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	<title>scipher</title>
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	<link>http://scipher.wordpress.com</link>
	<description>a science blog</description>
	<lastBuildDate>Fri, 09 Dec 2011 20:06:54 +0000</lastBuildDate>
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		<title>scipher</title>
		<link>http://scipher.wordpress.com</link>
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		<title>Evolution and gravity: theory? fact? law? Or: Why Ron Paul and other politicians must stop crying &#8216;theory&#8217;!</title>
		<link>http://scipher.wordpress.com/2011/12/08/evolution-and-gravity-theory-fact-law-or-why-ron-paul-and-other-politicians-must-stop-crying-theory/</link>
		<comments>http://scipher.wordpress.com/2011/12/08/evolution-and-gravity-theory-fact-law-or-why-ron-paul-and-other-politicians-must-stop-crying-theory/#comments</comments>
		<pubDate>Thu, 08 Dec 2011 19:58:00 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Background Science]]></category>
		<category><![CDATA[Current Science Events]]></category>
		<category><![CDATA[Other]]></category>
		<category><![CDATA[evolution]]></category>
		<category><![CDATA[fact]]></category>
		<category><![CDATA[gravity]]></category>
		<category><![CDATA[hypothesis]]></category>
		<category><![CDATA[just a theory]]></category>
		<category><![CDATA[law]]></category>
		<category><![CDATA[politicians]]></category>
		<category><![CDATA[Ron Paul]]></category>
		<category><![CDATA[science education]]></category>
		<category><![CDATA[theory]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=202</guid>
		<description><![CDATA[Background and Significance: Recently, a pretty old YouTube clip of Ron Paul explaining that he does not accept the &#8220;theory of evolution&#8221; showed up in my Facebook feed.   It was posted by the Secular Student Alliance and provoked quite a bit of debate in the comments.  The video is from late 2007 and the relevant question posed to Paul was <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=202&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2011/12/08/evolution-and-gravity-theory-fact-law-or-why-ron-paul-and-other-politicians-must-stop-crying-theory/feed/</wfw:commentRss>
		<slash:comments>2</slash:comments>
	
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		<title>siniXster&#8217;s cloaked spaceship hypothesis</title>
		<link>http://scipher.wordpress.com/2011/12/08/sinixsters-cloaked-spaceship-hypothesis/</link>
		<comments>http://scipher.wordpress.com/2011/12/08/sinixsters-cloaked-spaceship-hypothesis/#comments</comments>
		<pubDate>Thu, 08 Dec 2011 14:12:00 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Current Science Events]]></category>
		<category><![CDATA[Other]]></category>
		<category><![CDATA[Science Coverage in the News]]></category>
		<category><![CDATA[CME]]></category>
		<category><![CDATA[conspiracy theories]]></category>
		<category><![CDATA[coronal mass ejection]]></category>
		<category><![CDATA[current events]]></category>
		<category><![CDATA[Mercury]]></category>
		<category><![CDATA[skepticism]]></category>
		<category><![CDATA[UFO]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=254</guid>
		<description><![CDATA[Said the tin-foil-hat-wearing,  little-grey-men otaku (siniXster) of the coronal mass ejection (CME) as it passed Mercury and &#8220;seemed&#8221; to illuminate a near by object: &#8220;It&#8217;s cylindrical on either side and has a shape in the middle. It definitely looks like a ship to me, and very obviously, it&#8217;s cloaked&#8230;&#8221; Before I continue: for a much <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=254&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2011/12/08/sinixsters-cloaked-spaceship-hypothesis/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
	
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		<title>Simple Sliding Window Iterator in Python</title>
		<link>http://scipher.wordpress.com/2010/12/02/simple-sliding-window-iterator-in-python/</link>
		<comments>http://scipher.wordpress.com/2010/12/02/simple-sliding-window-iterator-in-python/#comments</comments>
		<pubDate>Thu, 02 Dec 2010 05:50:22 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Python]]></category>
		<category><![CDATA[bioinformatics]]></category>
		<category><![CDATA[git repo]]></category>
		<category><![CDATA[python]]></category>
		<category><![CDATA[sliding window]]></category>
		<category><![CDATA[transcription factor binding sites]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=175</guid>
		<description><![CDATA[A common task encountered in bioinformatics is the need to process a sequence bit-by-bit, sometimes with overlapping regions.  I have provided an example of a very simple; easy to extend; and stand-alone python iterator that returns a single defined window of any python string object per iteration to allow simple, intuitive handling of sliding window <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=175&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2010/12/02/simple-sliding-window-iterator-in-python/feed/</wfw:commentRss>
		<slash:comments>12</slash:comments>
	
