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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/4193?offset=1200</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/12288/genomic-medicine-bruce-korf-2014</guid>
	<pubDate>Tue, 24 Jun 2014 07:58:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/12288/genomic-medicine-bruce-korf-2014</link>
	<title><![CDATA[Genomic Medicine - Bruce Korf (2014)]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/FYldIrsXHKw" frameborder="0" allowfullscreen></iframe>May 21, 2014 - Current Topics in Genome Analysis 2014
A lecture series covering contemporary areas in genomics and bioinformatics. More: http://www.genome.gov/COURSE2014]]></description>
	
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/view/2379</guid>
	<pubDate>Wed, 14 Aug 2013 15:43:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/view/2379</link>
	<title><![CDATA[Which Perl distribution should I choose for bioinformatics study : ActivePerl, Strawberry Perl, DWIM Perl, Citrus Perl ?]]></title>
	<description><![CDATA[<p>I'm new to bioinformatics and recently started learning Perl. I found several rival distributions available for Windows platform, which confuse me at the begining.</p><p>I google it and found that Strawberry comes with additional dev tools to compile CPAN modules if necessary. Whereas&nbsp;ActivePerl has a lot of prepackaged modules which are easier to install with PPM. In addition,&nbsp;DWIM Perl contains the standard Perl and a lot of extension and Citrus Perl is a binary distribution of Perl created for GUI application developers.&nbsp;</p><p>Now, I wonder what should I pick to get started?&nbsp;</p><p>Note: I am going to use BioPerl in near future.</p><p>http://dwimperl.com/</p><p>http://www.activestate.com/activeperl</p><p>http://www.citrusperl.com/</p><p>http://strawberryperl.com/</p>]]></description>
	<dc:creator>Manshi Raghubanshi</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12594/faculty-positions-at-central-university-of-punjab</guid>
  <pubDate>Mon, 07 Jul 2014 23:33:33 -0500</pubDate>
  <link></link>
  <title><![CDATA[Faculty Positions at Central University of Punjab]]></title>
  <description><![CDATA[
<p>Faculty Positions: Rolling/Open Advertisement Advt.No: T-10 (2013)</p>

<p>Pay Scale: Pay Band Rs.15600-39100 with AGP of Rs.6,000/-</p>

<p>Essential Qualifications for Professors, Associate Professors, and Assistant Professors: As per “UGC REGULATIONS ON MINIMUM QUALIFICATIONS FOR APPOINTMENT OF TEACHERS AND OTHER ACADEMIC STAFF IN UNIVERSITIES AND COLLEGES AND MEASURES FOR THE MAINTENANCE OF STANDARDS IN HIGHER EDUCATION 2010“ and the 2nd Amendments to the regulation issued in June 2013.</p>

<p>For details: http://www.ugc.ac.in/oldpdf/regulations/revised_finalugcregulationfinal10.pdf http://www.ugc.ac.in/pdfnews/8539300_English.pdf and University rules.</p>

<p>Procedure to apply:</p>

<p>Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 500/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:</p>

<p>Registrar, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001</p>

<p>For more info visit: http://www.centralunipunjab.com/Teaching/Final%20Details-t10-2013.pdf, http://www.centralunipunjab.com/Teaching/Advertisement-t10-2013.jpg</p>

<p>Last Apply Date: 31 Dec 2014</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33586/genetic-mapper-svg-genetic-map-drawer</guid>
	<pubDate>Sun, 18 Jun 2017 14:11:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33586/genetic-mapper-svg-genetic-map-drawer</link>
	<title><![CDATA[Genetic-mapper: SVG Genetic Map Drawer]]></title>
	<description><![CDATA[<p><span>Genetic-mapper is a perl script able to draw publication-ready vectorial genetic maps.</span></p>
<p>Perl script for creating a publication-ready vectorial genetic/linkage map in Scalable Vector Graphics (SVG) format. The resulting file can either be submitted for publication and edited with any vectorial drawing software like&nbsp;<a href="https://inkscape.org/">Inkscape</a>&nbsp;and&nbsp;<a href="http://www.adobe.com/uk/products/illustrator.html">Abobe Illustrator(R)</a>.</p>
<p>The input file must be a text file with at least the marker name (ID), linkage group (LG) and the position (POS) separeted by tabulations. Additionally a logarithm of odds (LOD score) can be provided. Any extra parameter will be ignored.</p>
<pre><code>map.tsv

