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	<title>Comments on: Indispensable Applications</title>
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	<link>http://crookedtimber.org/2004/12/11/indispensible-applications/</link>
	<description>Out of the crooked timber of humanity, no straight thing was ever made</description>
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		<title>By: Crooked Timber &#187; &#187; Strategies for successful dissertation completion</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-122420</link>
		<dc:creator>Crooked Timber &#187; &#187; Strategies for successful dissertation completion</dc:creator>
		<pubDate>Fri, 18 Nov 2005 12:56:34 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-122420</guid>
		<description>[...] Related to all this, it may be a good time to revisit Kieran&#8217;s list of Indispensable Applications. [...]</description>
		<content:encoded><![CDATA[	<p>[...] Related to all this, it may be a good time to revisit Kieran&#8217;s list of Indispensable Applications. [...]</p>
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		<title>By: Andrew Leigh</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53909</link>
		<dc:creator>Andrew Leigh</dc:creator>
		<pubDate>Sun, 12 Dec 2004 22:52:56 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53909</guid>
		<description>I&#039;m a big fan of Google Desktop.http://desktop.google.com/about.html</description>
		<content:encoded><![CDATA[	<p>I&#8217;m a big fan of Google Desktop.<a href="http://desktop.google.com/about.html" rel="nofollow">http://desktop.google.com/about.html</a></p>
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		<title>By: nick</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53908</link>
		<dc:creator>nick</dc:creator>
		<pubDate>Sun, 12 Dec 2004 18:31:29 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53908</guid>
		<description>&lt;i&gt;I will go to my grave protesting that Latex documents look shit.&lt;/i&gt;Part of the learning curve was ensuring that my own stuff didn&#039;t look like shit. Adobe Caslon Pro, thank you very much, with old-style figures and proper spacing. The default styles are rather crappy, to my eyes. But &#039;\usepackage{palatino}&#039; (or even the &#039;times&#039; package) works wonders as a starting point.As for quotation management: something that hooks into BibTeX and its UIDs for texts, while offering a free-text search mapped to page references, would do me just fine.</description>
		<content:encoded><![CDATA[	<p><i>I will go to my grave protesting that Latex documents look shit.</i>Part of the learning curve was ensuring that my own stuff didn&#8217;t look like shit. Adobe Caslon Pro, thank you very much, with old-style figures and proper spacing. The default styles are rather crappy, to my eyes. But &#8216;usepackage{palatino}&#8217; (or even the &#8216;times&#8217; package) works wonders as a starting point.As for quotation management: something that hooks into BibTeX and its UIDs for texts, while offering a free-text search mapped to page references, would do me just fine.</p>
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		<title>By: Adam Kotsko</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53907</link>
		<dc:creator>Adam Kotsko</dc:creator>
		<pubDate>Sun, 12 Dec 2004 17:08:25 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53907</guid>
		<description>HA!</description>
		<content:encoded><![CDATA[	<p>HA!</p>
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		<title>By: ben wolfson</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53906</link>
		<dc:creator>ben wolfson</dc:creator>
		<pubDate>Sun, 12 Dec 2004 06:08:53 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53906</guid>
		<description>&lt;em&gt;Vim is a nice alternative to emacs for those who don’t want to develop emacs pinky&lt;/em&gt;The downside, of course, is that you get colon cancer.</description>
		<content:encoded><![CDATA[	<p><em>Vim is a nice alternative to emacs for those who don&#8217;t want to develop emacs pinky</em>The downside, of course, is that you get colon cancer.</p>
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		<title>By: bq</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53911</link>
		<dc:creator>bq</dc:creator>
		<pubDate>Sun, 12 Dec 2004 03:43:00 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53911</guid>
