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
