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	<title>Biohaskell</title>
	<link>http://blog.malde.org</link>
	<description>bioinformatics and haskell</description>
	<lastBuildDate>Tue, 20 Jul 2010 15:04:58 +0000</lastBuildDate>
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	<language>en</language>
	
	<item>
		<title>Updated software versions available</title>
		<description><![CDATA[I&#8217;ve just uploaded new versions of various software to HackageDB.  If you have cabal-install on your system, it should now be possible to do e.g. cabal install flowsim to automatically download and compile the program and its dependencies.
bio-0.4.6: A bioinformatics library
The library provides functions and data structures to work with various kinds of bioinformatics data.  [...]]]></description>
		<link>http://blog.malde.org/index.php/2010/07/20/updated-software-versions-available/</link>
			</item>
	<item>
		<title>A quick count of popular Haskell libraries in Debian and Ubuntu</title>
		<description><![CDATA[Don Stewart recently posted a summary of Hackage downloads, which can be seen as a metric of a package&#8217;s popularity.  Of course, there are many other ways to acquire libraries and applications, some may prefer to get the bleeding edge right from the source repository, others prefer the comfort of their distribution&#8217;s repositories.  For the [...]]]></description>
		<link>http://blog.malde.org/index.php/2010/07/01/a-quick-count-of-popular-haskell-libraries-in-debian-and-ubuntu/</link>
			</item>
	<item>
		<title>Snagged!</title>
		<description><![CDATA[Recently, I&#8217;ve been burned by a couple of, eh, issues.  Not exactly bugs, but some hidden surprises that have taken some work to iron out.  Below I&#8217;ll make a quick writeup of symptoms, diagnoses, and remedies, in the hope that other people running into the same problems will find it useful.
Static binaries relying on iconv
Symptoms
I [...]]]></description>
		<link>http://blog.malde.org/index.php/2010/05/22/snagged/</link>
			</item>
	<item>
		<title>Tools for pyrosequencing analysis</title>
		<description><![CDATA[I recently did a brief presentation of the set of tools I&#8217;ve developed for analyzing pyrosequences (the Roche 454 variety).  Nothing spectacular, just an overview of various ways of slicing and dicing SFF files using tools written in Haskell.  For lack of a better place to put it, I&#8217;ll drop my slides below.
flowers
]]></description>
		<link>http://blog.malde.org/index.php/2010/02/19/tools-for-pyrosequencing-analysis/</link>
			</item>
	<item>
		<title>Searching for poly(A) tails</title>
		<description><![CDATA[I&#8217;m currently involved in a project where we study, among other things, the 3&#8242;UTR and poly-A tails of certain genes.  For this, is of course important to accurately identify the poly-A tail in each transcript, but I couldn&#8217;t find any program or tool to do just that.  Presumably the task is considered too [...]]]></description>
		<link>http://blog.malde.org/index.php/2009/12/14/searching-for-polya-tails/</link>
			</item>
	<item>
		<title>Installing the software on Ubuntu 9.10</title>
		<description><![CDATA[Ubuntu 9.10, nicknamed Karmic Koala, is about to be released, and in a moment of idleness, I upgraded my old 9.04 install to the latest beta.  Upgrading is always generates a slight feeling of dread,  taking the plunge from the cozy stability of bugs I&#8217;ve learned to work around, into the great unknown, but it [...]]]></description>
		<link>http://blog.malde.org/index.php/2009/10/07/installing-the-software-on-ubuntu-910/</link>
			</item>
	<item>
		<title>A (too) brief Biohaskell presentation</title>
		<description><![CDATA[I was recently in Trondheim, and got an opportunity to present Haskell to an audience of bioinformaticians.  Alas, it is hard to describe Haskell in all its glory to the uninitiated in forty-five minutes, and especially when I also wanted to talk a bit about the application to bioinformatics.  I left in the belief that [...]]]></description>
		<link>http://blog.malde.org/index.php/2009/09/15/a-too-brief-biohaskell-presentation/</link>
			</item>
	<item>
		<title>Parsing ints</title>
		<description><![CDATA[A recurring theme on the Haskell mailing lists is how to quicly parse a file consisting of integers.  Often, this comes up in the contest of benchmarking, but a real example of integer-filled files are the quality data that often accompanies Fasta sequence files.  When investigating one of my programs that seemed a bit on [...]]]></description>
		<link>http://blog.malde.org/index.php/2009/08/31/parsing-ints/</link>
			</item>
	<item>
		<title>A set of tools for working with 454 sequences</title>
		<description><![CDATA[Pyrosequencing is often referred to as next-generation sequencing (although it would be increasingly more accurate to refer to traditional Sanger sequencing as previous-generation sequencing) as it produces large amounts of sequences at lower costs.  As the technology is radically different, so are the type of data that results from it, and while it is possible [...]]]></description>
		<link>http://blog.malde.org/index.php/2009/07/03/a-set-of-tools-for-working-with-454-sequences/</link>
			</item>
	<item>
		<title>Dephd updates</title>
		<description><![CDATA[Dephd is a small application for performing various analysis of nucleotide sequences.  Originally, it was used for analyzing/converting PHD-file output from the basecaller phred, but it has since grown a bit beyond that.  A new update was just pushed onto HackageDB, this is just a quick note describing new features.
Filtering out empty sequences.
Phred often produces [...]]]></description>
		<link>http://blog.malde.org/index.php/2009/06/16/dephd-updates/</link>
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