ID&lt;tab&gt;LG&lt;tab&gt;POS&lt;tab&gt;LOD
13519  12     0       0.250840894
2718   12     1.0     0.250840893
11040  12     1.6     0.252843341
...</code></pre>
<p>https://github.com/pseudogene/genetic-mapper</p><p>Address of the bookmark: <a href="https://github.com/pseudogene/genetic-mapper" rel="nofollow">https://github.com/pseudogene/genetic-mapper</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/12787/integrative-genomics-viewer-igv-tutorial</guid>
	<pubDate>Sat, 12 Jul 2014 15:16:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/12787/integrative-genomics-viewer-igv-tutorial</link>
	<title><![CDATA[Integrative Genomics Viewer (IGV) tutorial]]></title>
	<description><![CDATA[<p>The <a href="http://www.broadinstitute.org/igv/">Integrative Genomics Viewer (IGV)</a> from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.</p>
<p>http://www.broadinstitute.org/igv/</p><p>Address of the bookmark: <a href="https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial" rel="nofollow">https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/34864/installing-perl-environment-on-linux</guid>
	<pubDate>Tue, 26 Dec 2017 21:21:50 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/34864/installing-perl-environment-on-linux</link>
	<title><![CDATA[Installing Perl environment on Linux]]></title>
	<description><![CDATA[<p>By using&nbsp;<code>plenv</code>, you can easily install and switch among different version of Perl. This will be installed under your home directory in<code>~/.plenv</code>.</p><h4>Install latest Perl (with supporting multithreading) and CPANMinus.</h4><pre><code> $ cd
 $ git clone git://github.com/tokuhirom/plenv.git ~/.plenv
 $ git clone git://github.com/tokuhirom/Perl-Build.git ~/.plenv/plugins/perl-build/
 $ echo 'export PATH="$HOME/.plenv/bin:$PATH"' &gt;&gt; ~/.bashrc
 $ echo 'eval "$(plenv init -)"' &gt;&gt; ~/.bashrc
 $ source ~/.bashrc
 $ plenv install 5.18.1 -Dusethreads
 $ plenv rehash
 $ plenv global 5.18.1
 $ plenv install-cpanm
</code></pre><ul>
<li><code>git</code>&nbsp;is a distributed revision control and source code management software which can help you to download files from GitHub server.</li>
<li><code>echo</code>&nbsp;means "print".</li>
<li><code>&gt;&gt;</code>&nbsp;means adding the output into the end of the file, while&nbsp;<code>&gt;</code>&nbsp;means adding the output by overwriting the whole file. Please use<code>&gt;</code>&nbsp;with additional cares.</li>
<li>In Linux system, there are two types of outputs when you execute a command. One is called standard output (or sometimes STDOUT for short), and the other is a standard error (STDERR).&nbsp;<code>1&gt;</code>&nbsp;is for STDOUT only,&nbsp;<code>2&gt;</code>&nbsp;is for STDERR only, and&nbsp;<code>&amp;&gt;</code>means for both. In default&nbsp;<code>&gt;</code>&nbsp;is the same to&nbsp;<code>1&gt;</code>.</li>
<li><code>exec</code>&nbsp;is execution.</li>
<li>Remember to install Perl in supporting multithreading (with option&nbsp;<code>-Dusethreads</code>), which is important for many NGS analysis packages (e.g. Trinity). In this setting, you can use multiple CPU for Perl software.</li>
<li>Install the CPAN (Comprehensive Perl Archive Network) manager software, CPANMinus, by&nbsp;<code>install-cpanm</code>.</li>
</ul><p>You can use&nbsp;<code>plenv global</code>&nbsp;and&nbsp;<code>plenv local</code>&nbsp;to change the different version of Perl to fulfil different needs of your Perl software.</p><p>For example, if the&nbsp;specific version of Perl is not compatible with your script, you can switch to the different version by:</p><pre><code> $ plenv local 
</code></pre><ul>
<li>It is similar to set the local version of your script language when you use&nbsp;<code>pyenv</code>&nbsp;and&nbsp;<code>rbenv</code>&nbsp;as the following.</li>
</ul><p>Put the following path into&nbsp;<code>~/.bashrc file</code>.</p><pre><code>export PERL5LIB="$HOME/.plenv/build/perl-5.18.1/lib"
</code></pre><h4>Install BioPerl and PerlIO::gzip</h4><p>CPANMinus is a very good Perl module manager, use&nbsp;<code>cpanm</code>&nbsp;to install BioPerl can save you a lot of time. Here are some useful modules:</p><pre><code>$ cpanm Bio::Perl
$ cpanm Bio::SearchIO
$ cpanm PerlIO::gzip<br /></code></pre><p><span>For more information, please visit:&nbsp;</span><a href="https://github.com/tokuhirom/plenv">https://github.com/tokuhirom/plenv</a></p><pre><code>&nbsp;</code></pre>]]></description>
	<dc:creator>biogeek</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/12963/cosmos-our-workflow-management-system-for-ngs-data</guid>
	<pubDate>Wed, 23 Jul 2014 07:29:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/12963/cosmos-our-workflow-management-system-for-ngs-data</link>
	<title><![CDATA[COSMOS, our workflow management system for NGS data]]></title>
	<description><![CDATA[<p><strong>COSMOS</strong>, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via <a href="http://bioinformatics.oxfordjournals.org/content/early/2014/06/29/bioinformatics.btu385.abstract">Advance Access</a> in <em>Bioinformatics</em> (<a href="http://scholar.harvard.edu/lancaster/publications/cosmos-python-library-massively-parallel-workflows">Gafni et al. 2014</a>).&nbsp; It is also available for download for non-commercial academic and research purposes at:</p>
<p><strong>&nbsp;<a href="http://cosmos.hms.harvard.edu/">http://cosmos.hms.harvard.edu/</a></strong>.</p><p>Address of the bookmark: <a href="https://cosmos.hms.harvard.edu/" rel="nofollow">https://cosmos.hms.harvard.edu/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36927/restrictiondigest-a-powerful-perl-module-for-simulating-genomic-restriction-digests</guid>
	<pubDate>Tue, 12 Jun 2018 13:17:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36927/restrictiondigest-a-powerful-perl-module-for-simulating-genomic-restriction-digests</link>
	<title><![CDATA[RestrictionDigest: A powerful Perl module for simulating genomic restriction digests]]></title>
	<description><![CDATA[RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes at one run and generates concise comparison of enzyme(s) performance across the genomes.

