Comments for The Secret Microbe http://secretmicrobe.org Webial home of Aaron Darling, Ph.D. \\ Stories from a computational genomics geek Thu, 11 Mar 2010 10:31:28 +0000 http://wordpress.org/?v=2.6.2 Comment on KDE 4.1: Open the menu with the windows key by dan http://secretmicrobe.org/kde-41-open-the-menu-with-the-windows-key#comment-161 dan Fri, 01 Jan 2010 03:16:25 +0000 http://secretmicrobe.org/?p=9#comment-161 I got the same error as JasonD but a logout/login fixed the issue. I got the same error as JasonD but a logout/login fixed the issue.

]]> Comment on KDE 4.1: Open the menu with the windows key by Will http://secretmicrobe.org/kde-41-open-the-menu-with-the-windows-key#comment-157 Will Mon, 07 Dec 2009 14:20:45 +0000 http://secretmicrobe.org/?p=9#comment-157 Still works like a charm for Ubuntu 9.10 (64-bit). Thanks! Still works like a charm for Ubuntu 9.10 (64-bit). Thanks!

]]> Comment on KDE 4.1: Open the menu with the windows key by Herb http://secretmicrobe.org/kde-41-open-the-menu-with-the-windows-key#comment-156 Herb Sun, 06 Dec 2009 21:47:35 +0000 http://secretmicrobe.org/?p=9#comment-156 Is there a way to do it without changing the key? I actually use it for other things so it has to be mod4? I mean, come on, it should work as well or better that windows. I mean come on. I'm trying KDE 4.3 for the first thing, and nothing works. Volume buttons on my keyboard do nothing. KDE is SHIT. I'm going back to fluxbox. Is there a way to do it without changing the key? I actually use it for other things so it has to be mod4? I mean, come on, it should work as well or better that windows. I mean come on. I’m trying KDE 4.3 for the first thing, and nothing works. Volume buttons on my keyboard do nothing. KDE is SHIT. I’m going back to fluxbox.

]]> Comment on KDE 4.1: Open the menu with the windows key by **Juanito** http://secretmicrobe.org/kde-41-open-the-menu-with-the-windows-key#comment-141 **Juanito** Fri, 13 Nov 2009 23:33:08 +0000 http://secretmicrobe.org/?p=9#comment-141 Awesome! Works amazing in openSUSE 11.2 but instead of $HOME/.kde/Autostart/remap_keys.sh y write $HOME/.kde<b>4/Autostart/remap_keys.sh that is my version of KDE Awesome! Works amazing in openSUSE 11.2 but instead of $HOME/.kde/Autostart/remap_keys.sh y write $HOME/.kde4/Autostart/remap_keys.sh that is my version of KDE

]]> Comment on Hypocrisy inside open access journals by Mico http://secretmicrobe.org/open-access-hipocrisy#comment-140 Mico Wed, 28 Oct 2009 23:36:21 +0000 http://secretmicrobe.org/?p=55#comment-140 As many of you, I am very sympathetic to PLoS and its open-access policy but cannot understand the choice of a Word-based option, specially for its mathematically oriented journals. Although it's certainly good news that they now accept LaTeX submissions, we are still left with all the typographical imperfections derived from the suboptimal format all the manuscripts end up being converted to. Unnatural spacings in mathematical expressions, ugly mathematical fonts, or weird kernings are a sad and pervasive proof that PLoS made a poor choice. Possibly unrelated to the previous point: can anyone tell me the advantages of accepting only figures in tiff format (bitmap format)? Judging from the pixelation visible in the figures of too many articles, quality cannot be the reason behind this restriction. Sorry for the rant. As many of you, I am very sympathetic to PLoS and its open-access policy but cannot understand the choice of a Word-based option, specially for its mathematically oriented journals. Although it’s certainly good news that they now accept LaTeX submissions, we are still left with all the typographical imperfections derived from the suboptimal format all the manuscripts end up being converted to. Unnatural spacings in mathematical expressions, ugly mathematical fonts, or weird kernings are a sad and pervasive proof that PLoS made a poor choice.

Possibly unrelated to the previous point: can anyone tell me the advantages of accepting only figures in tiff format (bitmap format)? Judging from the pixelation visible in the figures of too many articles, quality cannot be the reason behind this restriction.

Sorry for the rant.

]]> Comment on KDE 4.1: Open the menu with the windows key by Stanley http://secretmicrobe.org/kde-41-open-the-menu-with-the-windows-key#comment-91 Stanley Fri, 29 May 2009 18:59:52 +0000 http://secretmicrobe.org/?p=9#comment-91 Thanks, man! this was exactly what I was looking for! Thanks, man! this was exactly what I was looking for!

