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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/34864?offset=20</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/396/bioinformatics-introduction-to-perl</guid>
	<pubDate>Thu, 11 Jul 2013 09:49:37 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/396/bioinformatics-introduction-to-perl</link>
	<title><![CDATA[Bioinformatics: Introduction to PERL]]></title>
	<description><![CDATA[<p>This course is aimed at those new to programming and provides an introduction to programming using <strong>Perl</strong>. By the end of this course, attendees should be able to write simple <strong>Perl</strong> programs and to understand more complex <strong>Perl</strong> programs written by others. The course will be taught using the online <a href="http://sofiarobb.com/learning-perl-toc/" title="http://sofiarobb.com/learning-perl-toc/">Learning Perl</a> materials created by <a href="http://stajich.bioinformatics.ucr.edu/members/sofia-robb" title="http://stajich.bioinformatics.ucr.edu/members/sofia-robb">Sofia Robb</a> of the <a href="http://www.ucr.edu/" title="http://www.ucr.edu/">University of California Riverside</a>. Further information is <a href="http://ruddles.bio.cam.ac.uk/%7Edpjudge/Descriptions/PERL.php" title="http://ruddles.bio.cam.ac.uk/~dpjudge/Descriptions/PERL.php">available</a>.</p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/1737/perl-in-a-day</guid>
	<pubDate>Sat, 10 Aug 2013 21:14:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/1737/perl-in-a-day</link>
	<title><![CDATA[Perl in a day !!]]></title>
	<description><![CDATA[<p>This pdf based tutorial in good resource to understand the basic of Perl in a day</p><p><a href="http://ritg.med.harvard.edu/training/perl/RC_Perl_Intro.pdf">http://ritg.med.harvard.edu/training/perl/RC_Perl_Intro.pdf</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</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/file/view/5307/clean-the-fasta-file</guid>
	<pubDate>Thu, 03 Oct 2013 14:19:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/5307/clean-the-fasta-file</link>
	<title><![CDATA[Clean the FASTA file]]></title>
	<description><![CDATA[<p>Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.</p><p>&nbsp;</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/5307" length="1408" type="text/x-perl" />
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/22388/perl-one-liner-basics</guid>
	<pubDate>Sun, 24 May 2015 09:28:33 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/22388/perl-one-liner-basics</link>
	<title><![CDATA[Perl One liner basics !!]]></title>
	<description><![CDATA[<p>Perl has a ton of command line switches (see perldoc perlrun), but I'm just going to cover the ones you'll commonly need to debug code. The most important switch is -e, for execute (or maybe "engage" :) ). The -e switch takes a quoted string of Perl code and executes it. For example:<br /><br />$ perl -e 'print "Hello, World!\n"'<br />Hello, World!<br /><br />It's important that you use single-quotes to quote the code for -e. This usually means you can't use single-quotes within the one liner code. If you're using Windows cmd.exe or PowerShell, you must use double-quotes instead.<br /><br />I'm always forgetting what Perl's predefined special variables do, and often test them at the command line with a one liner to see what they contain. For instance do you remember what $^O is?<br /><br />$ perl -e 'print "$^O\n"'<br />linux<br /><br />It's the operating system name. With that cleared up, let's see what else we can do. If you're using a relatively new Perl (5.10.0 or higher) you can use the -E switch instead of -e. This turns on some of Perl's newer features, like say, which prints a string and appends a newline to it. This saves typing and makes the code cleaner:<br /><br />$ perl -E 'say "$^O"'<br />linux<br /><br />Pretty handy! say is a nifty feature that you'll use again and again.</p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/22570/frequent-words-problem-solution-by-perl</guid>
	<pubDate>Tue, 09 Jun 2015 23:38:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/22570/frequent-words-problem-solution-by-perl</link>
	<title><![CDATA[Frequent words problem solution by Perl]]></title>
	<description><![CDATA[<div><p>Solved with perl <a href="http://rosalind.info/problems/1a/">http://rosalind.info/problems/1a/</a></p><p>#Find the most frequent k-mers in a string.<br />#Given: A DNA string Text and an integer k.<br />#Return: All most frequent k-mers in Text (in any order).<br /><br />use strict;<br />use warnings;<br /><br />my $string="ACGTTGCATGTCGCATGATGCATGAGAGCT";<br />my $kmer=4; <br />my %myHash;<br />my $max=0;<br /><br />for (my $aa=0; $aa&lt;=(length($string)-4); $aa++) {<br />&nbsp;&nbsp; &nbsp;my $myStr=substr&nbsp; $string, $aa,$kmer;<br />&nbsp;&nbsp; &nbsp;#print "$myStr\n";<br />&nbsp;&nbsp; &nbsp;my $km=kmerMatch ($string, $myStr, $kmer);<br />&nbsp;&nbsp; &nbsp;if ($km &gt; $max) { $max = $km;}<br />&nbsp;&nbsp; &nbsp;#print "$km\t$myStr\n";<br />&nbsp;&nbsp; &nbsp;$myHash{$myStr}=$km;<br />&nbsp;&nbsp; &nbsp;<br />}<br /><br />#Print all key which have matching values<br />foreach my $name (keys %myHash){<br />&nbsp;&nbsp;&nbsp; print "$name " if $myHash{$name} == $max;<br />}<br /><br />sub kmerMatch { #Check the exact matching kmers with sliding window<br />my ($string, $myStr, $kmer)=@_;<br />my $count=0;<br />for (my $aa=0; $aa&lt;=(length($string)-4); $aa++) {<br />&nbsp;&nbsp; &nbsp;my $myWin=substr&nbsp; $string, $aa,$kmer;<br />&nbsp;&nbsp; &nbsp;if ($myWin eq $myStr) {<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;#print "$myWin eq $myStr\n";<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$count++;<br />&nbsp;&nbsp; &nbsp;}<br />}<br />return $count;<br />}</p></div>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/26627/scientist-computational-genomics-two-positions</guid>
  <pubDate>Sat, 12 Mar 2016 18:07:56 -0600</pubDate>
  <link></link>
  <title><![CDATA[Scientist - Computational Genomics (Two Positions)]]></title>
  <description><![CDATA[
<p>ICRISAT is a non-profit, non-political organization that conducts agricultural research for development in Asia and sub-Saharan Africa with a wide array of partners throughout the world. Covering 6.5 million square kilometers of land in 55 countries, the semi-arid tropics is home to over 2 billion people, with 650 million of these being the poorest of the poor. ICRISAT and its partners help empower those living in the semi-arid tropics, especially smallholder farmers, to overcome poverty, hunger, malnutrition and a degraded environment through more efficient and profitable agriculture.</p>

