. It's a scary thing throwing your baby out into the street like that. Just some food for thought. Dave Young Alabama Supercomputer Center Dave Young dave.young^^^springmail.com Just another quantum chemistry geek. From owner-chemistry@ccl.net Tue Feb 28 15:02:00 2006 From: "Pablo Andres Denis pablod^^^bilbo.edu.uy" To: CCL Subject: CCL: PBC software Message-Id: <-31048-060228122420-6179-KiBGP+vpmP0X4sya0j7MJQ/./server.ccl.net> X-Original-From: "Pablo Andres Denis" Date: Tue, 28 Feb 2006 12:24:18 -0500 Sent to CCL by: "Pablo Andres Denis" [pablod^bilbo.edu.uy] Hi all, It is possible to work in ``molecular quantum chemistry with free programs like GAMESS, COLUMBUS, NWCHEM, DIRAC etc. but are there any free programs that work with periodic systems? (WIEN2k, CRYSTAL, VASP, CASTEP etc are all paid). Thanks, Pablo From owner-chemistry@ccl.net Tue Feb 28 15:37:02 2006 From: "=?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= jwegner(0)tibbe.JNJ.com" To: CCL Subject: CCL: Feature request: Wiki Message-Id: <-31049-060228125322-20218-K6tbzA+jmQQZK8dJikFcNg|*|server.ccl.net> X-Original-From: =?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C63C8F.D8D360CC" Date: Tue, 28 Feb 2006 18:53:14 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?=22Wegner=2C_J=F6rg_=5BTIBBE=5D=22?= [jwegner_._tibbe.JNJ.com] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C63C8F.D8D360CC Content-Type: text/plain; charset="iso-8859-1" Dear CCL members and maintainers, with respect to question redundancy and a facilitated design and maintenance of the web pages I was wondering why we have not already an CCL-Wiki running? 1. This will facilitate the work dramatically and contributors are rewarded due to the fact that every entry in a Wiki will be stored and you can look-up the history for it. 2. The software repository is nice, but to be honest, the benefit having a wiki with multiple categories and cross-linking options would it make much easier to find things;-) 3. Installing a wiki is trivial and could really boost the information transfer, by reducing redundancy on basic questions. Sure, there is also the archive, but there is IMHO a huge difference between proper written and summarized Wiki entries and an inhomogeneous e-mail collection. I recommend: http://www.mediawiki.org/wiki/MediaWiki because it the same engine like Wikipedia. 4. Especially with respect to citing publications in e-mails, I would really like that those references provide a DOI (Document Object Identifier) or PMID (PubMed ID) link-out. Since I know, that those links makes mail unreadable, the Wiki can help here enourmously. 5. So, what do you think ? Any further positive reactions on that? Best regards, Joerg Kurt Wegner ------_=_NextPart_001_01C63C8F.D8D360CC Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Feature request: Wiki

Dear CCL members and = maintainers,

with respect to question redundancy = and a facilitated design and maintenance of the web pages I was = wondering why we have not already an

CCL-Wiki running?

1. This will facilitate the work = dramatically and contributors are rewarded due to the fact that every = entry in a Wiki will be stored and you can look-up the history for = it.

2. The software repository is nice, = but to be honest, the benefit having a wiki with multiple categories = and cross-linking options would it make much easier to find = things;-)

3. Installing a wiki is trivial and = could really boost the information transfer, by reducing redundancy on = basic questions. Sure, there is also the archive, but there is IMHO a = huge difference between proper written and summarized Wiki entries and = an inhomogeneous e-mail collection. I recommend:

http://www.mediawiki.org/wiki/MediaWiki
because it the same engine like = Wikipedia.

4. Especially with respect to citing = publications in e-mails, I would really like that those references = provide a DOI (Document Object Identifier) or PMID (PubMed ID) = link-out. Since I know, that those links makes mail unreadable, the = Wiki can help here enourmously.

