From owner-chemistry@ccl.net Wed Jan 7 04:28:01 2015 From: "Eli Lam eli421^hku.hk" To: CCL Subject: CCL: Molecular dynamics for metal complexes Message-Id: <-50872-150107042526-21025-swZKIusWQsiwSs6K+Ci8+A],[server.ccl.net> X-Original-From: "Eli Lam" Date: Wed, 7 Jan 2015 04:25:24 -0500 Sent to CCL by: "Eli Lam" [eli421[*]hku.hk] Dear CCLers, I am totally new to molecular dynamics simulations. Yet I have heard from my seniors commenting that MD simulations is unrealistic towards transition metal complexes especially in non-convalent interactions. May I ask about the reasons? I would be grateful if CCLers can introduce me some materials about the basics on MD. Thank you so much in advance! Eli From owner-chemistry@ccl.net Wed Jan 7 09:40:01 2015 From: "Andrew Dalke dalke()dalkescientific.com" To: CCL Subject: CCL: Any regrets open-sourcing your programs? Message-Id: <-50873-150107003749-10996-FSqD4SAz9N5P78lY9Rgryg|-|server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 7 Jan 2015 06:37:39 +0100 Mime-Version: 1.0 (Apple Message framework v1283) Sent to CCL by: Andrew Dalke [dalke###dalkescientific.com] On Jan 6, 2015, at 1:13 PM, uekstrom/./gmail.com uekstrom/./gmail.com wrote: > I am involved in a discussion about open source scientific software. "Regret" is a very strong and specific word. There are other negatives. The earliest one I know is RasMol, which was released into the public domain. Glaxo-Wellcome hired Roger Sayle, the author of RasMol, to continue to develop the software as an employee, still in the public domain; "repaying its intellectual debt to the scientific community". MDL used it as part of their original Chime/Netscape plugin. Which they wanted to sell to Glaxo-Wellcome and others. This caused some difficulties. See: http://www.icis.com/resources/news/1996/06/17/3444/glaxo-wellcome-mdl-in-copyright-dispute/ http://www.umass.edu/microbio/chime/chimvras.htm for some of the background. I know the RasMol author did not like this perfectly legal use of the RasMol source code. I do not know if those negative feelings towards what happened extended to "regret". Had the software been under the GPL, this would not have happened, so you could interpret this as a regret over choice of license rather than specifically the choice to release the source. One of the reasons I've heard for releasing software under an open source/free license is because others will contribute. My own experience with VMD (I was the main author of VMD in the mid-1990s) was that very few people contribute. OpenEye distributed a commercial free software package called OELib, under the GPL. They had customers willing to pay for support. However, their experience was that customers would make patches to the local source, but not send the patches back (as I recall, such contributions might have had to go through lawyers). The problem is that a code branch that might be incompatible with newer versions of the software, ending up with an extra local maintenance cost to merge the branches, instead of a remote cost of asking for new features. After polling their clients, they decided that a traditional proprietary license would be more effective, which they used for their new OEChem library. OELib still exists; it's the basis for Open Babel. My memory on this is 10+ years old and likely inaccurate in the details. My point is if someone released software with the hope that others will volunteer significant new contributions, then the lack of any response can be, well, not a regret but a disappointment. Another negative is the expectation that you will support your software. I wrote one package for generating RSS feeds in Python. It took about 3 days, in the early 2000s. I still get a few support emails each year on it. It's also one of my most widely used pieces of software, oddly enough. Funding has always been the problem with free and open source projects. There are any number of projects which come from academic research, hobby projects, and research projects in industry. I'll note that the other replies so far have come from people employed at two national labs and a university. There are very few financially self-supported projects. One is/was PyMol. Warren DeLano was a very pro-open source advocate. His funding came from site and individual licenses for PyMol, which included early access to features, support, and pre-built binaries. (Again, my memory can be vague.) As Huub van Dam pointed out, managing license fees also takes time. Part of DeLano's day was spent managing these ~$100/user fee (as I recall) transactions. As well as doing user support. He did hire staff to help, but I don't think he made enough to employ someone else. Another, is my own "chemfp" package for fast Tanimoto search (http://chemfp.com/). I release it under the MIT license, but to get the latest version you have to pay me "non-trivial" money for it, or get it from someone else who has a copy. It's not quite there yet in the market to say it's successful, but it's the only other case I know of. I don't make enough to employ someone else. As van Dam further pointed out, the question is does your market support revenue? One comment I read elsewhere suggest that no-cost open source projects decrease the market size by about an order of magnitude compared to a proprietary market. There are people who would pay, if needed, to get the source code. By making it available at no cost that market segment disappears. What's left are people who are willing to pay for custom development, new features, support, etc. This applies even with academic groups. If there is a market for software at $250/seat/year then 500 seats is enough to fund a research programmer to work on it, rather than depend on grants and other external funding. I see you are in Oslo. I was planning to visit the city in a couple of weeks. Let me know if you would like to meet talk this over face-to-face. I've been involved with various aspects of open source in bioinformatics and cheminformatics since the late 1990s. Cheers, Andrew Dalke dalke/./dalkescientific.com From owner-chemistry@ccl.net Wed Jan 7 12:59:01 2015 From: "Chris Swain swain:mac.com" To: CCL Subject: CCL: Any regrets open-sourcing your programs? Message-Id: <-50874-150107120149-25311-up8sq4Sww+3xLge/1mgXww-x-server.ccl.net> X-Original-From: Chris Swain Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=utf-8 Date: Wed, 07 Jan 2015 17:01:36 +0000 MIME-version: 1.0 (Mac OS X