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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27432?offset=290</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/11441/assistant-professor-in-bioinformatics-at-dr-d-y-patil-biotechnology-bioinformatics-institute</guid>
  <pubDate>Tue, 03 Jun 2014 19:54:15 -0500</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor 	in Bioinformatics at Dr. D. Y. Patil Biotechnology &amp; Bioinformatics Institute]]></title>
  <description><![CDATA[
<p>Dr. D. Y. Patil Biotechnology &amp; Bioinformatics Institute <br />Tathawade, Pune 411033.</p>

<p>Assistant Professor 	in Bioinformatics </p>

<p>Essential :<br />First Class Master’s Degree in the appropriate branch of Life Sciences / Technology (Tech.)<br />OR<br />Ph.D in Life Sciences or in the respective subject area of specialization<br />OR<br />Good Academic record with at least 55% marks (or an equivalent grade) at the Master’s Degree level, in the relevant subject or an equivalent degree from an Indian / Foreign University.<br />Besides fulfilling the above qualifications, candidates should have cleared the eligibility test (NET) for lecturers conducted by the UGC, CSIR or similar test accredited by the UGC and as per the requirements of UGC guidelines.</p>

<p>Desirable :<br />Teaching, research industrial and/or professional experience in a reputed organization. <br />Papers presented at Conferences and/or in refereed journals</p>

<p>Note : Application are invited in prescribed form Click here for Application Form<br />Kindly send your applications to “Registrar, Dr. D. Y. Patil Vidyapeeth, Pune, Sant Tukaram Nagar, Pimpri, Pune – 411018., Maharashtra, India.” should reach in the University office within 15 days from the publication.</p>

<p>More Info: http://www.dpu.edu.in/BiotechResearchPositions.aspx</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34931/3d-dna-3d-de-novo-assembly-3d-dna-pipeline</guid>
	<pubDate>Thu, 28 Dec 2017 10:09:37 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34931/3d-dna-3d-de-novo-assembly-3d-dna-pipeline</link>
	<title><![CDATA[3d-dna: 3D de novo assembly (3D DNA) pipeline]]></title>
	<description><![CDATA[<p>This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in:&nbsp;<a href="http://science.sciencemag.org/content/early/2017/03/22/science.aal3327.full">Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017.</a></p>
<p>Unless otherwise noted, all terminology below is consistent with this paper, and all references to figures and tables in this readme refer to this paper. Specifically, some of the terminology used below is outlined in&nbsp;<code>Figure S2</code>. The assembly procedure is described in detail in the&nbsp;<a href="http://science.sciencemag.org/content/suppl/2017/03/22/science.aal3327.DC1?_ga=1.9816115.760837492.1490574064">Supporting Online Materials</a>, specifically in the section labelled &ldquo;Pipeline description&rdquo;.</p>
<p>In addition, the pipeline uses tools and methods from&nbsp;<a href="http://www.cell.com/cell-systems/abstract/S2405-4712(16)30219-8">Juicer (Durand &amp; Shamim et al., Cell Systems, 2016)</a>&nbsp;and&nbsp;<a href="http://www.cell.com/cell-systems/abstract/S2405-4712(15)00054-X">Juicebox (Durand &amp; Robinson et al., Cell Systems, 2016)</a>, as well as additional dependencies noted below.</p>
<p>Feel free to post your questions and comments at:&nbsp;<a href="http://www.aidenlab.org/forum.html">http://www.aidenlab.org/forum.html</a></p>
<p>http://aidenlab.org/documentation.html</p><p>Address of the bookmark: <a href="https://github.com/theaidenlab/3d-dna" rel="nofollow">https://github.com/theaidenlab/3d-dna</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/11656/faculty-post-at-zhejiang-university</guid>
  <pubDate>Tue, 10 Jun 2014 03:40:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Faculty post at Zhejiang University]]></title>
  <description><![CDATA[
<p>Zhejiang University (ZJU) is seeking faculty candidates for its newly launched, highly competitive and well funded “Hundred Talents Program”. This search covers all colleges and departments at ZJU. Applicants, expected to be about 35 years old, should hold PhD degree, and postdoctoral experiences are preferred for applicants in most fields. Applicants should have demonstrated commitment to excellence in teaching and research at a level comparable to the academic achievement of assistant professor or associate professor in world-renowned universities. Successful candidates must work full-time and are expected to establish internationally competitive and independent research program in cutting-edge areas of the relevant field at ZJU.</p>

<p>As one of the leading research-intensive universities in China, ZJU is located in the beautiful city of Hangzhou. Successful candidates will be employed as Principal Investigators and are qualified to supervise doctoral students. ZJU will offer an internationally competitive salary and the opportunity to purchase university's apartment at a price much lower than the market price, and will provide office and laboratory spaces as well as internationally competitive research startup packages.</p>

<p>Qualified applicants are strongly encouraged to submit their applications electronically to tr@zju.edu.cn. Applicants should include the following materials in pdf format: a comprehensive CV, a statement of research and teaching plan, and a list of 3 to 5 references with detailed contact information.</p>