5. So, what do you think ? Any further = positive reactions on that?

Best regards, Joerg Kurt Wegner

------_=_NextPart_001_01C63C8F.D8D360CC-- From owner-chemistry@ccl.net Tue Feb 28 16:12:00 2006 From: "Jan Labanowski janl---speakeasy.net" To: CCL Subject: CCL: Feature request: Wiki Message-Id: <-31050-060228133320-14826-4fv4VhIe1+ulSHLbN7kDtw=-=server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 28 Feb 2006 18:33:06 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl{:}speakeasy.net] Joerg Kurt Wegner writes: > with respect to question redundancy and a facilitated design and maintenance > of the web pages I was wondering why we have not already an > CCL-Wiki running? While there is no CCL-Wiki running, there is a Computational Chemistry Wiki running and does great things: http://en.wikipedia.org/wiki/Computational_chemistry Why there is no CCL-Wiki running? 1) I do not think we need another one... The one above is in great hands... 2) And beside, I have enough chores to take care of the current CCL as is... and a few others... Jan CCL Admin... From owner-chemistry@ccl.net Tue Feb 28 16:47:01 2006 From: "Tony Yuan TYuan]=[cambridgesoft.com" To: CCL Subject: CCL: How to post structures? Message-Id: <-31051-060228134537-21322-oZyCmmi1Zi6Saa9t56UyEA,+,server.ccl.net> X-Original-From: "Tony Yuan" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Feb 2006 13:45:22 -0500 MIME-Version: 1.0 Sent to CCL by: "Tony Yuan" [TYuan*o*cambridgesoft.com] This is nice to post a message containing Chemical Structure: http://forum.chemih.com/view.asp?aid=653&search=smiles -Tony From owner-chemistry@ccl.net Tue Feb 28 17:22:00 2006 From: "Alex Wang yawang*chem.ubc.ca" To: CCL Subject: CCL: CCCC6, 26-30 July 2006 at UBC, Vancouver, Canada Message-Id: <-31052-060228151245-25927-SyWYTT1KPiFQ4gR8sXBuvQ_+_server.ccl.net> X-Original-From: "Alex Wang" Date: Tue, 28 Feb 2006 15:12:43 -0500 Sent to CCL by: "Alex Wang" [yawang:chem.ubc.ca] Dear Colleagues, The Sixth Canadian Computational Chemistry Conference (CCCC6) will be held on July 26-30, 2006 at the beautiful campus of the University of British Columbia in Vancouver, Canada (http://www.chem.ubc.ca/CCCC6). Held every three years, the CCCC continues the tradition of showcasing the achievement and advances of computational chemistry in Canada and all over the world. The scope of the CCCC6 is devoted to all areas of computational chemistry, with special emphasis on novel method developments and state-of-the-art applications in life and materials sciences. We have assembled a star cast composed of forty-four world-renowned computational scientists from academia and industry for the CCCC6: Ruben Abagyan (Scripps) Yuriko Aoki (Kyushu, Japan) Rodney J. Bartlett (Florida) Axel D. Becke (Dalhousie) Richard Bowles (Saskatchewan) Russell J. Boyd (Dalhousie) Alexander Brown (Alberta) Emily A. Carter (Princeton) Jonathan W. Essex (Southampton, UK) Julian D. Gale (Curtin, Australia) Jiali Gao (Minnesota) Michael K. Gilson (Maryland) Radu I. Iftimie (Montreal) Andreas Klamt (COSMOlogic, Germany) Andriy Kovalenko (NRC, NINT, Alberta) Roman Krems (UBC) Peter Kusalik (Calgary) Themis Lazaridis (CUNY) Paul A. Madden (Edinburgh, UK) David E. Manolopoulos (Oxford) Todd J. Martinez (Illinois) Anne B. McCoy (Ohio State) Dan McKay (Merck-Frosst, Montreal) Nicolas Moitessier (McGill) Marcel Nooijen (Waterloo) Sergei Noskov (Calgary) Alexey Onufriev (Virginia Tech) Grenfell N. Patey (UBC) Gilles H. Peslherbe (Concordia) Piotr Piecuch (Michigan State) Regis Pomes (Toronto) Jeremy Schofield (Toronto) Moshe Shapiro (UBC) Woody Sherman (Schrodinger) Bruce Tidor (MIT) Peter Tieleman (Calgary) Troy Van Hoorhis (MIT) Tomasz A. Wesolowski (Geneva) Shoshana J. Wodak (Toronto & Brussells) Tom K. Woo (Ottawa) Weitao Yang (Duke) John Z. H. Zhang (NYU) Tom Ziegler (Calgary) Zsolt Zsoldos (SimBioSys, Toronto) The conference will begin in the evening (registration) on Wednesday, July 26 and will end in the afternoon on Sunday, July 30. The daily lecture sessions will be scheduled from July 27 to 30, between 8:30 AM and 6:15 PM. Two poster sessions will be held at 2-4 PM on July 28-29. The welcome reception will be held at 6-8 PM on July 27 and the banquet is scheduled at 7:30-10 PM on July 29. Very soon, the conference website will be open for abstract submission and registration. In the coming weeks, please visit the conference website (http://www.chem.ubc.ca/CCCC6) for more information and details. With extensive advertising all over the world, we anticipate that the total number of participants of the CCCC6 will probably reach 250. This will definitely be a wonderful opportunity to know the latest cutting-edge advances in computational chemistry and to network with your colleagues worldwide. We sincerely hope you will join us for a four-day scientific fest at UBC during the CCCC6. With best wishes, The CCCC6 Organizing Committee Alex Wang (British Columbia) Pierre-Nicholas Roy (Alberta) Enrico Purisima (BRI, NRC) Mark Thachuk (British Columbia) From owner-chemistry@ccl.net Tue Feb 28 17:57:01 2006 From: "Anthony Fejes