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	<title>When Brains Fly &#187; admin</title>
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	<link>http://www.whenbrainsfly.com</link>
	<description>An Awesome Blog About Neuroscience, Computer Science, and Technology</description>
	<lastBuildDate>Mon, 28 Jun 2010 01:03:21 +0000</lastBuildDate>
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			<item>
		<title>Theme Updated and Miscellaneous Code</title>
		<link>http://www.whenbrainsfly.com/2009/08/theme-updated/</link>
		<comments>http://www.whenbrainsfly.com/2009/08/theme-updated/#comments</comments>
		<pubDate>Sat, 22 Aug 2009 05:34:33 +0000</pubDate>
		<dc:creator>Ryan</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[admin]]></category>
		<category><![CDATA[java]]></category>
		<category><![CDATA[unix]]></category>

		<guid isPermaLink="false">http://www.whenbrainsfly.com/?p=131</guid>
		<description><![CDATA[I wasn&#8217;t really liking the Brain Power theme anymore, so I decided to make my own using the handy-dandy WordPress Theme Generator and then tweaked the details to my liking. It looks better now, in my opinion.
Hopefully these changes plus the smackdown on spam will encourage me to blog some more. (Comments will still be [...]]]></description>
			<content:encoded><![CDATA[<p>I wasn&#8217;t really liking the Brain Power theme anymore, so I decided to make my own using the handy-dandy <a href="http://www.yvoschaap.com/wpthemegen/">WordPress Theme Generator</a> and then tweaked the details to my liking. It looks better now, in my opinion.</p>
<p>Hopefully these changes plus the smackdown on spam will encourage me to blog some more. (Comments will still be moderated until I am sure spam is under control.)</p>
<p>Now for some miscellaneous things:</p>
<p>In the meantime, for my reference, I like to keep two aliases for my bash shell:</p>
<pre>
alias ll='ls -l'
alias ls='ls -aG' # for the BSD ls
alias ls='ls -a --color=auto' # for the GNU ls
</pre>
<p>I also like to change the default color for directories (blue) to cyan when in BSD (cyan foreground not otherwise used) so that I can see it better.</p>
<pre>
export LSCOLORS="gxfxcxdxbxegedabagacad"
</pre>
<p>In GNU ls, there is a different method and cyan is used for symbolic links, so rather than have two different colors for directories, which I see far more often than symbolic links, let&#8217;s change the directory color to blue and symbolic link color to yellow:</p>
<p>&#8212;-I&#8217;ll finish this up soon&#8212;-</p>
<p>For compiling a Java program using Cygwin and including the jxl.jar library (typical bin, lib, src setup):</p>
<pre>
#!/bin/bash
javac -cp `cygpath -wp lib/jxl.jar:.` -d bin $(find src -name '*.java')
</pre>
<p>For running a Java program using Cygwin and including the jxl.jar library (two parameters passed):</p>
<pre>
#!/bin/bash
java -cp `cygpath -wp lib/jxl.jar:src/:.` main.class.Name $1 $2
</pre>
<p>For running the above Java program on a Mac without the Mac top menu bar and with a specified dock name:</p>
<pre>
#!/bin/bash
java -cp lib/jxl.jar:src/:. -Dapple.laf.useScreenMenuBar=true
-Xdock:name="Program Name" main.class.Name $1 $2
</pre>
<p>Note to self: &lt;pre&gt; tags do not have word wrap. Consider using a special scrollable text field or plugin for displaying code.</p>
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		</item>
		<item>
		<title>Whoo! WordPress Upgraded and Akismet Installed</title>
		<link>http://www.whenbrainsfly.com/2009/08/whoo-wordpress-upgraded-and-akismet-installed/</link>
		<comments>http://www.whenbrainsfly.com/2009/08/whoo-wordpress-upgraded-and-akismet-installed/#comments</comments>
		<pubDate>Thu, 20 Aug 2009 22:43:23 +0000</pubDate>
		<dc:creator>Ryan</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[admin]]></category>
		<category><![CDATA[spam]]></category>
		<category><![CDATA[svn]]></category>
		<category><![CDATA[wordpress]]></category>