Mail 8.1 \(1993\)) Sent to CCL by: Chris Swain [swain:mac.com] This is very nice summary. In my very limited experience the the long term ongoing support for contributed portions of code can be a pretty onerous (and thankless) task. On the other hand my interactions with people working on OpenBabel has lead to relationships which I’m delighted to say still hold dear decades later. Cheers, Chris > On 7 Jan 2015, at 05:37, Andrew Dalke dalke()dalkescientific.com wrote: > > > Sent to CCL by: Andrew Dalke [dalke###dalkescientific.com] > On Jan 6, 2015, at 1:13 PM, uekstrom/./gmail.com uekstrom/./gmail.com wrote: >> I am involved in a discussion about open source scientific software. > > "Regret" is a very strong and specific word. There are other negatives. > > The earliest one I know is RasMol, which was released into the public domain. Glaxo-Wellcome hired Roger Sayle, the author of RasMol, to continue to develop the software as an employee, still in the public domain; "repaying its intellectual debt to the scientific community". MDL used it as part of their original Chime/Netscape plugin. Which they wanted to sell to Glaxo-Wellcome and others. > > This caused some difficulties. See: > http://www.icis.com/resources/news/1996/06/17/3444/glaxo-wellcome-mdl-in-copyright-dispute/ > http://www.umass.edu/microbio/chime/chimvras.htm > > for some of the background. I know the RasMol author did not like this perfectly legal use of the RasMol source code. I do not know if those negative feelings towards what happened extended to "regret". Had the software been under the GPL, this would not have happened, so you could interpret this as a regret over choice of license rather than specifically the choice to release the source. > > > One of the reasons I've heard for releasing software under an open source/free license is because others will contribute. My own experience with VMD (I was the main author of VMD in the mid-1990s) was that very few people contribute. OpenEye distributed a commercial free software package called OELib, under the GPL. They had customers willing to pay for support. However, their experience was that customers would make patches to the local source, but not send the patches back (as I recall, such contributions might have had to go through lawyers). The problem is that a code branch that might be incompatible with newer versions of the software, ending up with an extra local maintenance cost to merge the branches, instead of a remote cost of asking for new features. > > After polling their clients, they decided that a traditional proprietary license would be more effective, which they used for their new OEChem library. OELib still exists; it's the basis for Open Babel. > > My memory on this is 10+ years old and likely inaccurate in the details. My point is if someone released software with the hope that others will volunteer significant new contributions, then the lack of any response can be, well, not a regret but a disappointment. > > Another negative is the expectation that you will support your software. I wrote one package for generating RSS feeds in Python. It took about 3 days, in the early 2000s. I still get a few support emails each year on it. It's also one of my most widely used pieces of software, oddly enough. > > Funding has always been the problem with free and open source projects. There are any number of projects which come from academic research, hobby projects, and research projects in industry. I'll note that the other replies so far have come from people employed at two national labs and a university. > > There are very few financially self-supported projects. One is/was PyMol. Warren DeLano was a very pro-open source advocate. His funding came from site and individual licenses for PyMol, which included early access to features, support, and pre-built binaries. (Again, my memory can be vague.) > > As Huub van Dam pointed out, managing license fees also takes time. Part of DeLano's day was spent managing these ~$100/user fee (as I recall) transactions. As well as doing user support. He did hire staff to help, but I don't think he made enough to employ someone else. > > Another, is my own "chemfp" package for fast Tanimoto search (http://chemfp.com/). I release it under the MIT license, but to get the latest version you have to pay me "non-trivial" money for it, or get it from someone else who has a copy. It's not quite there yet in the market to say it's successful, but it's the only other case I know of. I don't make enough to employ someone else. > > As van Dam further pointed out, the question is does your market support revenue? One comment I read elsewhere suggest that no-cost open source projects decrease the market size by about an order of magnitude compared to a proprietary market. There are people who would pay, if needed, to get the source code. By making it available at no cost that market segment disappears. What's left are people who are willing to pay for custom development, new features, support, etc. > > This applies even with academic groups. If there is a market for software at $250/seat/year then 500 seats is enough to fund a research programmer to work on it, rather than depend on grants and other external funding. > > I see you are in Oslo. I was planning to visit the city in a couple of weeks. Let me know if you would like to meet talk this over face-to-face. I've been involved with various aspects of open source in bioinformatics and cheminformatics since the late 1990s. > > Cheers, > > Andrew Dalke > dalke:dalkescientific.com> > From owner-chemistry@ccl.net Wed Jan 7 14:53:01 2015 From: "rjensen:+:ualberta.ca" To: CCL Subject: CCL: Any regrets open-sourcing your programs? Message-Id: <-50875-150107143703-5715-tgcPs67quQpsv+1k6xuA2w]_[server.ccl.net> X-Original-From: rjensen]_[ualberta.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 07 Jan 2015 12:36:56 -0700 MIME-Version: 1.0 Sent to CCL by: rjensen]=[ualberta.ca I am currently putting together an article looking at limitations and challenges associated with Creative Commons licensing of instructional material. I would greatly appreciate a few people interested in this topic reviewing my draft article. (It will be ready in two weeks -- I hope!) Interested persons can contact me via email: rjensen _ ualberta.ca Thanks, Dr. Roy Jensen (==========)-----------------------------------------¤ Lecturer, Chemistry E5-33F, University of Alberta 780.248.1808