fejes-*-zymeworks.com" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31053-060228152450-30956-w54ZkMXt2qe0qJoD5Qe+qw++server.ccl.net> X-Original-From: Anthony Fejes Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Feb 2006 12:24:42 -0800 MIME-Version: 1.0 Sent to CCL by: Anthony Fejes [fejes()zymeworks.com] I had planned to stay out of this discussion, but I figured I should toss in my 2 cents as well, to counter some of the other arguments presented. I'm not a lawyer, so what I have to contribute is simply my opinion. (I also provide the warning that this email is quite long.) > As compared to patents, software copyrights excessively reward > innovation, and they provide no reasonable mechanism > through which such innovation could eventually become available to the > community as a whole in a royalty-free fashion. Copyright laws in most countries have "fair use" clauses, and those classes are designed to encourage innovation. Fair use typically includes personal use, academic use and the ability to create personal backup copies. There is every provision (in North American copyright, in any case) for others to build upon what other people have done. The final part of the above quotation is somewhat mistaken. Copyrights do expire, and the copyrighted material does become public domain. However, as stated it was pointed out in the parent email, the time frame required may be in terms of lifetimes, which is ridiculously long, in terms of software usefulness. The most disturbing trend visible today in copyright is found in the entertainment industry, where a lot of lobbying for governments is going on to remove "fair use" and the rights to other non-infringing uses. (Which the parent alluded to in discussing the RIAA and other current lawsuits.) > Thus, copyrights are > the real problem we need to focus on. They involve applying an > extremely strong form of legal protection intended for books and > unique works of art to an important modern class of productive tool. For the most part, copyright isn't a "strong" form of legal protection. It simply provides the author of any material the ability to exert control over his own creation. If someone else has access to that creation and decides to make their own similar but non-identical (derivative) version, there is no legal way to stop them in copyright law. (This level of restriction can only be achieved by patenting the invention, where derivative copies are prohibited.) The strength of copyright law is that it is difficult to circumvent: If I write a program, copyright assures me that I get to decide who is allowed to make a copy of my program, which prevents anyone else from stealing, redistributing and presumably profiting from the results of my work. GPL is dependent upon those strengths to carry any weight. Furthermore, GPL allows people to share their copyrighted material - thus retaining the protection from having other people misappropriate the work of the developers, which promoting collaboration. Thus, whether you want to share your work or not, copyright allows the creator to decide the level of access granted to the original work. You can always waive your rights (given to you by copyright law) to your own work. However, as much as we would all like to have access to other people's work, the decision to share it should always remain with the person who did the work in the first place. > Prior to the invention of computers, analogous tools could only be > protected by short-lived patents and trade secrets. To touch on trade secrets, they can be and are still used by simply refusing to distribute the source code. I think Microsoft is a good example of a company that has used trade secrets in the computer software world to create a monopoly. However, I find the argument about copyright and tools to be somewhat difficult to follow. My interpretation of the above statement is that copyright doesn't prevent someone from using an analogous tool, it prevents someone from taking your tool and selling it without respecting your rights. > Software is mis-treated as a work of art because centuries-old > intellectual property laws weren't written with software in mind. > Open-source and copyleft/GPL are merely work-arounds for this serious > defect (or bug!) in our legal system. Ultimately, copyright law needs > to softened for software works in order to bring their protections > more in line with patented inventions. And finally, I'd like to make the opposite case to the one presented by the original poster: Patent law is where the reform needs to be taken. Patents were originally designed to foster innovation, by publishing methods and technologies, and allowing other users to reasonably license the innovations so that everyone could benefit. At this point, we're seeing a lot of cases (i.e. NTP vs. RIM) where patents are being used to stifle innovation. So long as this is allowed to go on, patents fail to achieve their original purpose, and innovation is replaced by legal extortion. In the case of the patent that originally started this discussion, it's already been remarked numerous times on CCL that it's likely unenforceable. In the current climate of