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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30015?offset=790</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/29479/how-to-install-perl-modules-on-mac-os-x-in-easy-steps</guid>
	<pubDate>Thu, 20 Oct 2016 07:26:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/29479/how-to-install-perl-modules-on-mac-os-x-in-easy-steps</link>
	<title><![CDATA[How to install Perl modules on Mac OS X in easy steps !!]]></title>
	<description><![CDATA[<p>Today at work, I learned how to install Perl modules using&nbsp;<a href="http://en.wikipedia.org/wiki/CPAN">CPAN</a>. It&rsquo;s a lot easier than I thought.</p><p>You see, for the past couple of years, I&rsquo;ve been a bit frustrated because OS X does not come with a whole lot of Perl modules pre-installed, and for all I googled, I couldn&rsquo;t find an &ldquo;idiot&rsquo;s&rdquo; guide for moderately-savvy-but-not-expert users like myself to install modules and dependencies on demand.</p><p>The only instructions I could find point to&nbsp;<a href="http://fink.sourceforge.net/">Fink</a>, which basically installs modules in a path that isn&rsquo;t included in the Perl @INC variable, meaning you have to manually specify the full path to the modules in every script &mdash; which is not a lot of fun if you&rsquo;re developing on OS X and deploying on Red Hat, for instance.</p><p>Moreover, Fink doesn&rsquo;t seem to make every module available, and it&rsquo;s not very easy to determine which Fink package you need to install if you need a particular module.</p><p>So, with a script that called on several apparently unavailable modules, and a deadline looming, I finally decided to suck it up and figure out how to use CPAN to install them:</p><h4>1) Make sure you have the Apple Developer Tools (XCode) installed.</h4><p>These are on one of your install discs, or available as a huge but free download from the&nbsp;<a href="https://developer.apple.com/xcode/">Apple Developer Connection</a>&nbsp;[free registration required] or the Mac App Store. I thought I had them, but apparently when we upgraded that computer to Tiger, they went missing.</p><p>If you don&rsquo;t have this stuff installed, your installation will fail with errors about unavailable commands.</p><h4>1.5) Install Command Line Tools (Recent XCode versions only)</h4><p>(Thank you to Tom Marchioro for informing me about this step.)</p><p>Older versions of XCode installed the command line tools (which are required to properly install CPAN modules) by default, but apparently newer ones do not. To check whether you have the command line tools already installed, run the following from the Terminal:</p><p><code>$ which make</code></p><p>This command checks the system for the &ldquo;<code>make</code>&rdquo; tool. If it spits out something like&nbsp;<code>/usr/bin/make</code>&nbsp;you&rsquo;re golden and can skip ahead to Step 2. If you just get a new prompt and no output, you&rsquo;ll need to install the tools:</p><ol>
<li>Launch XCode and bring up the Preferences panel.</li>
<li>Click on the Downloads tab</li>
<li>Click to install the Command Line Tools</li>
</ol><p>If you like, you can run&nbsp;<code>which make</code>&nbsp;again to confirm that everything&rsquo;s installed correctly.</p><h4>2) Configure CPAN.</h4><p><code>$ sudo perl -MCPAN -e shell</code></p><p><code>perl&gt; o conf init</code></p><p>This will prompt you for some settings. You can accept the defaults for almost everything (just hit &ldquo;return&rdquo;). The two things you must fill in are the path to&nbsp;<code>make</code>&nbsp;(which should be&nbsp;<code>/usr/bin/make</code>&nbsp;or the value returned when you run&nbsp;<code>which make</code>&nbsp;from the command line) and your choice of CPAN mirrors (which you actually choose don&rsquo;t really matter, but it won&rsquo;t let you finish until you select at least one). If you use a proxy or a very restrictive firewall, you may have to configure those settings as well.</p><p>If you skip Step 2, you may get errors about&nbsp;<code>make</code>&nbsp;being unavailable.</p><h4>3) Upgrade CPAN</h4><p><code>$ sudo perl -MCPAN -e 'install Bundle::CPAN'</code></p><p>Don&rsquo;t forget the&nbsp;<code>sudo</code>, or it&rsquo;ll fail with permissions errors, probably when doing something relatively unimportant like installing&nbsp;<code>man</code>&nbsp;files.</p><p>This will spend a long time downloading, testing, and compiling various files and dependencies. Bear with it. It will prompt you a few times about dependencies. You probably want to enter &ldquo;yes&rdquo;. I agreed to everything it asked me, and everything turned out fine. YMMV of course. If everything installs properly, it&rsquo;ll give you an &ldquo;OK&rdquo; at the end.</p><h4>4) Install your modules. For each module&hellip;.</h4><p><code>$ sudo perl -MCPAN -e 'install Bundle::Name'</code></p><p>or</p><p><code>$ sudo perl -MCPAN -e 'install Module::Name'</code></p><p>This will install the module&nbsp;<em>and</em>&nbsp;its dependencies. Nice, eh? Again, don&rsquo;t forget the&nbsp;<code>sudo</code>.</p><p>The first time you run this after upgrading CPAN, it may prompt you to configure again (see Step 2). If you accept its offer to try to configure itself automatically, it may just run through everything without a problem.</p><p>There are a couple of potential pitfalls with specific modules (such as the<code>LWP::UserAgent</code>&nbsp;/&nbsp;<code>HEAD</code>&nbsp;issue), but most have workarounds, and I haven&rsquo;t run into anything that wasn&rsquo;t easily recoverable.</p><p>And that&rsquo;s it!</p><p>Did you find this useful? Is there anything I missed?</p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29953/traineeship-at-jawaharlal-nehru-tropical-botanic-garden-and-research-institute</guid>
  <pubDate>Fri, 25 Nov 2016 08:07:59 -0600</pubDate>
  <link></link>
  <title><![CDATA[Traineeship at JAWAHARLAL NEHRU TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE]]></title>
  <description><![CDATA[
<p>JAWAHARLAL NEHRU TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE</p>

