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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30698?offset=330</link>
	<atom:link href="https://bioinformaticsonline.com/related/30698?offset=330" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<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/37230/navigator-network-analysis-visualization-and-graphing-toronto</guid>
	<pubDate>Tue, 03 Jul 2018 05:05:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37230/navigator-network-analysis-visualization-and-graphing-toronto</link>
	<title><![CDATA[NAViGaTOR: Network Analysis, Visualization and Graphing Toronto]]></title>
	<description><![CDATA[NAViGaTOR –  Network Analysis, Visualization, &amp; Graphing TORonto is a software system for scaleable visualizing and analyzing networks.

The current version, NAViGaTOR 3, increases modularity, improves scaleability, extends input/output options, brings new network views and analysis algorithms.

http://142.150.188.236/navigatorwp/<p>Address of the bookmark: <a href="http://142.150.188.236/navigatorwp/" rel="nofollow">http://142.150.188.236/navigatorwp/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<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>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38819/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties</guid>
	<pubDate>Mon, 28 Jan 2019 18:38:44 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38819/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties</link>
	<title><![CDATA[UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties]]></title>
	<description><![CDATA[<p>UpSetR generates static&nbsp;<a href="http://vcg.github.io/upset/">UpSet</a>&nbsp;plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.</p>
<p>For further details about the original technique see the&nbsp;<a href="http://vcg.github.io/upset/about/">UpSet website</a>. You can also check out the&nbsp;<a href="https://gehlenborglab.shinyapps.io/upsetr/">UpSetR shiny app</a>.&nbsp;<a href="https://github.com/hms-dbmi/UpSetR-shiny">Here is the source code</a>&nbsp;for the shiny wrapper.</p>
<p>A&nbsp;<a href="https://github.com/ImSoErgodic/py-upset">Python package</a>&nbsp;called&nbsp;<a href="https://github.com/ImSoErgodic/py-upset">py-upset</a>&nbsp;to create UpSet plots has been created by GitHub user&nbsp;<a href="https://github.com/ImSoErgodic">ImSoErgodic</a>.</p><p>Address of the bookmark: <a href="https://github.com/hms-dbmi/UpSetR/" rel="nofollow">https://github.com/hms-dbmi/UpSetR/</a></p>]]></description>
	<dc:creator>BioStar</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/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx</guid>
	<pubDate>Sun, 31 May 2020 02:01:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx</link>
	<title><![CDATA[SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.]]></title>
	<description><![CDATA[<p>SynVisio lets you explore the results of&nbsp;<a href="http://chibba.pgml.uga.edu/mcscan2/">McScanX</a>&nbsp;a popular synteny and collinearity detection toolkit and generate publication ready images.</p>
<p>SynVisio requires two files to run:</p>
<ul>
<li>The&nbsp;<strong>simplified gff file</strong>&nbsp;that was used as an input for a McScanX query.</li>
<li>The&nbsp;<strong>collinearity file</strong>&nbsp;generated as an output by McScanX for the same input query.</li>
<li>Optional&nbsp;<strong>track file</strong>&nbsp;in bedgraph format to annotate the generated charts.</li>
</ul>
<p>SynVisio offers different types of visualizations such as&nbsp;<strong>Linear Parallel plots</strong>,&nbsp;<strong>Hive plots</strong>,&nbsp;<strong>Stacked Parallel Plots&nbsp;</strong>and&nbsp;<strong>Dot plots</strong>. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.</p><p>Address of the bookmark: <a href="https://synvisio.github.io/#/" rel="nofollow">https://synvisio.github.io/#/</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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33693/circleator</guid>
	<pubDate>Sun, 25 Jun 2017 18:04:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33693/circleator</link>
	<title><![CDATA[Circleator]]></title>