patent law, where companies like the assignee of the patent (VeraChem) are trying to innovate, the only way to exist is to file defensive patents. These patents are rarely designed to be used against competitors, and are rarely innovative - but they do have the ability to protect a company from other entities that might try to assert a patent against them. Thus, they are "defensive patents". As long as companies find the need to file patents defensively, this argument will continue. By reforming patent law in the U.S., there may be hope for a more innovation friendly environment - both for academics and for industry. At any rate, I'm happy to continue this dialog, although I suspect the CCL list is not the appropriate place for it, so I won't post anything further here on the subject. For a good reference on a lot of these subjects, I highly suggest following the copyright discussions on www.groklaw.net. Anthony Fejes From owner-chemistry@ccl.net Tue Feb 28 18:32:00 2006 From: "Charles McCallum mmccallum^pacific.edu" To: CCL Subject: CCL: Antivirus software and VPN clients Message-Id: <-31054-060228135009-23928-UBYGUH3eSeYoR1xe8OMhUQ[]server.ccl.net> X-Original-From: Charles McCallum Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 28 Feb 2006 10:12:05 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Charles McCallum [mmccallum|-|pacific.edu] I'm not sure this is especially helpful. Unfortunately, people have constraints placed upon them by what they use, or perhaps their IT departments. I myself use OS X machines, but I cringe when I see comments like this. Comments that also suggest simply using ssh are incomplete, too. For example, I can't use ssh without going through VPN to my campus. Ssh and a VPN are not interchangable always. The best bet for John may be to find another AV agent, or work with the VPN server admin to see what suggestions they have. I'm not sure what types of organizations you must work with and through, but knowing that may help others make more constructive suggestions. Cheers On Feb 28, 2006, at 6:59 AM, kefalidi]=[chem.auth.gr wrote: > Sent to CCL by: kefalidi:+:chem.auth.gr > My suggestions is to install a Unix based system like Linux or to > buy a Mac, > because this OS does not have viruses. > > > > > Christos E. Kefalidis > PhD Student > Laboratory of Applied Quantum Chemistry > Department of Chemistry > Aristotle University of Thessaloniki > -- C. Michael McCallum http://www.pacific.edu/college/ chemistry/McCallum/cmccallum.html Associate Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax From owner-chemistry@ccl.net Tue Feb 28 19:07:01 2006 From: "David F. Green dfgreen..ams.sunysb.edu" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31055-060228160215-31639-B1RHRwRIany0WkSsL81BfA,,server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Feb 2006 16:02:05 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen]-[ams.sunysb.edu] US patent law explicitly allows an exception for "experimental use." This includes testing, and would most certainly allow for validation of published results. It is true that the law does not make an exception for non-commercial or personal use -- you are not allowed to use a patented method for anything beyond testing unless you obtain permission > from the patent holder -- but that is a separate issue. The arguments that patenting scientific work prevents it from being independently verified simply does not hold water. This is equally true for computational and non-computational methods. DG. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Math Tower, Room 1-117 Voice: +1-631-632-9344 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Ross Walker ross _ rosswalker.co.uk wrote: > Sent to CCL by: "Ross Walker" [ross-*-rosswalker.co.uk] > Dear Warren > > I believe you have misinterpreted the intent of my previous message. I was > referring to whether software (algorithm) patent applications should also be > publishable not arguing the virtues of software copyrights. > > The point I was trying to make is that someone can, at least in the US, > patent an algorithm and then publish work based on that algorithm in a peer > reviewed journal. Now, as you rightly point out, the vast majority of such > patent holders choose not to assert their patent and thus reproduction of > their results by other researchers is possible. However, they still reserve > the right to assert that patent at a later date and should they choose to do > that the reproduction of their published work will only be possible by > negotiating with the patent holder. I am not a lawyer but as a reviewer I > would not look favourably on publications where I am prevented from testing > the hypothesises discussed in that paper or indeed from extending the work > discussed in the paper. > > Such issues I feel require a clear and precise definition of what is > acceptable and what isn't with regards to published scientific research. > > With regards to the issue of software copyright the point I am trying to > raise is not how easily the results of a published paper can be reproduced > but the fact that they can be reproduced. Copyrighted