For more information, please see the academic paper published online (http://www.sciencedirect.com/science/article/pii/S071734581630001X).<p>Address of the bookmark: <a href="https://github.com/JINPENG-WANG/RestrictionDigest" rel="nofollow">https://github.com/JINPENG-WANG/RestrictionDigest</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/12995/national-center-for-bioinformatics-ncb</guid>
  <pubDate>Wed, 23 Jul 2014 14:10:49 -0500</pubDate>
  <link></link>
  <title><![CDATA[National Center for Bioinformatics (NCB)]]></title>
  <description><![CDATA[
<p>NCB is offering M.Phil and Ph.D programs in the area of Bioinformatics. The major goal of NCB is to promote quality training and research in the area of Bioinformatics. Bioinformatics originated as a cross-disciplinary field as the need for computational sections to research problem raised in biomedicine. </p>

<p>More at http://ncb.qau.edu.pk/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38067/metaplotr-a-perlr-pipeline-for-plotting-metagenes-of-nucleotide-modifications-and-other-transcriptomic-sites</guid>
	<pubDate>Mon, 05 Nov 2018 08:12:45 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38067/metaplotr-a-perlr-pipeline-for-plotting-metagenes-of-nucleotide-modifications-and-other-transcriptomic-sites</link>
	<title><![CDATA[MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites]]></title>
	<description><![CDATA[<p><span>An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.</span></p><p>Address of the bookmark: <a href="https://github.com/olarerin/metaPlotR" rel="nofollow">https://github.com/olarerin/metaPlotR</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

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