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			<media:title type="html">xguse</media:title>
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			<media:title type="html">Crystal_Clear_mimetype_source_py</media:title>
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		<item>
		<title>SciPlore: Mind-mapping for academic writing</title>
		<link>http://scipher.wordpress.com/2010/09/03/sciplore-mind-mapping-for-academic-writing/</link>
		<comments>http://scipher.wordpress.com/2010/09/03/sciplore-mind-mapping-for-academic-writing/#comments</comments>
		<pubDate>Fri, 03 Sep 2010 18:38:08 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Nerd Awesome]]></category>
		<category><![CDATA[free]]></category>
		<category><![CDATA[mind maps]]></category>
		<category><![CDATA[reference management]]></category>
		<category><![CDATA[software]]></category>
		<category><![CDATA[writing]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=159</guid>
		<description><![CDATA[As a Ph.D. student, I am constantly trying to improve my ability to communicate the findings of our lab and my work to others.  A central part of this effort in any academic setting is the composition and publishing of scholarly articles and presentations.  One of the keys to a great paper or presentation (other <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=159&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2010/09/03/sciplore-mind-mapping-for-academic-writing/feed/</wfw:commentRss>
		<slash:comments>3</slash:comments>
	
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			<media:title type="html">xguse</media:title>
		</media:content>

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			<media:title type="html">SciPloreIcon</media:title>
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	</item>
		<item>
		<title>Sgt. John McCary: Tribute to the fallen.</title>
		<link>http://scipher.wordpress.com/2010/06/01/sgt-john-mccary-tribute-to-the-fallen/</link>
		<comments>http://scipher.wordpress.com/2010/06/01/sgt-john-mccary-tribute-to-the-fallen/#comments</comments>
		<pubDate>Tue, 01 Jun 2010 17:50:02 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Other]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=148</guid>
		<description><![CDATA[I was just listening to Wisconsin Public Radio&#8217;s To The Best of Our Knowledge, a great podcast/radio show (if you can get it in your area) that takes an hour each week to examine topics from whether Shakespeare is still relevant to high energy physics to something as &#8220;simple&#8221; as salt.  And they make it astonishingly interesting.  Like to the point where <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=148&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2010/06/01/sgt-john-mccary-tribute-to-the-fallen/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
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			<media:title type="html">xguse</media:title>
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		<title>A biologist&#8217;s Mother&#8217;s Day musical tribute</title>
		<link>http://scipher.wordpress.com/2010/05/11/a-biologists-mothers-day-musical-tribute/</link>
		<comments>http://scipher.wordpress.com/2010/05/11/a-biologists-mothers-day-musical-tribute/#comments</comments>
		<pubDate>Tue, 11 May 2010 17:28:40 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Nerd Awesome]]></category>
		<category><![CDATA[mother's day]]></category>
		<category><![CDATA[nerd awesome]]></category>
		<category><![CDATA[pz]]></category>
		<category><![CDATA[video]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=141</guid>
		<description><![CDATA[So I do know that its a bit late for Mother&#8217;s Day but I just ran across the most adorable musical tribute to moms and had to post it.  As PZ warns (which is where I found it), this is MASSIVELY chock full of nerd power.  So try not to be too embarrassed when you realize that you really <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=141&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2010/05/11/a-biologists-mothers-day-musical-tribute/feed/</wfw:commentRss>
		<slash:comments>1</slash:comments>
	
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		<item>
		<title>Setting Your PYTHONPATH environment variable (Linux/Unix/OsX)</title>
		<link>http://scipher.wordpress.com/2010/05/10/setting-your-pythonpath-environment-variable-linuxunixosx/</link>
		<comments>http://scipher.wordpress.com/2010/05/10/setting-your-pythonpath-environment-variable-linuxunixosx/#comments</comments>
		<pubDate>Mon, 10 May 2010 21:04:28 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Python]]></category>
		<category><![CDATA[environment variables]]></category>
		<category><![CDATA[python]]></category>
		<category><![CDATA[PYTHONPATH]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=123</guid>
		<description><![CDATA[Environment variables are lovely little shortcuts that your system uses to give many programs the ability to find certain shared resources easily.  In the *nix environments, these variables are set up for you when you log in to your terminal.  In order to customize these, you will need to modify a little shell script that <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=123&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2010/05/10/setting-your-pythonpath-environment-variable-linuxunixosx/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
	