software does not in > any way block somebody from implementing algorithms discussed in a > scientific journal it simply involves more work on their part. The point I > am trying to hammer home is that anything published in a peer reviewed > journal must be able to be subjected, independently, to careful scrutiny. > The best way to test the results is to re-implement the algorithms from > scratch. Simply re-using the same software the authors of the paper did does > nothing to address any errors that they may have made in their > implementation. Independent verification is an important foundation of our > scientific research infrastructure and something we should not disregard > lightly. > > All the best > Ross > > /\ > \/ > |\oss Walker > > | Department of Molecular Biology TPC15 | > | The Scripps Research Institute | > | Tel: +1 858 784 8889 | EMail:- ross.:.rosswalker.co.uk | > | http://www.rosswalker.co.uk | PGP Key available on request | > > Note: Electronic Mail is not secure, has no guarantee of delivery, may not > be read every day, and should not be used for urgent or sensitive issues. > > >>-----Original Message----- >>From: owner-chemistry.:.ccl.net [mailto:owner-chemistry.:.ccl.net] >>Sent: Tuesday, February 28, 2006 00:54 >>To: Walker, Ross >>Subject: CCL: software pattents in chemistry? >> >>Sent to CCL by: "Warren DeLano" [warren|-|delsci.com] >> >> >>>The problem being that if you patent the algorithm you use other >>>researchers can't use that algorithm to reproduce and >> >>verify your work >> >> >>>and therefore such work does not belong in a peer reviewed journal. >> >>>If the algorithm itself is patented then nobody can verify your >>>results without paying you royalties. >> >>Nonsense -- if the above were true, vast areas of academic research >>simply wouldn't exist. In fact, there are many issued patents that >>cover procedures used everyday in research. Case in point: PCR >>Patents! >> >>In almost all cases, patent holders choose not to assert >>their rights to >>block research because there isn't any money in doing so. Patent >>lawsuits are very expensive, and it can even be in their interest to >>allow academics to infringe provided that they can preserve a claim to >>the proceeds of any subsequent commercialization. So in practice, >>patents do nothing to directly inhibit academic research -- they are >>largely irrelevant so long as you are not making money. >> >>In contrast, software copyrights greatly obstruct progress by >>making it >>necessary for every new developer to reimplement the same old tired >>algorithms from scratch instead of using good implementations which >>already exist. That is just not efficient, and it doesn't makes sense >>for enabling cumulative progress in research. Consequently, computer >>scientists have come to appreciate the shared benefits of open-source >>and copy-"lefted" approaches where royalty-free derivative usage is >>possible and even encoraged. We now see the fruits of that all around >>us in terms of the Internet, BSD-Unix, GCC, Perl/Python/Apache, Linux, >>etc. >> >>Though software copyrights in computational chemistry have >>historically >>prevented derivative reuse of existing publicly-funded implementations >>(e.g. TINKER, AMBER, DOCK, GAMESS, NAMD, VMD, etc.), many modern >>computational chemistry tools are now either open-source or >>copy-lefted >>(e.g. APBS, GROMACS, MMTK, Jmol, PyMOL, OpenBabel, CDK, JOElib, >>JChemPaint, etc.). That is no accident -- we developers are actively >>trying to avoid the mistakes of the past. Perhaps someday funding >>agencies will even make open-source licensing a requirement for >>publication of software? One can only hope! >> >>As for Jan's astute comments on Bayh Dole, that is one of the big >>reasons why "DeLano Scientific" is a private company and not >>simply the >>"DeLano Laboratory" at some local University of California. Mandatory >>software licensing policies in academia actively prevent the kind of >>collaborative software development that could best enable cumulative >>reseach progress. Change is needed! >> >>Cheers, >>Warren >> >>PS. For more discussion on open-source, see pro/con arguments in Drug >>Discovery Today: and >>, as well as >>our about >>page: >> >>-- >>Warren L. DeLano, Ph.D. >>Principal Scientist >> >>. DeLano Scientific LLC >>. 400 Oyster Point Blvd., Suite 213 >>. South San Francisco, CA 94080 USA >>. Biz:(650)-872-0942 Tech:(650)-872-0834 >>. Fax:(650)-872-0273 Cell:(650)-346-1154 >>. mailto:warren!A!delsci.com >> >> >> >>>-----Original Message----- >>>From: owner-chemistry!A!ccl.net [mailto:owner-chemistry!A!ccl.net] >>>Sent: Monday, February 27, 2006 6:48 PM >>>To: Warren DeLano >>>Subject: CCL: software pattents in chemistry? >>> >>>Sent to CCL by: "Ross Walker" [ross]_[rosswalker.co.uk] >>> >>> >>>>For what it's worth, the same figure appears to be included >>> >>>in their >>> >>>>publication of similar name, and is entirely legible in >> >>that format: >> >>>> J Chem Inf Comput Sci. 2003 Nov-Dec;43(6):1982-97. >>>> >>>>It appears they filed provisional patents, and then proceeded to >>>>publish the same material. >>> >>>And