On Wed, May 16, 2012 at 9:07 PM, Geoffrey Hutchison firstname.lastname@example.org 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:
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
- 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?
Dr E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)