		<description>&lt;a href=&quot;http://www.vim.org&quot;&gt;Vim&lt;/a&gt; is a nice alternative to emacs for those who don&#039;t want to develop emacs pinky.  I usually use LaTeX and vim, but I know people who use LyX as their interface to LaTeX on UNIX and TeXnicCenter on Windows (it&#039;s better than WinEDT and completely free.)Revision control is a necessity if you care about your work, and I&#039;ve recently converted from CVS to subversion (with the fsfs repository, not the BDB one.)  Fixing a set of mistakes by typing &quot;svn revert&quot; just once makes the relatively minor effort of learning svn completely worthwhile.Firefox for browsing, Thunderbird for email, and Sharpreader for reading RSS feeds on Windows.  I haven&#039;t found a UNIX RSS aggregator that I&#039;m completely happy with yet.  Thunderbird might be good, but it doesn&#039;t import or export OPML files yet.  I was surprised to see a discussion on a blog about software tools without a mention of RSS aggregators.  I wouldn&#039;t have the time to follow blogs without one.I use python (with numarray) and Mathematica for most mathematics and programming work; I use perl for munging text, and I use bash for managing files.  While almost everything leaves Windows Explorer in the dust and Konqueror is both pretty and powerful, nothing compares to a good shell like bash for ease of use and ability to automate.</description>
		<content:encoded><![CDATA[	<p><a href="http://www.vim.org">Vim</a> is a nice alternative to emacs for those who don&#8217;t want to develop emacs pinky.  I usually use LaTeX and vim, but I know people who use LyX as their interface to LaTeX on <span class="caps">UNIX</span> and TeXnicCenter on Windows (it&#8217;s better than WinEDT and completely free.)Revision control is a necessity if you care about your work, and I&#8217;ve recently converted from <span class="caps">CVS</span> to subversion (with the fsfs repository, not the <span class="caps">BDB</span> one.)  Fixing a set of mistakes by typing &#8220;svn revert&#8221; just once makes the relatively minor effort of learning svn completely worthwhile.Firefox for browsing, Thunderbird for email, and Sharpreader for reading <span class="caps">RSS</span> feeds on Windows.  I haven&#8217;t found a <span class="caps">UNIX RSS</span> aggregator that I&#8217;m completely happy with yet.  Thunderbird might be good, but it doesn&#8217;t import or export <span class="caps">OPML</span> files yet.  I was surprised to see a discussion on a blog about software tools without a mention of <span class="caps">RSS</span> aggregators.  I wouldn&#8217;t have the time to follow blogs without one.I use python (with numarray) and Mathematica for most mathematics and programming work; I use perl for munging text, and I use bash for managing files.  While almost everything leaves Windows Explorer in the dust and Konqueror is both pretty and powerful, nothing compares to a good shell like bash for ease of use and ability to automate.</p>
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		<title>By: bza</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53910</link>
		<dc:creator>bza</dc:creator>
		<pubDate>Sun, 12 Dec 2004 02:23:20 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53910</guid>
		<description>&lt;i&gt; I’ve seen plenty of them with really dodgy kerning and justification too.&lt;/i&gt;I really, really doubt this.  Kerning can go wrong in LaTeX for basically two reasons:  Incorrect font metrics, which is not a problem with LaTeX, but with the font, and end-users trying to insert manual spacing  adjustments as if they were still working in a word processor, which is also not a problem with LaTeX. </description>
		<content:encoded><![CDATA[	<p><i> I&#8217;ve seen plenty of them with really dodgy kerning and justification too.</i>I really, really doubt this.  Kerning can go wrong in LaTeX for basically two reasons:  Incorrect font metrics, which is not a problem with LaTeX, but with the font, and end-users trying to insert manual spacing  adjustments as if they were still working in a word processor, which is also not a problem with LaTeX.</p>
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		<title>By: ben wolfson</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53905</link>
		<dc:creator>ben wolfson</dc:creator>
		<pubDate>Sat, 11 Dec 2004 21:42:10 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53905</guid>