		<guid isPermaLink="false">http://www.whenbrainsfly.com/?p=122</guid>
		<description><![CDATA[Finally, I have upgraded to WordPress 2.8.4 and installed Akismet seemingly successfully. Spam be gone! I also set up svn upgrading of WordPress so that I don&#8217;t have to do so many steps next time around.
For reference, I used:
http://codex.wordpress.org/WordPress_Backups to backup my stuff first
http://codex.wordpress.org/Upgrading_WordPress to do the upgrade
And then realizing that I could upgrade by [...]]]></description>
			<content:encoded><![CDATA[<p>Finally, I have upgraded to WordPress 2.8.4 and installed Akismet seemingly successfully. Spam be gone! I also set up svn upgrading of WordPress so that I don&#8217;t have to do so many steps next time around.</p>
<p>For reference, I used:<br />
<a href="http://codex.wordpress.org/WordPress_Backups">http://codex.wordpress.org/WordPress_Backups</a> to backup my stuff first<br />
<a href="http://codex.wordpress.org/Upgrading_WordPress">http://codex.wordpress.org/Upgrading_WordPress</a> to do the upgrade<br />
And then realizing that I could upgrade by svn, I used <a href="http://codex.wordpress.org/Installing/Updating_WordPress_with_Subversion">http://codex.wordpress.org/Installing/Updating_WordPress_with_Subversion</a>. Very nice.</p>
<p>Update: It has been nearly 24 hours and I have gotten no spam comments to moderate in my inbox. Akismet caught 8 of them. Thank goodness. That was really annoying to see a new email every couple hours only to realize that it is spam. Kinda makes me really appreciate Gmail&#8217;s spam filter, even though it has screwed up somewhat majorly once.</p>
<p>Edit (2009-12-15):<br />
To upgrade to the latest stable version of wordpress via svn, run the following command from /home/public/ (assuming 2.8.6 is the latest stable version):</p>
<pre>svn sw http://core.svn.wordpress.org/tags/2.8.6/ . </pre>
<p>and then go to <a href="http://www.whenbrainsfly.com/wp-admin/upgrade.php">http://www.whenbrainsfly.com/wp-admin/upgrade.php</a></p>
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		</item>
		<item>
		<title>Usefulness</title>
		<link>http://www.whenbrainsfly.com/2009/07/usefulness/</link>
		<comments>http://www.whenbrainsfly.com/2009/07/usefulness/#comments</comments>
		<pubDate>Fri, 31 Jul 2009 20:55:37 +0000</pubDate>
		<dc:creator>Ryan</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[admin]]></category>
		<category><![CDATA[remote desktop]]></category>
		<category><![CDATA[spam]]></category>

		<guid isPermaLink="false">http://www.whenbrainsfly.com/?p=119</guid>
		<description><![CDATA[I think this blog has paid off! I&#8217;ve used what I wrote in this post on remote desktop many times already because I just can&#8217;t remember how to do it right whenever working with a new mac. Plus, it is now the first result when you google &#8220;remote desktop into mac os x&#8221;, even without [...]]]></description>
			<content:encoded><![CDATA[<p>I think this blog has paid off! I&#8217;ve used what I wrote in <a href="http://www.whenbrainsfly.com/2009/01/remote-desktop…d-from-windowsremote-desktop-into-mac-os-x-leopard-from-windows/">this post on remote desktop</a> many times already because I just can&#8217;t remember how to do it right whenever working with a new mac. Plus, it is now the first result when you google &#8220;remote desktop into mac os x&#8221;, even without quotes! Too bad most of the comments I get around here are spam. So far, there have been 3 real comments (I think) and 124 spam comments. Joy.</p>
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		</item>
		<item>
		<title>An Update</title>
		<link>http://www.whenbrainsfly.com/2009/06/an-update/</link>
		<comments>http://www.whenbrainsfly.com/2009/06/an-update/#comments</comments>
		<pubDate>Thu, 25 Jun 2009 22:18:45 +0000</pubDate>
		<dc:creator>Ryan</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[admin]]></category>

		<guid isPermaLink="false">http://www.whenbrainsfly.com/2009/06/an-update/</guid>
		<description><![CDATA[OMG Why do I get so much spam and no real comments?! Ugh. 
Anyway. 
TODO list for this site: 

update blogroll
maybe change the images
make link to comments more visible from front page (e.g. at end of post)
update biographical info
add $$ to web hosting account
make text less wide looking
add adsense?
Make top links more distinctive or move [...]]]></description>
			<content:encoded><![CDATA[<p>OMG Why do I get so much spam and no real comments?! Ugh. </p>
<p>Anyway. </p>
<p>TODO list for this site: </p>
<ul>
<li>update blogroll</li>
<li>maybe change the images</li>
<li>make link to comments more visible from front page (e.g. at end of post)</li>
<li>update biographical info</li>
<li>add $$ to web hosting account</li>
<li>make text less wide looking</li>
<li>add adsense?</li>
<li>Make top links more distinctive or move them to the right side</li>
<li>make lists not indent so much within a post</li>
</ul>
]]></content:encoded>
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		</item>
		<item>
		<title>Switch to WordPress</title>
		<link>http://www.whenbrainsfly.com/2009/01/switch-to-wordpress/</link>
		<comments>http://www.whenbrainsfly.com/2009/01/switch-to-wordpress/#comments</comments>
		<pubDate>Wed, 14 Jan 2009 19:25:00 +0000</pubDate>
		<dc:creator>Ryan</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[admin]]></category>
		<category><![CDATA[tutorial]]></category>
		<category><![CDATA[wordpress]]></category>