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			<media:title type="html">xguse</media:title>
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		<item>
		<title>Simple Python FastQ Parser</title>
		<link>http://scipher.wordpress.com/2010/05/06/simple-python-fastq-parser/</link>
		<comments>http://scipher.wordpress.com/2010/05/06/simple-python-fastq-parser/#comments</comments>
		<pubDate>Thu, 06 May 2010 18:02:48 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Python]]></category>
		<category><![CDATA[bioinformatics]]></category>
		<category><![CDATA[fastq]]></category>
		<category><![CDATA[github]]></category>
		<category><![CDATA[high-throughput sequencing]]></category>
		<category><![CDATA[python]]></category>
		<category><![CDATA[solexa]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=92</guid>
		<description><![CDATA[UPDATED (Tue Sep  7 09:51:46 PDT 2010) High-throughput sequencing (HTS) is rapidly advancing our ability to understand how the genome responds to its environment.  It also presents a challenge to those tasked with analyzing the results.  Massive files can be produced that can overwhelm a modest computer&#8217;s store of available memory.  The simplest way around this problem is to only <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=92&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2010/05/06/simple-python-fastq-parser/feed/</wfw:commentRss>
		<slash:comments>8</slash:comments>
	
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			<media:title type="html">xguse</media:title>
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			<media:title type="html">Crystal_Clear_mimetype_source_py</media:title>
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		<title>Researching a Scientific Topic</title>
		<link>http://scipher.wordpress.com/2010/05/02/researching-a-scientific-topic/</link>
		<comments>http://scipher.wordpress.com/2010/05/02/researching-a-scientific-topic/#comments</comments>
		<pubDate>Sun, 02 May 2010 18:44:10 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Other]]></category>
		<category><![CDATA[pubmed]]></category>
		<category><![CDATA[research]]></category>
		<category><![CDATA[tutorial]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/?p=73</guid>
		<description><![CDATA[A friend of mine recently asked me what types of resources I used to read up on and explore areas of science that I might be studying or planing to delve into with more focus. I remember how she feels. It can be quite daunting to stare at the screen and wonder, &#8220;where do I <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=73&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2010/05/02/researching-a-scientific-topic/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
	
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			<media:title type="html">xguse</media:title>
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			<media:title type="html">800px-Old_book_bindings</media:title>
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			<media:title type="html">hubble10-google</media:title>
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			<media:title type="html">pubmed</media:title>
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		<title>Baldwin&#8217;s &#8220;These are not negotiable&#8221;</title>
		<link>http://scipher.wordpress.com/2009/10/14/baldwins-these-are-not-negotiable/</link>
		<comments>http://scipher.wordpress.com/2009/10/14/baldwins-these-are-not-negotiable/#comments</comments>
		<pubDate>Wed, 14 Oct 2009 16:58:59 +0000</pubDate>
		<dc:creator>xguse</dc:creator>
				<category><![CDATA[Other]]></category>
		<category><![CDATA[politics]]></category>
		<category><![CDATA[vaccines]]></category>

		<guid isPermaLink="false">http://scipher.wordpress.com/2009/10/14/baldwins-these-are-not-negotiable/</guid>
		<description><![CDATA[A very dear friend of mine posted an essay by Chuck Baldwin, a politician, pastor, and radio personality titled &#8220;These are not negotiable&#8220;.  I do not exactly belong to the same school of thought as the essay&#8217;s author, so I tried to compose a response to the essay.  I have posted a version of the <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=scipher.wordpress.com&amp;blog=1213071&amp;post=46&amp;subd=scipher&amp;ref=&amp;feed=1" width="1" height="1" />]]></description>
		<wfw:commentRss>http://scipher.wordpress.com/2009/10/14/baldwins-these-are-not-negotiable/feed/</wfw:commentRss>
		<slash:comments>3</slash:comments>
	
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