		<description>I think the default TeX font is real purty, especially the capital Qs.I bet it would be pretty easy, though maybe not so elegant, to hack together a quotation-management system using textfiles and &lt;a href=&quot;http://swish-e.org/&quot;&gt;swish-e&lt;/a&gt;.  You&#039;d have to use some sort of standard format for the files (überdorks would use XML, but that&#039;s basically human-unwriteable) so that you could programmatically extract author, work, page, etc (keywords, I guess), then use the prog input type for swish-e, your program feeding the metadata to swish-e&#039;s engine using the MetaNames or PropertyNames (or something, it&#039;s been a while since I looked at swish-e last) features.  Then you could search doing something like &quot;swish-e -w author=&#039;(someone or someonelse)&#039;&quot;.  If that&#039;s actually what you mean by quotation management.  I just rely on my PRODIGIOUS MEMORY.</description>
		<content:encoded><![CDATA[	<p>I think the default TeX font is real purty, especially the capital Qs.I bet it would be pretty easy, though maybe not so elegant, to hack together a quotation-management system using textfiles and <a href="http://swish-e.org/">swish-e</a>.  You&#8217;d have to use some sort of standard format for the files (&#252;berdorks would use <span class="caps">XML</span>, but that&#8217;s basically human-unwriteable) so that you could programmatically extract author, work, page, etc (keywords, I guess), then use the prog input type for swish-e, your program feeding the metadata to swish-e&#8217;s engine using the MetaNames or PropertyNames (or something, it&#8217;s been a while since I looked at swish-e last) features.  Then you could search doing something like &#8220;swish-e -w author=&#8217;(someone or someonelse)&#8217;&#8221;.  If that&#8217;s actually what you mean by quotation management.  I just rely on my <span class="caps">PRODIGIOUS MEMORY</span>.</p>
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		<title>By: Kieran Healy</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53904</link>
		<dc:creator>Kieran Healy</dc:creator>
		<pubDate>Sat, 11 Dec 2004 21:07:20 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53904</guid>
		<description>&lt;i&gt;For some reason they’re always in this yacky skinny serif font&lt;/i&gt;That&#039;s Computer Modern, the default Latex font. Standard installations come with three or four more (Times and Palatino, in particular), if you don&#039;t like it (and many don&#039;t, especially for online PDFs). If you want other ones you have to buy them. I forked out for Adobe&#039;s versions of Sabon and Caslon, and I use those (especially Sabon) for my papers these days.Easy installation of new fonts is one area where LaTeX falls down in a big way, though things have improved considerably in recent years. You&#039;ll get a lot more of an argument from me and others about the quality of kerning and justification in Latex, as opposed to things like MS Word.</description>
		<content:encoded><![CDATA[	<p><i>For some reason they&#8217;re always in this yacky skinny serif font</i>That&#8217;s Computer Modern, the default Latex font. Standard installations come with three or four more (Times and Palatino, in particular), if you don&#8217;t like it (and many don&#8217;t, especially for online PDFs). If you want other ones you have to buy them. I forked out for Adobe&#8217;s versions of Sabon and Caslon, and I use those (especially Sabon) for my papers these days.Easy installation of new fonts is one area where LaTeX falls down in a big way, though things have improved considerably in recent years. You&#8217;ll get a lot more of an argument from me and others about the quality of kerning and justification in Latex, as opposed to things like <span class="caps">MS </span>Word.</p>
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		<title>By: BenA</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53903</link>
		<dc:creator>BenA</dc:creator>
		<pubDate>Sat, 11 Dec 2004 21:00:08 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53903</guid>
		<description>I&#039;ve been using &lt;a href=&quot;http://www.eastgate.com/Tinderbox/&quot;&gt;Tinderbox&lt;/a&gt; as a note-taking/information management tool for the last three months or so.  I love it, though feel that I&#039;ve only scratched the surface of its usefulness (my feeling about it is similar to the way Kieran describes Quicksilver, which I downloaded weeks ago, but have yet to try).  Right now Tinderbox is Mac-only, though they&#039;re working on porting it to Windows.</description>
