Re: [Avogadro-Discuss] [Avogadro-devel] Avogadro Manuscript
On Thu, May 17, 2012 at 4:22 PM, Geoffrey Hutchison geo...@pitt.edu wrote: Some feedback; it's a nice read: Drat. Now I can't use you as a reviewer. ;-) :) - in the reference section, many of the cited webpage do not author(s) yet. Those should be added. E.g. 55. OpenSMILES 2012, [http://opensmiles.org/].; This is a specification, much more than a random webpage. BMC allows authors on webpages, and is the right thing to do. It's a good idea. I'll have to look through all contributors to the specification. It applies to several webpage / references... - in section 5 you should explain why Avogadro stuck with GPL, when Qt moved to LGPL, because the text now seems to suggest the latter is better and you were forced into GPL when Qt still had that license. Good point. As you're aware, the restriction is on Open Babel. This is one incentive for the MolCore and ChemKit pushes, and I think it's fair to state that Avogadro 2.0 will be released under the BSD license. OK. I thoughts so, but the next did not say much about strong dependencies in that part... But nothing wrong with clarifying such things in the paper, IMHO. aspect is of OpenGL... there are plenty of *new* but crappy ThinkPads around which only have a mobile graphics processor. I have one, and it really sucks, and makes Avogadro very slow on my laptop (surfaces are impossible, but even default rotation is awkward…). I appreciate your suggestions here, but I'm curious about your performance issues. As you know, I use Mac, and many of my students use Windows. My group has several of these slow integrated GPUs and have good performance. I know you're using Linux, but what driver are you using? Fair point, indeed. It's running 'i915'... that's kind of something I miss in Debian GNU/Linux... clear suggestions on what less free but better performing modules I can use. - and to balance things, OpenGL also makes Avagadro more crash-prone (and fairly, with just 2 minutes of working with it, it crashed again, though I could not reproduce it in the next 2 minutes) One issue we've identified with OpenGL is the existence of different pipelines. Most of the tutorials out there for OpenGL, and indeed many other viewer programs use an older pipeline, rather than uploading shapes onto the GPU. The latter strategy is used by modern games. So better performance is found in this modern pipeline, and this aspect of the card and driver are more heavily tested. But is this Avogadro's crash because the driver has a bug? I'm happy to look at crash logs and stack traces, but 90% of these random crashes turn out to be the drafting. Dunno, unfortunately :( The command line only said 'Segmentation fault'... how do I turn on debugging? - fig 10: explain the coloring in the caption - Other requirements (if compiling): CMake 2.6+ Should Qt, OB, ... not be listed here too? Good points. - Any restrictions to use by non-academics: None That's a BMC thing, but obviously non-academics do have restrictions too: they are equally copy-lefted like anyone else :) Do you have a suggestion for wording? This is something I should pick up with Kuras and Bailey... None additional or No specific? What about a scripting language, like Jmol and Bioclipse have? You can script Avogadro using Python. I'm investigating use of JavaScript through QtScript, but there are cases of Python extensions -- it's probably worth us linking to a few of these. Yeah, I saw the Python binding... but I could not find how to use that via the GUI... if that is possible, then I would certainly mention that in the paper. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] [Avogadro-devel] Avogadro Manuscript
Hi Geoff, On Wed, May 16, 2012 at 9:07 PM, Geoffrey Hutchison geo...@pitt.edu wrote: We're currently finishing up a manuscript on Avogadro, to be submitted as part of an upcoming special topic issue of J. Cheminformatics. I realized last night, that in submitting to an open access journal, we can let everyone see the article before, during, and after submission: https://github.com/avogadropaper/avogadropaper/raw/master/AvogadroPaper/AvogadroPaper.pdf Some feedback; it's a nice read: - in the reference section, many of the cited webpage do not author(s) yet. Those should be added. E.g. 55. OpenSMILES 2012, [http://opensmiles.org/].; This is a specification, much more than a random webpage. BMC allows authors on webpages, and is the right thing to do. - intro: Jmol is with a lower case 'm' - in section 5 you should explain why Avogadro stuck with GPL, when Qt moved to LGPL, because the text now seems to suggest the latter is better and you were forced into GPL when Qt still had that license. - 'OpenGL 1.1 and below is used in most of the rendering code, and so Avogadro can be used even on modest, older computer systems. Remove 'modest'; that has nothing to do with an older OpenGL version, and instead suggests that OpenGL is the only way to get something to work in structure viz on older machines, which is incorrect. A second aspect is of OpenGL... there are plenty of *new* but crappy ThinkPads around which only have a mobile graphics processor. I have one, and it really sucks, and makes Avogadro very slow on my laptop (surfaces are impossible, but even default rotation is awkward...). Bottom line: there is new hardware too without proper hardware accelleration, so even the 'older computer systems' in that statement is incorrect. Maybe just update to computers without modern accellerated graphics. - and to balance things, OpenGL also makes Avagadro more crash-prone (and fairly, with just 2 minutes of working with it, it crashed again, though I could not reproduce it in the next 2 minutes) - fig 10: explain the coloring in the caption - Other requirements (if compiling): CMake 2.6+ Should Qt, OB, ... not be listed here too? - Any restrictions to use by non-academics: None That's a BMC thing, but obviously non-academics do have restrictions too: they are equally copy-lefted like anyone else :) What about a scripting language, like Jmol and Bioclipse have? Grtz, Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] [Avogadro-devel] Avogadro Manuscript
It applies to several webpage / references… Done. OK. I thoughts so, but the next did not say much about strong dependencies in that part... But nothing wrong with clarifying such things in the paper, IMHO. Done. Fair point, indeed. It's running 'i915'... that's kind of something I miss in Debian GNU/Linux... clear suggestions on what less free but better performing modules I can use. Dunno. A quick search turns up: https://launchpad.net/~glasen/+archive/intel-driver Dunno, unfortunately :( The command line only said 'Segmentation fault'... how do I turn on debugging? ulimit -c unlimited # dump core files gdb /path/to/binary core This is something I should pick up with Kuras and Bailey... None additional or No specific? Ok, I went with none additional, which seems appropriate. Thanks! Yeah, I saw the Python binding... but I could not find how to use that via the GUI... if that is possible, then I would certainly mention that in the paper. If Python is enabled, there will be a Python terminal window: http://avogadro.openmolecules.net/wiki/Tutorials:Console I've added this to the paper. Thanks for the suggestions! -Geoff -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