]]> Comment on Hypocrisy inside open access journals by Peter Binfield http://secretmicrobe.org/open-access-hipocrisy#comment-90 Peter Binfield Mon, 16 Mar 2009 21:22:30 +0000 http://secretmicrobe.org/?p=55#comment-90 As an update, PLoS ONE is now open for LaTeX submissions :) http://www.plos.org/cms/node/451 Pete Binfield, Managing Editor, PLoS ONE As an update, PLoS ONE is now open for LaTeX submissions :)

http://www.plos.org/cms/node/451

Pete Binfield,
Managing Editor, PLoS ONE

]]> Comment on Hypocrisy inside open access journals by Mailund on the Internet » Blog Archive » This week in the blogs … well, last week http://secretmicrobe.org/open-access-hipocrisy#comment-87 Mailund on the Internet » Blog Archive » This week in the blogs … well, last week Mon, 16 Feb 2009 08:47:09 +0000 http://secretmicrobe.org/?p=55#comment-87 [...] Hypocrisy inside open access journals (The secret microbe) [...] [...] Hypocrisy inside open access journals (The secret microbe) [...]

]]> Comment on Hypocrisy inside open access journals by koadman http://secretmicrobe.org/open-access-hipocrisy#comment-86 koadman Fri, 13 Feb 2009 22:29:56 +0000 http://secretmicrobe.org/?p=55#comment-86 Jonathan Eisen just pointed me to some comments about this post on his friendfeed (http://friendfeed.com/treeoflife). Somebody there points out the Topaz project (http://www.topazproject.org/). I had not come across Topaz before, but it looks like they're well on their way to addressing exactly the issues I raised above. So cool! That really made my Friday. Jonathan Eisen just pointed me to some comments about this post on his friendfeed (http://friendfeed.com/treeoflife). Somebody there points out the Topaz project (http://www.topazproject.org/). I had not come across Topaz before, but it looks like they’re well on their way to addressing exactly the issues I raised above. So cool! That really made my Friday.

]]> Comment on Hypocrisy inside open access journals by koadman http://secretmicrobe.org/open-access-hipocrisy#comment-85 koadman Fri, 13 Feb 2009 20:01:36 +0000 http://secretmicrobe.org/?p=55#comment-85 @Ian: Yes, I did try latex2rtf, in fact I tried all the options listed on the PLoS page for converting latex to Microsoft-friendly formats. Of the bunch, latex2rtf did the most admirable job. If I absolutely had to convert the document myself, I would definitely use that software as a starting point. Unfortunately, latex2rtf stumbled over several of the equations. They do not appear at all when the document is opened in OpenOffice 3.0. I also have MS Word XP running in wine, but the equations turn up with LaTeX commands still embedded, and when I launch the Equation Editor the equation disappears entirely?! Nor do the equations appear in OS X's TextEdit, but maybe that's not surprising. I had Office 2007 running in wine at one point and recall that at least some equations did appear but weren't editable -- wine balked at loading the equation editor. Could it be that if I used Office 2007 on Windows that everything would just work? I've been trying to exterminate all Microsoftware from my laptop, but maybe that's too ambitious... @Peter: That's great news about PLoS One beta testing LaTeX submission, yes, I would like to be part of that group. I never expected anyone from PLoS to read this post, much less respond, so maybe I can ask you more directly: is there any hope of having a scientific publishing platform that is based on well-supported open document format standards? Such a system could do the entire publishing industry a huge favor by helping them move away from closed-proprietary software, cutting costs and improving operability, and most importantly, enabling me to avoid microsoft entirely :^) I do think LaTeX support at PLoS One would be great, but it's not a good general solution... By its very nature, TeX is inherently difficult to support because its command language is not well specified and zillions of variants and extensions exist. That's where the cooperatively developed XML-based standards come in. @Ian: Yes, I did try latex2rtf, in fact I tried all the options listed on the PLoS page for converting latex to Microsoft-friendly formats. Of the bunch, latex2rtf did the most admirable job. If I absolutely had to convert the document myself, I would definitely use that software as a starting point. Unfortunately, latex2rtf stumbled over several of the equations. They do not appear at all when the document is opened in OpenOffice 3.0. I also have MS Word XP running in wine, but the equations turn up with LaTeX commands still embedded, and when I launch the Equation Editor the equation disappears entirely?! Nor do the equations appear in OS X’s TextEdit, but maybe that’s not surprising. I had Office 2007 running in wine at one point and recall that at least some equations did appear but weren’t editable — wine balked at loading the equation editor. Could it be that if I used Office 2007 on Windows that everything would just work? I’ve been trying to exterminate all Microsoftware from my laptop, but maybe that’s too ambitious…

@Peter: That’s great news about PLoS One beta testing LaTeX submission, yes, I would like to be part of that group. I never expected anyone from PLoS to read this post, much less respond, so maybe I can ask you more directly: is there any hope of having a scientific publishing platform that is based on well-supported open document format standards? Such a system could do the entire publishing industry a huge favor by helping them move away from closed-proprietary software, cutting costs and improving operability, and most importantly, enabling me to avoid microsoft entirely :^) I do think LaTeX support at PLoS One would be great, but it’s not a good general solution… By its very nature, TeX is inherently difficult to support because its command language is not well specified and zillions of variants and extensions exist. That’s where the cooperatively developed XML-based standards come in.

]]>