		<content:encoded><![CDATA[	<p>I&#8217;ve been using <a href="http://www.eastgate.com/Tinderbox/">Tinderbox</a> as a note-taking/information management tool for the last three months or so.  I love it, though feel that I&#8217;ve only scratched the surface of its usefulness (my feeling about it is similar to the way Kieran describes Quicksilver, which I downloaded weeks ago, but have yet to try).  Right now Tinderbox is Mac-only, though they&#8217;re working on porting it to Windows.</p>
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		<title>By: dsquared</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53902</link>
		<dc:creator>dsquared</dc:creator>
		<pubDate>Sat, 11 Dec 2004 20:35:11 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53902</guid>
		<description>I know I am in a minority of one on this subject, but I will go to my grave protesting that Latex documents look shit.  For some reason they&#039;re always in this yacky skinny serif font and the linespacing always looks too wide.  I&#039;ve seen plenty of them with really dodgy kerning and justification too.</description>
		<content:encoded><![CDATA[	<p>I know I am in a minority of one on this subject, but I will go to my grave protesting that Latex documents look shit.  For some reason they&#8217;re always in this yacky skinny serif font and the linespacing always looks too wide.  I&#8217;ve seen plenty of them with really dodgy kerning and justification too.</p>
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		<title>By: schwa</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53901</link>
		<dc:creator>schwa</dc:creator>
		<pubDate>Sat, 11 Dec 2004 19:30:03 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53901</guid>
		<description>What I wouldn&#039;t give for an editor with the adaptability of emacs, but without the creeping kudzu of emacs. And with key combinations which aren&#039;t &lt;i&gt;stupid&lt;/i&gt;. Every time I&#039;ve tried to learn emacs, I find myself completely unable to get past the sheer dumbness, from a usability point of view, of C-x C-f.I&#039;d love to get shot of MS Word and move to a TeX-based writing environment, but the lack of a decent editor prevents me. (Vi sucks for this purpose in a whole different way.)</description>
		<content:encoded><![CDATA[	<p>What I wouldn&#8217;t give for an editor with the adaptability of emacs, but without the creeping kudzu of emacs. And with key combinations which aren&#8217;t <i>stupid</i>. Every time I&#8217;ve tried to learn emacs, I find myself completely unable to get past the sheer dumbness, from a usability point of view, of C-x C-f.I&#8217;d love to get shot of <span class="caps">MS </span>Word and move to a TeX-based writing environment, but the lack of a decent editor prevents me. (Vi sucks for this purpose in a whole different way.)</p>
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		<title>By: Alun Carr</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53900</link>
		<dc:creator>Alun Carr</dc:creator>
		<pubDate>Sat, 11 Dec 2004 19:26:44 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53900</guid>
		<description>There is a more pleasant alternative to Emacs available: Alpha. The original Alpha was coded in a mixture of C and Tcl for Classic Mac OS, but now there is the cross-platform AlphaTk (coded entirely in Tcl/Tk, for all platforms that support Tcl/Tk, including Windows and Mac OS X); in addition, the original Alpha project has migrated to OS X as AlphaX.The LaTeX mode in Alpha is very good, and the whole editor is very user-friendly (and it even supports many Emacs key combinations).Links:AlphaTk:http://www.santafe.edu/~vince/Alphatk.htmlAlphaXhttp://www.maths.mq.edu.au/~steffen/Alpha/AlphaX/Note that in both cases you must have Tcl/Tk installed (links are on both sites).Alun</description>
		<content:encoded><![CDATA[	<p>There is a more pleasant alternative to Emacs available: Alpha. The original Alpha was coded in a mixture of C and Tcl for Classic Mac OS, but now there is the cross-platform AlphaTk (coded entirely in Tcl/Tk, for all platforms that support Tcl/Tk, including Windows and Mac <span class="caps">OS X</span>); in addition, the original Alpha project has migrated to <span class="caps">OS X</span> as AlphaX.The LaTeX mode in Alpha is very good, and the whole editor is very user-friendly (and it even supports many Emacs key combinations).Links:AlphaTk:<a href="http://www.santafe.edu/~vince/Alphatk.html" rel="nofollow">http://www.santafe.edu/~vince/Alphatk.html</a>AlphaX<a href="http://www.maths.mq.edu.au/~steffen/Alpha/AlphaX/" rel="nofollow">http://www.maths.mq.edu.au/~steffen/Alpha/AlphaX/</a>Note that in both cases you must have Tcl/Tk installed (links are on both sites).Alun</p>