<p>Contact：Talents Office, ZJU</p>

<p>Tel：+86-571-88981345, +86-571-88981390</p>

<p>Fax：+86-571-88981976</p>

<p>E-mail:tr@zju.edu.cn</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38666/mcat-motif-combining-and-association-tool</guid>
	<pubDate>Sun, 13 Jan 2019 06:27:28 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38666/mcat-motif-combining-and-association-tool</link>
	<title><![CDATA[MCAT: Motif Combining and Association Tool]]></title>
	<description><![CDATA[<p>This is a pipeline for finding motifs in fasta files.<br>It can be run from the command line as follows:</p>
<p>usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C]<br>[-s S] [-d] [-ff] [-v V]<br>positive_seq negative_seq</p>
<p>positional arguments:<br>positive_seq the fasta file for the positive sequences<br>negative_seq the fasta file for the negative sequences</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="https://github.com/yanshen43/MCAT" rel="nofollow">https://github.com/yanshen43/MCAT</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu</guid>
	<pubDate>Sat, 07 Jun 2014 05:52:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu</link>
	<title><![CDATA[XAMPP: Starting Apache fail Ubuntu]]></title>
	<description><![CDATA[<p>Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.</p><p>sudo /etc/init.d/apache2 stop</p><p>sudo /etc/init.d/mysql stop</p><p>sudo /etc/init.d/proftpd stop</p><p>sudo /opt/lampp/lampp start</p><p>&nbsp;</p><p><strong>PhpMyAdmin &ldquo;Wrong permissions on configuration file, should not be world writable!&rdquo;</strong></p><p>Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:</p><p>Just chmod 0755 the file</p><pre>sudo chmod 0755 config.inc.php</pre>]]></description>
	<dc:creator>Ram Yash Pal</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39856/tritex-sequence-assembly-pipeline-for-triticeae-genomes</guid>
	<pubDate>Tue, 20 Aug 2019 09:47:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39856/tritex-sequence-assembly-pipeline-for-triticeae-genomes</link>
	<title><![CDATA[TRITEX sequence assembly pipeline for Triticeae genomes]]></title>
	<description><![CDATA[<div>
<p>The pipeline is open-source and hosted in a public Bitbucket&nbsp;<a href="https://bitbucket.org/tritexassembly/tritexassembly.bitbucket.io/src/master/">repository</a>.</p>
</div>
<div>
<p>TRITEX has been run on highly inbred genotypes of barley (<em>Hordeum vulgare</em>), tetraploid wheat (<em>Triticum turgidum</em>) and hexaploid wheat (<em>T. aestivum</em>) with reasonable results: super-scaffold N50 values in the range of dozens of Mb and pseudomolecules with better gene space representation than a BAC-by-BAC assembly. It has never been tested and is not expected to work on heterozygous or autopolyploid genomes.</p>
</div>
<div>
<p>A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use with the pipeline is described in&nbsp;<a href="https://bio-protocol.org/e2955">Himmelbach et al. 2018</a>. Refer to the&nbsp;<a href="https://www.10xgenomics.com/resources/technical-notes/">technical notes</a>&nbsp;of 10X Genomics on how to generate Chromium data.</p>
</div><p>Address of the bookmark: <a href="https://tritexassembly.bitbucket.io/" rel="nofollow">https://tritexassembly.bitbucket.io/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<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/bookmarks/view/40856/3d-de-novo-assembly-3d-dna-pipeline</guid>
	<pubDate>Sun, 02 Feb 2020 13:41:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40856/3d-de-novo-assembly-3d-dna-pipeline</link>
	<title><![CDATA[3D de novo assembly (3D DNA) pipeline]]></title>
	<description><![CDATA[<p>For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see&nbsp;<a href="http://aidenlab.org/assembly/manual_180322.pdf">Genome Assembly Cookbook</a>&nbsp;on&nbsp;<a href="http://aidenlab.org/assembly">http://aidenlab.org/assembly</a>.</p>
<p>For the original version of the pipeline and to reproduce the Hs2-HiC and the AaegL4 genomes reported in&nbsp;<a href="http://science.sciencemag.org/content/356/6333/92">(Dudchenko et al.,&nbsp;<em>Science</em>, 2017)</a>&nbsp;see the&nbsp;<a href="https://github.com/theaidenlab/3d-dna/tree/745779bdf64db6e55bddb70c24e9b58825938c33">original commit</a>.</p>
<p>For the detailed description of the merge section see&nbsp;<a href="https://github.com/theaidenlab/AGWG-merge">https://github.com/theaidenlab/AGWG-merge</a>.</p><p>Address of the bookmark: <a href="https://github.com/theaidenlab/3d-dna" rel="nofollow">https://github.com/theaidenlab/3d-dna</a></p>]]></description>
	<dc:creator>Jit</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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41998/wgddetector-a-pipeline-for-detecting-whole-genome-duplication-events-using-the-genome-or-transcriptome-annotations</guid>
	<pubDate>Thu, 23 Jul 2020 05:52:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41998/wgddetector-a-pipeline-for-detecting-whole-genome-duplication-events-using-the-genome-or-transcriptome-annotations</link>
	<title><![CDATA[WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations]]></title>
	<description><![CDATA[<p><span>WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (</span><em>Arabidopsis thaliana</em><span>,<span>&nbsp;</span></span><em>Juglans regia</em><span>,<span>&nbsp;</span></span><em>Populus trichocarpa</em><span><span>&nbsp;</span>and<span>&nbsp;</span></span><em>Xenopus laevis</em><span>) representing herb, wood and animal, to test its practicability. Our final results showed a high degree of accuracy with the previous studies using both genome and transcriptome data.</span></p>
<p><span>More at <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2670-3">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2670-3</a></span></p><p>Address of the bookmark: <a href="https://github.com/yongzhiyang2012/wgddetector" rel="nofollow">https://github.com/yongzhiyang2012/wgddetector</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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