		<guid isPermaLink="false">http://www.whenbrainsfly.com/?p=30</guid>
		<description><![CDATA[After using Movable Type for an hour or so and trying to customize it, I found it to be irritatingly slow. I tried installing the Open Source version, but it was not much faster. It would take around 30 seconds to publish and 20 seconds to go to a different admin page, which got really [...]]]></description>
			<content:encoded><![CDATA[<p>After using Movable Type for an hour or so and trying to customize it, I found it to be irritatingly slow. I tried installing the Open Source version, but it was not much faster. It would take around 30 seconds to publish and 20 seconds to go to a different admin page, which got really frustrating after a while, especially after installing Movable Type four times (see <a href="http://www.whenbrainsfly.com/2009/01/installing-movable-type/">previous post</a>). </p>
<p>So, I decided to switch to WordPress, one of the other two popular blogging applications (the other being Blogger). The install was very simple and very fast. For my reference and yours, here is what I did:</p>
<p>First, I created a MySQL database called wordpress. Then, I downloaded <code>latest.tar.gz</code> from the <a href="http://wordpress.org/download/">WordPress website</a> onto my web server. Next, I unzipped that file and moved all of its contents to <code>/home/public/</code>. Then, I copied the file <code>config-sample.php</code> to <code>config.php</code>, and in <code>config.php</code>, I entered my database information and put in four security keys randomly generated from <a href="http://api.wordpress.org/secret-key/1.1/">the wordpress random key generator</a>. Finally, I opened a web browser and went to <code>wp-admin/install.php</code> where I entered a name for my blog and my email address, hit continue, and then I was done! Amazing.</p>
<p>I ran into some early problems with permissions, such as uploaded images not appearing. So I changed the group of all of the files in <code>/home/public</code> to web, changed all file permissions to 644 so my web server could write to them, and changed the permissions for <code>/home/public/wp-content/</code> and <code>/home/public/wp-content/uploads</code> to 775 so that my web server could put my uploaded files in the uploads directory. I think that was it.</p>
<p>Finally, I searched for a brainy WordPress theme and first found <a href="http://www.harrr.org/rrr/bigbluebrain-theme/">Big Blue Brain Theme</a> but later found <a href="http://wordpress.org/extend/themes/brain-power#post-534">Brain Power Theme</a>, which is an awesome theme. I tweaked it in many places to make spacing, color, and other little things nicer to me, and this modified theme is what is currently styling this site. I hope you like it too!</p>
<p>WordPress is not lightning fast, but not agonizingly slow either, so I think I&#8217;ll stick with it. Plus, this theme rocks!</p>
<p>Reference:<br />
<a href="http://codex.wordpress.org/Installing_WordPress">http://codex.wordpress.org/Installing_WordPress</a></p>
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		<item>
		<title>Installing Movable Type</title>
		<link>http://www.whenbrainsfly.com/2009/01/installing-movable-type/</link>
		<comments>http://www.whenbrainsfly.com/2009/01/installing-movable-type/#comments</comments>
		<pubDate>Wed, 14 Jan 2009 03:55:36 +0000</pubDate>
		<dc:creator>Ryan</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[admin]]></category>
		<category><![CDATA[movable type]]></category>
		<category><![CDATA[nfsn]]></category>
		<category><![CDATA[tutorial]]></category>