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		<title>By: Andrew Case</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53899</link>
		<dc:creator>Andrew Case</dc:creator>
		<pubDate>Sat, 11 Dec 2004 18:35:25 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53899</guid>
		<description>I second the recommendation for emacs and LaTeX, though I don&#039;t have experience with the other software.  I&#039;m a physicsist, and the number one app that I want is a simple photo markup program.  Just the ability to add arrows with numbers on them to pictures would be great.In the longer term I&#039;d like to have a dynamic lab notebook which automagically downloads pictures from my cell phone and allows me to mark them up and include text with change tracking.  Something along the lines of a Wiki would be ideal.  That way I can shoot snaps of equipment as I&#039;m building it or installing it and add comments to keep track of what I did when. The notebook should also include the ability to link to data files and data processing scripts, again with change tracking.  One other necessary element would be automatic backup to a remote RAID server. It seems to me that all the elements exist but nobody has yet integrated them into a single seamless app.Plain old paper lab notebooks are great, but you can&#039;t beat a picture for certain kinds of information.  Done right the Sooper Dooper Electronic Lab Notebook could seamlessly integrate the nitty-gritty of lab work with data analysis and publication.That said, simple photo markup would be a huge step in the right direction.  I&#039;ve tried doing it with photoshop, but it&#039;s too big to just leave idling in the background while I do other things.</description>
		<content:encoded><![CDATA[	<p>I second the recommendation for emacs and LaTeX, though I don&#8217;t have experience with the other software.  I&#8217;m a physicsist, and the number one app that I want is a simple photo markup program.  Just the ability to add arrows with numbers on them to pictures would be great.In the longer term I&#8217;d like to have a dynamic lab notebook which automagically downloads pictures from my cell phone and allows me to mark them up and include text with change tracking.  Something along the lines of a Wiki would be ideal.  That way I can shoot snaps of equipment as I&#8217;m building it or installing it and add comments to keep track of what I did when. The notebook should also include the ability to link to data files and data processing scripts, again with change tracking.  One other necessary element would be automatic backup to a remote <span class="caps">RAID</span> server. It seems to me that all the elements exist but nobody has yet integrated them into a single seamless app.Plain old paper lab notebooks are great, but you can&#8217;t beat a picture for certain kinds of information.  Done right the Sooper Dooper Electronic Lab Notebook could seamlessly integrate the nitty-gritty of lab work with data analysis and publication.That said, simple photo markup would be a huge step in the right direction.  I&#8217;ve tried doing it with photoshop, but it&#8217;s too big to just leave idling in the background while I do other things.</p>
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		<title>By: Adam Kotsko</title>
		<link>http://crookedtimber.org/2004/12/11/indispensible-applications/comment-page-1/#comment-53898</link>
		<dc:creator>Adam Kotsko</dc:creator>
		<pubDate>Sat, 11 Dec 2004 18:02:43 +0000</pubDate>
		<guid isPermaLink="false">http://crookedtimber.org/wp/?p=2634#comment-53898</guid>
		<description>I second Nick&#039;s call for a software package to handle quotations!  This whole setup has my techno-glands salivating, and that seems to be the only missing piece.  </description>
		<content:encoded><![CDATA[	<p>I second Nick&#8217;s call for a software package to handle quotations!  This whole setup has my techno-glands salivating, and that seems to be the only missing piece.</p>
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