<p>THIRUVANANTHAPURAM - 695 562</p>

<p>Traineeship on Bioinformatics(2)</p>

<p>First class M.Sc. Bioinformatics/ Agriculture/ Botany/ Biotechnology @ Rs.8000</p>

<p>Those candidates who fulfill the above criteria may attend a walk PCC Coordinator in-interview on 28th November 2016 at Saraswathy Thangavelu center, JNTBGRI, Puthenthope, Thiruvananthapuram between at 10.00 am and 2.00 pm with all the relevant document and testimonials.</p>

<p>No TA/DA will be given to candidates for attending the interview.</p>

<p>More Info : http://jntbgri.res.in/downloads/traineeship_notification.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/29652/bioistats-ppt</guid>
	<pubDate>Tue, 08 Nov 2016 07:09:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/file/view/29652/bioistats-ppt</link>
	<title><![CDATA[Bioistats PPT]]></title>
	<description><![CDATA[<p>Basics concepts of&nbsp;Probability: The Study of Randomness</p><p>Biostatistics is the application of statistics to a wide range of topics in biology. The science of biostatistics encompasses the design of biological experiments, especially in medicine, pharmacy, agriculture and fishery; the collection, summarization, and analysis of data from those experiments; and the interpretation of, and inference from, the results. A major branch of this is medical biostatistics, which is exclusively concerned with medicine and health.</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/29652" length="1663809" type="application/pdf" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29679/comparative-genomics-educational-material-and-papers-bookmarks</guid>
	<pubDate>Wed, 09 Nov 2016 16:23:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29679/comparative-genomics-educational-material-and-papers-bookmarks</link>
	<title><![CDATA[Comparative genomics educational material and papers bookmarks]]></title>
	<description><![CDATA[<p><span>Alignment of the porcine genome against seven other mammalian genomes (</span><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#supplementary-information">Supplementary Information</a><span>) identified homologous synteny blocks (HSBs). Using porcine HSBs and stringent filtering criteria, 192 pig-specific evolutionary breakpoint regions (EBRs) were located. The number of porcine EBRs </span><span>is comparable to the number of bovine-lineage-specific EBRs (100) reported earlier using a slightly lower resolution (500</span><span><span>&thinsp;</span></span><span>kilobases (kb)), indicating that both lineages evolved with an average rate of ~2.1 large-scale rearrangements per million years after the divergence from a common cetartiodactyl ancestor ~60</span><span><span>&thinsp;</span></span><span>Myr ago</span><sup><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#ref2" title="Meredith, R. W. et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334, 521-524 (2011)">2</a></sup><span>. This rate compares to ~1.9 rearrangements per million years within the primate lineage (</span><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#supplementary-information">Supplementary Table 11</a><span>). A total of 20 and 18 cetartiodactyl EBRs (shared by pigs and cattle) were detected using the pig and human genomes as a reference, respectively.</span></p><p>Address of the bookmark: <a href="http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html" rel="nofollow">http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29849/ra-bioinformatics-at-national-institute-of-cancer-prevention-research-icmr</guid>
  <pubDate>Thu, 17 Nov 2016 04:11:09 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at NATIONAL INSTITUTE OF CANCER PREVENTION &amp; RESEARCH (ICMR)]]></title>
  <description><![CDATA[
<p>NATIONAL INSTITUTE OF CANCER PREVENTION &amp; RESEARCH (ICMR)</p>