		<guid isPermaLink="false">http://www.whenbrainsfly.com/?p=22</guid>
		<description><![CDATA[Installing Movable Type is pretty simple. Unfortunately, I still messed it up, multiple times. So, for my reference and for yours, here are the steps to installing Movable Type on my web server.
This site is hosted on NearlyFreeSpeech.NET (NFSN), which is an awesome, pay-for-what-you-use hoster. It already has the right PHP and Perl things installed [...]]]></description>
			<content:encoded><![CDATA[<p>Installing Movable Type is pretty simple. Unfortunately, I still messed it up, multiple times. So, for my reference and for yours, here are the steps to installing Movable Type on my web server.</p>
<p>This site is hosted on <a href="http://nearlyfreespeech.net/">NearlyFreeSpeech.NET</a> (NFSN), which is an awesome, pay-for-what-you-use hoster. It already has the right PHP and Perl things installed for Movable Type. Since I recently made this site, I had no MySQL databases yet, so first, I created a MySQL process via the NFSN admin pages and then made a database named &#8220;movabletype.&#8221;</p>
<p>Next, I downloaded the file <code>MT-4.23-en.tar.gz</code> onto my computer from the <a href="http://www.movabletype.com/download/">Movable Type Download Page</a> under Movable Type Pro for Bloggers. (Note: the version offered at <a href="http://movabletype.org/">their .org website</a> offers their open source version for developers, which is different.) </p>
<p>Then, since unzipping the file and copying its contents to the web server was taking too long, I aborted that and scp&#8217;d <code>MT-4.23-en.tar.gz</code> from my computer to my root web directory of my web server, <code>/home/public/</code>. (Note: I am running Windows with Cygwin installed.) I then ssh&#8217;d into the web server and unzipped the file there. </p>
<p>I then made the directory mt in <code>/home/public</code>, and based on some suggestion from somewhere, I moved mt-static out of <code>/home/public/MT-4.23-en</code> (which was just created) to <code>/home/public/</code> and copied all of the other contents of <code>MT-4.23-en/</code> into <code>mt/</code>. </p>
<p>Next, I changed the group of mt to web, changed permissions of <code>mt-static/support</code> to 777, and removed the empty directory <code>MT-4.23-en</code>.</p>
<p>Then, I opened <code>http://www.whenbrainsfly.com/mt/mt.cgi</code> in my browser and began the installation wizard. I entered <code>/mt-static</code> as the static web path and hit continue. My web server&#8217;s PHP and Perl requirements checked out so I hit continue. At the Database Configuration prompt, I changed the database server from <code>localhost</code> to <code>my_mysql_process_name.db</code> because NFSN requires it, entered the other database info, and hit continue. At the next prompt, the Mail Configuration prompt, I selected sendmail, put in the path to it, <code>/usr/bin/sendmail/</code>, sent a test email, received the test email, and hit continue. The configuration file was successfully created so I hit continue there, and the configuration was finished!</p>
<p>Finally, I created an account, named my website, <code>chgrp web /home/public</code> so that my web server could write to it, told the prompt that I wanted my site at <code>/home/public</code>, selected the Professional Website theme, hit continue, and it was all done!</p>
<p>I then signed in and made my first post! =)</p>
<p>Sadly, this took me four times to get right.</p>
<p>The first time, I made the directory <code>/home/public/blog</code> and told Movable Type that I wanted my site there, not realizing that Movable Type is also a full-fledged Content Management System and that it would create a subdirectory called blog within <code>/home/public/blog</code> where my blog would lie.</p>
<p>The second time, I forgot to drop the movabletype MySQL database.</p>
<p>The third time, I got an error saying that my web server could not write to <code>/home/public/</code> which was true at the time. So, I chgrp&#8217;d it and continued, but the style changed to something other than Professional Website. I&#8217;m pretty sure I had changed it, so maybe this is a bug in Movable Type. I tried changing the style afterward but after selecting the Professional Blue style and publishing, the site was obviously missing elements and not how it was supposed to look. </p>
<p>The fourth time, I thought I had failed yet again because after the last step, I went to <code>http://www.whenbrainsfly.com</code> and got a 404. I thought that maybe if I wrote a post, it would appear, and sure enough, it did after saving my first entry.</p>
<p>References:<br />
<a href="http://www.movabletype.org/documentation/installation/quick-start.html">http://www.movabletype.org/documentation/installation/quick-start.html</a><br />
<a href="http://www.movabletype.org/documentation/installation/detailed-instructions.html">http://www.movabletype.org/documentation/installation/detailed-instructions.html</a><br />
<a href="http://www.superxm.com/2007/08/movable-type-4-installation-step-by-step-with-screenshots.html">http://www.superxm.com/2007/08/movable-type-4-installation-step-by-step-with-screenshots.html</a></p>
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		<item>
		<title>Hello, World!</title>
		<link>http://www.whenbrainsfly.com/2009/01/hello-world-2/</link>
		<comments>http://www.whenbrainsfly.com/2009/01/hello-world-2/#comments</comments>
		<pubDate>Tue, 13 Jan 2009 03:49:03 +0000</pubDate>
		<dc:creator>Ryan</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[admin]]></category>

		<guid isPermaLink="false">http://www.whenbrainsfly.com/?p=3</guid>
		<description><![CDATA[Hello, world!
]]></description>
			<content:encoded><![CDATA[<p>Hello, world!</p>
]]></content:encoded>
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		<slash:comments>2</slash:comments>
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