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<channel>
	<title>michael barton</title>
	
	<link>http://www.michaelbarton.me.uk</link>
	<description>genomics, phylogenetics and molecular evolution</description>
	<lastBuildDate>Mon, 08 Mar 2010 10:00:17 +0000</lastBuildDate>
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		<title>Estimating genome scaffold order using reference genomes</title>
		<link>http://www.michaelbarton.me.uk/2010/03/estimating-genome-scaffold-order-using-reference-genomes/</link>
		<comments>http://www.michaelbarton.me.uk/2010/03/estimating-genome-scaffold-order-using-reference-genomes/#comments</comments>
		<pubDate>Mon, 08 Mar 2010 10:00:17 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[genomics]]></category>
		<category><![CDATA[results]]></category>
		<category><![CDATA[mummer]]></category>
		<category><![CDATA[nucmer]]></category>
		<category><![CDATA[R124]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=163</guid>
		<description><![CDATA[The P. fluorescens genome sequencing results arrived last week and so far I&#8217;ve been looking at how we can begin to assemble the scaffolds from the smaller of the two genomes R124 into a complete draft. The are small holes in the scaffolds which we will PCR across but the harder task is cross the [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2010/03/estimating-genome-scaffold-order-using-reference-genomes/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Find repeating N regions in a fasta file with bioruby</title>
		<link>http://www.michaelbarton.me.uk/2010/03/find-repeating-n-regions-in-a-fasta-file-with-bioruby/</link>
		<comments>http://www.michaelbarton.me.uk/2010/03/find-repeating-n-regions-in-a-fasta-file-with-bioruby/#comments</comments>
		<pubDate>Wed, 03 Mar 2010 10:00:47 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[code]]></category>
		<category><![CDATA[methods]]></category>
		<category><![CDATA[bioruby]]></category>
		<category><![CDATA[contigs]]></category>
		<category><![CDATA[gaps]]></category>
		<category><![CDATA[Ruby]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=151</guid>
		<description><![CDATA[Useful for designing primers to PCR across gaps in genome contigs