this is part of the problem with software patents I feel. >>>If you are going to patent an algorithm you can't then expect to >>>publish work that uses that algorithm in peer reviewed >> >>journals. The >> >>>problem being that if you patent the algorithm you use other >>>researchers can't use that algorithm to reproduce and >> >>verify your work >> >> >>>and therefore such work does not belong in a peer reviewed journal. >>> >>>Copyrighted code is a very different situation, however, >> >>since even if >> >> >>>you use a commercial implementation of an algorithm to do >> >>the research >> >> >>>other scientists can simply implement the algorithm >> >>described in your >> >>>paper to reproduce the results. If the algorithm itself is patented >>>then nobody can verify your results without paying you royalties. >>> >>>Thus perhaps the discussion should be whether publication of an >>>algorithm, by the authors of a patent, in scientific journals then >>>invalidates the scope of that patent. >>> >>>Just my 2c. >>> >>>All the best >>>Ross >>> >>>/\ >>>\/ >>>|\oss Walker >>> >>>| Department of Molecular Biology TPC15 | The Scripps >>>Research Institute >>>| | >>>| Tel: +1 858 784 8889 | EMail:- ross###rosswalker.co.uk | >>>| http://www.rosswalker.co.uk | PGP Key available on request | >>> >>>Note: Electronic Mail is not secure, has no guarantee of >> >>delivery, may >> >> >>>not be read every day, and should not be used for urgent or >> >>sensitive >> >>>issues. >> >> >> >>-= This is automatically added to each message by the mailing >>script =- >>To recover the email address of the author of the message, >>please change> Conferences: >>http://server.ccl.net/chemistry/announcements/conferences/ >> >>Search Messages: http://www.ccl.net/htdig (login: ccl, >>Password: search)> >>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >>-+-+-+-+-+> > > From owner-chemistry@ccl.net Tue Feb 28 19:42:00 2006 From: "Curt M. Breneman brenec[]rpi.edu" To: CCL Subject: CCL: Antivirus software and VPN clients Message-Id: <-31056-060228154805-19910-R/vEVnk/eM/Gsob6F+Dz1Q**server.ccl.net> X-Original-From: "Curt M. Breneman" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Feb 2006 14:47:53 -0500 MIME-Version: 1.0 Sent to CCL by: "Curt M. Breneman" [brenec]-[rpi.edu] Dear Folks, I have had problems with the Cisco VPN Client (both 3.6 and 4.6 versions) with the (XP Pro) Windows Firewall system - this was solved by listing the VPN client executable (ipsec.exe in this case) as an Exclusion (as mentioned in another post), but that alone didn't do the trick. I also needed to open UDP port 62515 in order for the system to work correctly with the firewall enabled. Prior to doing that, the secure link was apparently established, but would not communicate properly. (I use the UDP tunneling transport). Cheers, Curt Breneman RPI Chemistry -----Original Message----- > From: owner-chemistry-,-ccl.net [mailto:owner-chemistry-,-ccl.net] Sent: Tuesday, February 28, 2006 1:59 PM To: Breneman, Curt Subject: CCL: Antivirus software and VPN clients Sent to CCL by: Thomas H Dr Pierce [TPierce-,-rohmhaas.com] This is a multipart message in MIME format. --=_alternative 00547CAE85257123_= Content-Type: text/plain; charset="US-ASCII" Too funny. John, I do not have the Antivirus system you have. However, one often can tell the software firewall that a particular application is "authorized and safe". Can you do that with your VPN application inside the 2005 Norton SystemWorks Premier? You may have to allow it to both communicate to and > from your computer as well. ------ Sincerely, Tom Pierce Bldg 7/ Rm 207D - Spring House, PA 215-641-7475 - Office "kefalidi]=[chem.auth.gr" Sent by: owner-chemistry-,-ccl.net 02/28/2006 09:48 AM Please respond to "CCL Subscribers" To "Pierce, Tom " cc Subject CCL: Antivirus software and VPN clients Sent to CCL by: kefalidi:+:chem.auth.gr My suggestions is to install a Unix based system like Linux or to buy a Mac, because this OS does not have viruses. Quoting "John McKelvey jmmckel-$-attglobal.net" : > Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net] > > CClers, > > This may be off topic, Jan, but perhaps someone on the list can help. > > I currently am running 2005 Norton SystemWorks Premier, which of course > includes their antivirus package. At the same time I am using Nortel > VPN client to connect to a cluster. Now, I can not do both at the same > time as Norton antivirus thinks that the VPN client is a worm!!! I have > to disable the worm protection part of Norton inorder to get through. > Am running W2K which connects to the internet through a Netgear firewall > > Does anyone have a suggestion for a different approach where I would not > have to turn off worm protection? [Have queried Norton on this, but no > answer yet...] > > John McKelvey> Christos E. Kefalidis PhD Student Laboratory of Applied Quantum Chemistry Department of Chemistry Aristotle University of Thessalonikihttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.ne t/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 00547CAE85257123_= Content-Type: text/html; charset="US-ASCII"
Too funny.