<p>Noida 201301 (U.P)</p>

<p>Applications are invited upto 21.11.2016 from interested candidates as per details available on NICPR website (www.nicpr.res.in)/ ICMR website (www.icmr.nic.in) to fill up following temporary position in the time bound DHR Project entitled “Next generation EGFR inhibitor identification using ligand based QSAR technique” under Dr. Subhash M. Agarwal, Scientist-D, Division of Bioinformatics.</p>

<p>Research Assistant (One)</p>

<p>Rs.27000/- p.m. (Fixed/temporary)</p>

<p>Essential: M.Sc. in Bioinformatics or related field.</p>

<p>Desirable: Experience in QSAR and structure based drug designing.</p>

<p>More Info : www.icmr.nic.in/icmrnews/NICPR_Advertisement%20for%20RA.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29998/csir-nehru-science-postdoctoral-research-fellowship</guid>
  <pubDate>Tue, 29 Nov 2016 12:34:59 -0600</pubDate>
  <link></link>
  <title><![CDATA[CSIR Nehru Science Postdoctoral Research Fellowship]]></title>
  <description><![CDATA[
<p>CSIR Nehru Science Postdoctoral Research Fellowship</p>

<p>About Fellowship: <br />CSIR Nehru Science Postdoctoral Research Fellowship Scheme is an Research Fellowship awarded/given by HRD Ministry, Govt. of India every year to more than 100 fellows.</p>

<p>It was started to identify promising and young researchers with novel ideas and provide them research opportunities in the areas of basic science, engineering, medicine &amp; agriculture.</p>

<p>The fellowship aims at facilitating their transition from mentored to independent research career.</p>

<p>In addition, check these ICTS Research Fellowships:<br />1.) Max-Planck Partner Group Fellowships 2017-18<br />2.) ICTS-Simons Postdoctoral Fellowships 2017<br />3.) ICTS Post Doctoral Fellowships 2017<br />4.) Airbus Prize Postdoctoral Fellowship 2017-18</p>

<p>Eligibility: To be eligible for this fellowship, you:<br />1.) PhD degree (within 3 years of award of PhD degree), OR<br />2.) Those who have submitted PhD theses.<br />3.) Applicants should have research publications in good impact factor SCI journals.<br />4.) Indian nationals, Persons of Indian Origin (PIO) &amp; Overseas Citizen of India (OCI), a can also apply.<br />5.) Maximum Age Limit: 32 years.</p>

<p>Duration: <br />– 2 Years.<br />– extendable for a maximum of 1 more year based on performance.</p>

<p>Remuneration: <br />– Rs. 50,000/- per month plus House Rent Allowance (HRA)<br />– A contingency grant of Rs. 3.0 lakh per annum.<br />– 25% of the contingency grant can be used for domestic and international travel.</p>

<p>Mode of Selection: You can apply throughout the year, but selection will be made twice a year, in June and December.</p>

<p>How to Apply: <br />– Read the instructions, given at Annexure-I in this PDF file.<br />– And, application form is given as, Annexure-II.<br />– Fill the form &amp; send it to the given address in the PDF file.</p>

<p>Deadline: Rolling Deadline (Applications accepted throughout the year)</p>

<p>Also See: Research Internship/ Fellowship in India:<br />1.) IIT Bombay Research Internship Awards Programme 2016-17<br />2.) IIT Delhi Internship Program 2016-17<br />3.) DAAD WISE – International Internship in Germany<br />4.) Summer Research Fellowship Programme| JNCASR Bangalore<br />5.) Indian Academy of Sciences Summer Internships 2017<br />6.) Winter Internship – IIT Bombay NPDE-TCA<br />7.) Viterbi – India Program 2017 | Research Internship in US<br />8.) Internship – Centre for Stem Cell Research, Vellore</p>