]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2010/03/find-repeating-n-regions-in-a-fasta-file-with-bioruby/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>First look at Pseudomonas fluorescens sequencing results</title>
		<link>http://www.michaelbarton.me.uk/2010/03/pseudomonas-fluorescens-sequencing-results/</link>
		<comments>http://www.michaelbarton.me.uk/2010/03/pseudomonas-fluorescens-sequencing-results/#comments</comments>
		<pubDate>Mon, 01 Mar 2010 10:00:07 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[results]]></category>
		<category><![CDATA[454]]></category>
		<category><![CDATA[assembly]]></category>
		<category><![CDATA[fluorescens]]></category>
		<category><![CDATA[genome size]]></category>
		<category><![CDATA[sequencing]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=131</guid>
		<description><![CDATA[We have received the 454 results for our two samples thanks to the University of Kentucky AGCT sequencing centre. The genomes sequenced were P. fluorescens isolates, R124 and KY485, cultured from two separate caves sites. The relationships of these cave strains to other P.fluorescens strains is shown below in the phylogenetic tree constructed from a [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2010/03/pseudomonas-fluorescens-sequencing-results/feed/</wfw:commentRss>
		<slash:comments>3</slash:comments>
		</item>
		<item>
		<title>Querying pubmed on the command line</title>
		<link>http://www.michaelbarton.me.uk/2010/02/querying-pubmed-on-the-command-line/</link>
		<comments>http://www.michaelbarton.me.uk/2010/02/querying-pubmed-on-the-command-line/#comments</comments>
		<pubDate>Mon, 22 Feb 2010 10:00:14 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[methods]]></category>
		<category><![CDATA[bioruby]]></category>
		<category><![CDATA[boson]]></category>
		<category><![CDATA[pubmed]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=122</guid>
		<description><![CDATA[I&#8217;ve had to read a lot of papers since I&#8217;ve started my post-doc. Something that particularly bothers me is that it takes rather a lot of effort to get the pubmed record for interesting references in the paper I&#8217;m reading. I&#8217;m annoyed by the effort it takes to refine pubmed queries to find the specific [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2010/02/querying-pubmed-on-the-command-line/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>A combined approach to genome sequencing</title>
		<link>http://www.michaelbarton.me.uk/2010/02/a-combined-approach-to-genome-sequencing/</link>
		<comments>http://www.michaelbarton.me.uk/2010/02/a-combined-approach-to-genome-sequencing/#comments</comments>
		<pubDate>Mon, 15 Feb 2010 09:30:01 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[future-work]]></category>
		<category><![CDATA[genomics]]></category>
		<category><![CDATA[methods]]></category>
		<category><![CDATA[post doc]]></category>
		<category><![CDATA[research]]></category>
		<category><![CDATA[454]]></category>
		<category><![CDATA[AB SOLiD]]></category>
		<category><![CDATA[comparative]]></category>
		<category><![CDATA[de novo]]></category>
		<category><![CDATA[fluorescens]]></category>
		<category><![CDATA[sequencing]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=116</guid>
		<description><![CDATA[The aim of this research project is to sequence the genomes of four Pseudomonas fluorescens isolates from two different cave environments. The resulting genome sequences will allow us to estimate of the selective pressure on the same species in two caves and then understand the overall selection pressures in nutrient starved caves. The additional P. [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2010/02/a-combined-approach-to-genome-sequencing/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Adapting to generating my own data</title>
		<link>http://www.michaelbarton.me.uk/2010/02/adapting-to-generating-my-own-data/</link>
		<comments>http://www.michaelbarton.me.uk/2010/02/adapting-to-generating-my-own-data/#comments</comments>
		<pubDate>Thu, 11 Feb 2010 09:30:57 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[genomics]]></category>
		<category><![CDATA[planning]]></category>
		<category><![CDATA[post doc]]></category>
		<category><![CDATA[research]]></category>
		<category><![CDATA[454]]></category>
		<category><![CDATA[fluorescens]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=108</guid>
		<description><![CDATA[I&#8217;ve spent the last five years as a computational scientist and my research begins with pulling data out of files. I&#8217;m far removed from the laboratories that generated the data in the first place. This past month however I&#8217;ve had to learn and decide about producing enough data to generate a complete genome. Prior to [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2010/02/adapting-to-generating-my-own-data/feed/</wfw:commentRss>
		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>Genomics in a small microbiology lab</title>
		<link>http://www.michaelbarton.me.uk/2010/01/genomics-in-a-small-microbiology-lab/</link>
		<comments>http://www.michaelbarton.me.uk/2010/01/genomics-in-a-small-microbiology-lab/#comments</comments>
		<pubDate>Tue, 05 Jan 2010 09:30:22 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[post doc]]></category>
		<category><![CDATA[research]]></category>
		<category><![CDATA[bioinformatics]]></category>
		<category><![CDATA[ec2]]></category>
		<category><![CDATA[on demand computing]]></category>
		<category><![CDATA[sequencing]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=102</guid>
		<description><![CDATA[My post-doc is doing genomics of micro-organisms from starved cave environments. Several universities in the Kentucky area have banded together to get a sequencer which allows a small microbiology lab like ourselves to do sequencing for a few thousand dollars. The biology department here doesn&#8217;t have the dedicated computing cluster required for genomic assembly and [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2010/01/genomics-in-a-small-microbiology-lab/feed/</wfw:commentRss>
		<slash:comments>3</slash:comments>
		</item>
		<item>
		<title>Deciding what genomes to sequence</title>
		<link>http://www.michaelbarton.me.uk/2009/12/deciding-what-genomes-to-sequence/</link>
		<comments>http://www.michaelbarton.me.uk/2009/12/deciding-what-genomes-to-sequence/#comments</comments>
		<pubDate>Tue, 22 Dec 2009 14:32:30 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=99</guid>
		<description><![CDATA[﻿﻿﻿﻿
We&#8217;re aiming to sequence three genomes from three different cave environments, where each cave differs in the degree of nutrient starvation. We will sequence P. fluorescens isolates from each cave and examine how the genomes have adapted to the starved cave environments compared with the available genomes of P. fluorescens from soil or plants.
We&#8217;ll be [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2009/12/deciding-what-genomes-to-sequence/feed/</wfw:commentRss>
		<slash:comments>4</slash:comments>
		</item>
		<item>
		<title>Starting a new post doc at NKU</title>
		<link>http://www.michaelbarton.me.uk/2009/12/starting-a-new-post-doc-at-nku/</link>
		<comments>http://www.michaelbarton.me.uk/2009/12/starting-a-new-post-doc-at-nku/#comments</comments>
		<pubDate>Tue, 15 Dec 2009 09:30:57 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[career]]></category>
		<category><![CDATA[new job]]></category>
		<category><![CDATA[nku]]></category>
		<category><![CDATA[post doc]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=90</guid>
		<description><![CDATA[Two weeks ago I started my new job as a post-doctoral researcher at Northern Kentucky University. I&#8217;ll be working in the Barton geomicrobiology lab doing bioinformatics. I&#8217;m looking forward to being a bioinformatician in a microbiology laboratory and I think the combination of computation and wet skills in the lab complement each other.
I&#8217;ll be working [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2009/12/starting-a-new-post-doc-at-nku/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>ActiveRecord and extremely large tables or queries</title>
		<link>http://www.michaelbarton.me.uk/2008/10/activerecord-and-extremely-large-tables-or-queries/</link>
		<comments>http://www.michaelbarton.me.uk/2008/10/activerecord-and-extremely-large-tables-or-queries/#comments</comments>
		<pubDate>Sun, 12 Oct 2008 16:43:18 +0000</pubDate>
		<dc:creator>Mike</dc:creator>
				<category><![CDATA[methods]]></category>
		<category><![CDATA[activerecord]]></category>
		<category><![CDATA[database]]></category>
		<category><![CDATA[large datasets]]></category>
		<category><![CDATA[mysql]]></category>
		<category><![CDATA[rails]]></category>
		<category><![CDATA[Ruby]]></category>

		<guid isPermaLink="false">http://www.michaelbarton.me.uk/?p=69</guid>
		<description><![CDATA[Using larger and larger datasets, ActiveRecord has performance problems when trying to iterate over the data. Consider this simple example to iterate over a table of genes, and print out the name of each. This is an common use case for accessing database rows.
Gene.all.each {&#124;gene&#124; puts gene.name}

Unfortunately, if the gene table contains millions of rows, [...]]]></description>
		<wfw:commentRss>http://www.michaelbarton.me.uk/2008/10/activerecord-and-extremely-large-tables-or-queries/feed/</wfw:commentRss>
		<slash:comments>3</slash:comments>
		</item>
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