John,

I do not have the Antivirus system you have. However, one often can tell the software firewall that a particular application is "authorized and safe". Can you do that with your VPN application inside the 2005 Norton SystemWorks Premier? You may have to allow it to both communicate to and from your computer as well.

------
Sincerely,

  Tom Pierce
   Bldg 7/ Rm 207D - Spring House, PA
   215-641-7475 - Office


"kefalidi]=[chem.auth.gr" <owner-chemistry-,-ccl.net>
Sent by: owner-chemistry-,-ccl.net

02/28/2006 09:48 AM
Please respond to
"CCL Subscribers" <chemistry-,-ccl.net>
To
"Pierce, Tom " <tpierce-,-rohmhaas.com>
cc
Subject
CCL: Antivirus software and VPN clients





Sent to CCL by: kefalidi:+:chem.auth.gr
My suggestions is to install a Unix based system like Linux or to buy a Mac,
because this OS does not have viruses.


Quoting "John McKelvey jmmckel-$-attglobal.net" <owner-chemistry-*-ccl.net>:

> Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net]
>
> CClers,
>
> This may be off topic, Jan, but perhaps someone on the list can help.
>
> I currently am running 2005 Norton SystemWorks Premier, which of course
> includes their antivirus package.  At the same time I am using  Nortel
> VPN client to connect to a cluster.  Now, I can not do both at the same
> time as Norton antivirus thinks that the VPN client is a worm!!!  I have
> to disable the worm protection part of Norton inorder to get through.
> Am running W2K which connects to the internet through a Netgear firewall

>
> Does anyone have a suggestion for a different approach where I would not
> have to turn off worm protection?  [Have queried Norton on this, but no
> answer yet...]
>
> John McKelvey>




        Christos E. Kefalidis
            PhD Student
Laboratory of Applied Quantum Chemistry
      Department of Chemistry
Aristotle University of Thessaloniki