<p>Accommodation &amp; other benefits: <br />– Accommodation may be provided by CSIR, if available.<br />– Medical benefits as per CSIR norms.</p>

<p>For more details: <br />– Check this PDF Notification of Fellowship.<br />– List of CSIR Labs &amp; their work/activities can be seen at www.csir.res.in.</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30198/faculty-at-indian-institute-of-science-education-and-research-berhampur</guid>
  <pubDate>Mon, 19 Dec 2016 03:34:26 -0600</pubDate>
  <link></link>
  <title><![CDATA[Faculty at Indian Institute of Science Education and Research Berhampur]]></title>
  <description><![CDATA[
<p>Advt. No: IISERBPR/DoFA/2016/2</p>

<p>Advertisement for Faculty Positions</p>

<p>The IISER Berhampur, an Institute of national importance, established through an act of Parliament is an autonomous organization under the Ministry of HRD, Govt. of India, to promote quality education and cutting edge research in basic sciences and to provide a platform for the faculty to engage in high quality education, at undergraduate and postgraduate levels. The Institute invites applications for faculty positions at the level of Assistant Professor (C) /Assistant Professor in the following disciplines:</p>

<p>1. Biological Sciences</p>

<p>2. Chemistry</p>

<p>3. Computer Sciences</p>

<p>4. Mathematics</p>

<p>5. Physics</p>

<p>Only hard copy of application in the prescribed format, via Speed Post should be sent to the Dean, Faculty Affairs, IISER Berhampur, Industrial Training Institute (ITI) Berhampur, Engineering School Road, Berhampur - 760 010, Ganjam District, Odisha, before 1700 hrs., December 30, 2016.</p>

<p>http://www.iiserbpr.ac.in</p>

<p>More Info : http://www.iiserbpr.ac.in/vacancies/Advertisement%20for%20Faculty%20Positions%20at%20IISER%20Berhampur.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30149/mypro-a-seamless-pipeline-for-automated-prokaryotic-genome-assembly-and-annotation</guid>
	<pubDate>Thu, 15 Dec 2016 05:47:35 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30149/mypro-a-seamless-pipeline-for-automated-prokaryotic-genome-assembly-and-annotation</link>
	<title><![CDATA[MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation]]></title>
	<description><![CDATA[<p>MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requires minimal programming skills. High-quality prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de novo assemblers and contig integration software. Produces more contiguous assemblies, higher N50 values and lower number of contigs.</p>
<p>More at https://sourceforge.net/projects/sb2nhri/files/MyPro/</p><p>Address of the bookmark: <a href="http://www.sciencedirect.com/science/article/pii/S0167701215001207" rel="nofollow">http://www.sciencedirect.com/science/article/pii/S0167701215001207</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30207/gam-ngs-genomic-assemblies-merger-for-next-generation-sequencing</guid>
	<pubDate>Mon, 19 Dec 2016 06:07:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30207/gam-ngs-genomic-assemblies-merger-for-next-generation-sequencing</link>
	<title><![CDATA[GAM-NGS: genomic assemblies merger for next generation sequencing]]></title>
	<description><![CDATA[<p><span>GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic&nbsp;</span><em>locus</em><span>&nbsp;(called&nbsp;</span><em>blocks</em><span>) are identified through reads' alignments and stored in a&nbsp;</span><em>weighted</em><span>graph. The merging phase is carried out with the help of this weighted graph that allows an&nbsp;</span><em>optimal</em><span>&nbsp;resolution of&nbsp;</span><em>local</em><span>&nbsp;problematic regions.</span></p><p>Address of the bookmark: <a href="https://github.com/vice87/gam-ngs" rel="nofollow">https://github.com/vice87/gam-ngs</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30249/genome-assembly-tutorial</guid>
	<pubDate>Tue, 20 Dec 2016 07:56:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30249/genome-assembly-tutorial</link>
	<title><![CDATA[Genome Assembly Tutorial]]></title>
	<description><![CDATA[<p><span>If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard to assemble using overlap-consensus-layout approach. De Bruijn graph-based assembly approach was originally proposed to handle the assembly of repetitive regions better.</span></p>
<p><span>More at&nbsp;http://www.homolog.us/Tutorials/index.php?p=1.4&amp;s=1</span></p><p>Address of the bookmark: <a href="http://www.homolog.us/Tutorials/index.php?p=1.4&amp;s=1" rel="nofollow">http://www.homolog.us/Tutorials/index.php?p=1.4&amp;s=1</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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