<p>ICRISAT is headquartered in Patancheru near Hyderabad, India, with two regional hubs and five country offices in sub-Saharan Africa. ICRISAT, established in 1972, is a member of the CGIAR Consortium. For more details, see www.icrisat.org.</p>

<p>Responsibilities:Design efficient SQL queries for pulling large sequencing projects.<br />Serve as a technical adviser to the project leadership and provide computational perspective on product design and deliverability.<br />Develop and oversee a rapid and incremental software development and release schedule.<br />Design the software architecture, oversee the implementation and evolution of the design on appropriate hardware platforms.<br />Working collaboratively in a team environment to design, code, test, debug, and document programs for an integrated genomic analysis pipeline in a rapid and incremental software development and release schedule.<br />Supervise and review code development and ensure that software products meet project objectives in terms of functionality, scalability, robustness and user experience.<br />Implement and oversee the QA/QC practices to ensure the development team is adhering to quality standards.<br />Work closely with the application specialist to integrate feedbacks from teams in each CGIAR center into software customization and improvement.<br />Assist in training of breeders in the CGIAR centers to use software developed.<br /> Personal Profile:</p>

<p>The applicant should have:</p>

<p>Understanding of genomics data and advanced knowledge of Java, and C/C++ as the programming languages and any of the scripting language like perl and/or Python, SQL<br />High Performance Computing, data architecture, database platforms and QA/QC practices in software engineering.<br />She/he should have solid experience in software development projects, preferably as a senior programmer or in the software project management role, and in projects involving big data.<br />Excellent communication skills are needed to work in this multi-disciplinary, multi-location and multi-cultural team.<br />Ability to mentor colleagues in quality software development practices is desired.<br />Educational Qualification : Ph. D or Masters Degree in Computational Biology / Computational Genomics or Equivalent with Research Experience in Mentioned Areas.</p>

<p>More at http://www.icrisat.org/careers/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31976/snpgenie</guid>
	<pubDate>Thu, 30 Mar 2017 17:38:02 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31976/snpgenie</link>
	<title><![CDATA[SNPGenie]]></title>
	<description><![CDATA[<p>SNPGenie is a Perl script for estimating evolutionary parameters, mainly from pooled next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data. SNP reports (acceptable in a variety of formats) much each correspond to a single population, with variants called relative to a single reference sequence (one sequence in one FASTA file). Just run the main script, <strong>snpgenie.pl</strong>, in a directory containing the necessary <a href="https://github.com/hugheslab/snpgenie#snpgenie-input">input files</a>, and we take care of the rest! For the earlier version, see <a href="http://ww2.biol.sc.edu/~austin/">Hughes Lab Bioinformatics Resource</a>.</p><p>Address of the bookmark: <a href="https://github.com/hugheslab/snpgenie" rel="nofollow">https://github.com/hugheslab/snpgenie</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl</guid>
	<pubDate>Tue, 26 Dec 2017 18:06:57 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl</link>
	<title><![CDATA[Building Web UIs With Mojolicious Perl]]></title>
	<description><![CDATA[<p>Mojolicious is one of 3 leading web frameworks available in the perl ecosystem (along with Dancer and Catalyst) and by far my favorite.</p>
<p>Mojolicious aims to provide a complete web development experience. It thus has no hard dependencies, comes with a built-in development and production server and many other features one needs to build a web application. It's easy to install, has an applciation generator script and many plugins and extensions.</p>
<p><em>Libraries for developing Web applications</em></p>
<ul>
<li><a href="https://metacpan.org/pod/Amon2">Amon2</a></li>
<li><a href="https://metacpan.org/pod/Catalyst">Catalyst</a>&nbsp;- Overflowing with features. Very popular.</li>
<li><a href="https://metacpan.org/pod/Dancer">Dancer</a>&nbsp;(<a href="http://perldancer.org/">Official site</a>)</li>
<li><a href="https://metacpan.org/pod/Dancer2">Dancer2</a></li>
<li><a href="https://metacpan.org/pod/Gantry">Gantry</a>&nbsp;- Web application framework for mod_perl, cgi, etc.</li>
<li><a href="https://metacpan.org/pod/Kossy">Kossy</a>&nbsp;- A Web framework with simple interface.</li>
<li><a href="https://metacpan.org/pod/Mojolicious">Mojolicious</a>&nbsp;- An all in one framework.</li>
<li><a href="https://metacpan.org/pod/Poet">Poet</a>&nbsp;- a modern Perl web framework for Mason developers</li>
</ul><p>Address of the bookmark: <a href="https://www.ynonperek.com/2017/09/28/perl-mojolicious-web-development/" rel="nofollow">https://www.ynonperek.com/2017/09/28/perl-mojolicious-web-development/</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>

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