     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/chemistry/sub_unsub.shtml

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
     http://www.ccl.net/spammers.txt
--=_alternative 00547CAE85257123_=--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 Tue Feb 28 20:18:30 2006 From: "Jim Kress ccl_nospam{=}kressworks.com" To: CCL Subject: CCL: PBC software Message-Id: <-31057-060228165633-1863-AreCK9YjsV+Rt9KGX3AzSg[]server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 28 Feb 2006 16:56:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam*o*kressworks.com] pwSCF, CPMD, Siesta Jim > -----Original Message----- > From: Pablo Andres Denis pablod^^^bilbo.edu.uy > [mailto:owner-chemistry a ccl.net] > Sent: Tuesday, February 28, 2006 3:39 PM > To: Kress, Jim > Subject: CCL: PBC software > > Sent to CCL by: "Pablo Andres Denis" [pablod^bilbo.edu.uy] Hi all, > > It is possible to work in ``molecular quantum chemistry > with free programs like GAMESS, COLUMBUS, NWCHEM, DIRAC etc. > but are there any free programs that work with periodic > systems? (WIEN2k, CRYSTAL, VASP, CASTEP etc are all paid). > > > Thanks, > > Pablo > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the a sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Tue Feb 28 20:52:00 2006 From: "Ivanciuc, Ovidiu I. oiivanci_+_utmb.edu" To: CCL Subject: CCL: software & chemistry: where to publish Message-Id: <-31058-060228182740-31669-wwp8ngrHlYsoWuc4MhYpEw,,server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Tue, 28 Feb 2006 17:27:31 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci|*|utmb.edu] David van der Spoel: >>If there were a repository for software >>that is in a public place, like a scientific journal (e.g. JCC or JCTC), >>where one could upload new versions of the code (together with a >>one-page description of the software) then there would be a public >>track-record of software >> ... >> if there is enough support from the community we could >> convince one of the journals to do something like this. http://sourceforge.net/ or similar sites are good places to deposit programs. If you do not have a better option for publishing a software paper, you can submit it to the Internet Electronic Journal of Molecular Design, http://www.biochempress.com/ Ross Walker: >>The point I was trying to make is that someone can, >>at least in the US, patent an algorithm and then publish >> work based on that algorithm in a peer reviewed journal. >>... >>I am not a lawyer but as a reviewer I >>would not look favourably on publications where >> I am prevented from testing the hypothesises discussed in >>that paper or indeed from extending the work discussed in the paper. A well-known patented software is CoMFA, used in more than 600 papers (PubMed, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed). It seems that many reviewers and editors accept patented software. Also, as a reviewer, you are entitled to a "fair use" of the patented software, in which case you can actually implement and test it. A problem is not patented software, but "black box" software, i.e., software (commercial or free) distributed only as binaries. Just because a "black box" program gives good results on a finite number of test cases, we cannot conclude that it is a reliable implementation of a certain algorithm. Regards, Ovidiu From owner-chemistry@ccl.net Tue Feb 28 21:27:27 2006 From: "Denys Bashtovyy bashtovyy(0)go.com" To: CCL Subject: CCL: free energy of TM proteins Message-Id: <-31059-060228184529-7333-SBgfL4AAwvdLnfLZmnNIzQ\a/server.ccl.net> X-Original-From: "Denys Bashtovyy" Date: Tue, 28 Feb 2006 18:45:22 -0500 Sent to CCL by: "Denys Bashtovyy" [bashtovyy .. go.com] Dear CCL members, would it be correct to state that every properly folded transmembrane protein structure will have its lowest possible free energy? Are there any known TM structures folded "improperly" from the free energy point of view? thank you, Denys From owner-chemistry@ccl.net Tue Feb 28 22:02:01 2006 From: "Brian Salter-Duke b_duke(a)octa4.net.au" To: CCL Subject: CCL: Feature request: Wiki Message-Id: <-31060-060228181233-27871-9ZtgIFAhCKB7QCadvm88KQ() server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 1 Mar 2006 09:41:38 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke*|*octa4.net.au] On Tue, Feb 28, 2006 at 04:34:14PM -0500, Jan Labanowski janl---speakeasy.net wrote: > Sent to CCL by: "Jan Labanowski" [janl{:}speakeasy.net] > Joerg Kurt Wegner writes: > > > with respect to question redundancy and a facilitated design and maintenance > > of the web pages I was wondering why we have not already an > > CCL-Wiki running? > > While there is no CCL-Wiki running, there is a Computational Chemistry Wiki > running and does great things: > > http://en.wikipedia.org/wiki/Computational_chemistry This is the Wikipedia article and not a Computational Chemistry Wiki. Do you not mean:- http://www.compchemwiki.org/index.php?title=Main_Page Brian. > Why there is no CCL-Wiki running? > 1) I do not think we need another one... The one above is in great hands... > 2) And beside, I have enough chores to take care of the current CCL as is... > and a few others... > > Jan > CCL Admin...> > > -- Brian Salter-Duke (Brian Duke) b_duke[*]octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. From owner-chemistry@ccl.net Tue Feb 28 22:37:01 2006 From: "Deskins, Nathaniel A nathaniel.deskins[A]pnl.gov" To: CCL Subject: CCL: PBC software Message-Id: <-31061-060228190539-26476-OUT/MN3pEjiQzPdF+i/wdA|server.ccl.net> X-Original-From: "Deskins, Nathaniel A" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Tue, 28 Feb 2006 15:06:45 -0800 MIME-version: 1.0 Sent to CCL by: "Deskins, Nathaniel A" [nathaniel.deskins---pnl.gov] Here's a few. Abinit http://www.abinit.org/ Dacapo http://dcwww.camp.dtu.dk/campos//Dacapo/ NWChem http://www.emsl.pnl.gov/docs/nwchem/nwchem.html DFT++ http://dft.physics.cornell.edu/ Siesta http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ PWscf http://www.pwscf.org/ CPMD http://www.cpmd.org/ I've used the first two (though it's been a while) and Abinit seemed to be the slower of the two, but seems to be very much geared towards solid-state physics and materials science work. Dacapo has been used extensively for surface work and comes from one of the world leaders in computational surface/catalysis work. One of the benefits with NWChem is that it's supposed to be optimized for parallel computations. I can't say much about the rest. Aaron Deskins -----Original Message----- Sent to CCL by: "Pablo Andres Denis" [pablod^bilbo.edu.uy] Hi all, It is possible to work in ``molecular quantum chemistry with free programs like GAMESS, COLUMBUS, NWCHEM, DIRAC etc. but are there any free programs that work with periodic systems? (WIEN2k, CRYSTAL, VASP, CASTEP etc are all paid). Thanks, Pablo From owner-chemistry@ccl.net Tue Feb 28 23:12:00 2006 From: "Greg Landrum Landrum-#-RationalDiscovery.com" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31062-060228215724-12710-wCzzRfwZkowG12YxJa6UTQ]*[server.ccl.net> X-Original-From: Greg Landrum Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Feb 2006 17:57:21 -0800 MIME-Version: 1.0 Sent to CCL by: Greg Landrum [Landrum[*]RationalDiscovery.com] David F. Green dfgreen..ams.sunysb.edu wrote: > Sent to CCL by: "David F. Green" [dfgreen]-[ams.sunysb.edu] > US patent law explicitly allows an exception for "experimental use." > This includes testing, and would most certainly allow for validation of > published results. It is true that the law does not make an exception > for non-commercial or personal use -- you are not allowed to use a > patented method for anything beyond testing unless you obtain permission > from the patent holder -- but that is a separate issue. The arguments > that patenting scientific work prevents it from being independently > verified simply does not hold water. This is equally true for > computational and non-computational methods. Though things may have changed in the last couple of years, a court decision in 2003 (Maday vs Duke U.) pretty much gutted the "experimental use" exemption: http://www.localtechwire.com/article.cfm?u=10135 http://www.wiggin.com/db30/cgi-bin/pubs/Rev%20IP%20Advisory%20-%20Summer%2003%20this%20one.pdf -greg From owner-chemistry@ccl.net Tue Feb 28 23:47:22 2006 From: "Greg Landrum Landrum#,#RationalDiscovery.com" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31063-060228215903-13666-cIJXanajna8XTEPZRTYTjQ%%server.ccl.net> X-Original-From: Greg Landrum Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Feb 2006 17:59:04 -0800 MIME-Version: 1.0 Sent to CCL by: Greg Landrum [Landrum|,|RationalDiscovery.com] Greg Landrum wrote: > Though things may have changed in the last couple of years, a court > decision in 2003 (Maday vs Duke U.) pretty much gutted the "experimental I meant, of course, "Madey" vs Duke U., not "Maday" sorry for the typo, -greg