	<description><![CDATA[<p>The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the&nbsp;<a href="http://igs.umaryland.edu/">Institute for Genome Sciences</a>&nbsp;in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:</p>
<p><a href="https://camo.githubusercontent.com/0b414f050a7dcb672386932ee0cd83e5f42d2271/687474703a2f2f6a6f6e617468616e63726162747265652e6769746875622e696f2f436972636c6561746f722f696d616765732f43503030323732352d322d3432302e706e673f7261773d74727565" target="_blank"><img src="https://camo.githubusercontent.com/0b414f050a7dcb672386932ee0cd83e5f42d2271/687474703a2f2f6a6f6e617468616e63726162747265652e6769746875622e696f2f436972636c6561746f722f696d616765732f43503030323732352d322d3432302e706e673f7261773d74727565" alt="Sample Circleator image" title="Sample Circleator Image" style="border: 0px;"></a></p>
<p>Common uses of the tool include:</p>
<ul>
<li>Displaying the sequence and/or genes in a&nbsp;<a href="http://www.ncbi.nlm.nih.gov/genbank/">GenBank</a>&nbsp;flat file.</li>
<li>Highlighting differences and/or similarities in gene content between related organisms.</li>
<li>Comparing SNPs and indels between closely-related strains or serovars.</li>
<li>Comparing gene expression values across multiple samples or timepoints.</li>
<li>Visualizing coverage plots of RNA-Seq read alignments.</li>
</ul>
<h3><a href="https://github.com/jonathancrabtree/Circleator#key-features"></a>Key Features</h3>
<p>Circleator...</p>
<ul>
<li>Builds on&nbsp;<a href="http://www.bioperl.org/">BioPerl</a>&nbsp;and the input file formats that it supports, including:
<ul>
<li><a href="http://www.ncbi.nlm.nih.gov/genbank/">GenBank</a>&nbsp;flat files, GFF, FASTA</li>
</ul>
</li>
<li>Accepts a number of other commonly-used datatypes and file formats:
<ul>
<li><a href="http://bsr.igs.umaryland.edu/">BSR</a>&nbsp;and&nbsp;<a href="http://tandem.bu.edu/trf/trf.html">TRF</a>&nbsp;output,&nbsp;<a href="http://samtools.sourceforge.net/">SAM/BAM</a>&nbsp;files,&nbsp;<a href="http://vcftools.sourceforge.net/">VCF</a>-encoded SNPs, tab-delimited files</li>
</ul>
</li>
<li>Outputs publication-ready figures in the&nbsp;<a href="http://www.w3.org/Graphics/SVG/">SVG</a>&nbsp;(Scalable Vector Graphics) format.</li>
<li>Requires only a single configuration file whose layout mirrors that of the figure itself.
<ul>
<li>Predefined configuration files and "track" types are supplied for common datasets.</li>
<li>Advanced features allow limited analyses to be performed as a figure is drawn.</li>
</ul>
</li>
<li>Includes an extensive set of regression tests.</li>
<li>Offers a prototype web-based GUI (under the "Ringmaster" project.)</li>
</ul>
<p>https://github.com/jonathancrabtree/Circleator</p><p>Address of the bookmark: <a href="https://github.com/jonathancrabtree/Circleator" rel="nofollow">https://github.com/jonathancrabtree/Circleator</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34562/harvest-a-suite-of-core-genome-alignment-and-visualization-tools</guid>
	<pubDate>Fri, 08 Dec 2017 07:16:03 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34562/harvest-a-suite-of-core-genome-alignment-and-visualization-tools</link>
	<title><![CDATA[Harvest: a suite of core-genome alignment and visualization tools]]></title>
	<description><![CDATA[<p>Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.</p>
<p><a href="https://harvest.readthedocs.io/en/latest/_images/screen.png"><img src="https://harvest.readthedocs.io/en/latest/_images/screen.png" alt="_images/screen.png" style="border: 0px;"></a><span></span></p>
<p><strong>Tools</strong></p>
<ul>
<li><a href="https://harvest.readthedocs.io/en/latest/content/parsnp.html">Parsnp</a>&nbsp;- Core-genome alignment and analysis</li>
<li><a href="https://harvest.readthedocs.io/en/latest/content/gingr.html">Gingr</a>&nbsp;- Interactive visualization of alignments, trees and variants</li>
<li><a href="https://harvest.readthedocs.io/en/latest/content/harvest-tools.html">HarvestTools</a>&nbsp;- Archiving and postprocessing</li>
<li></li>
</ul><p>Address of the bookmark: <a href="https://harvest.readthedocs.io/en/latest/" rel="nofollow">https://harvest.readthedocs.io/en/latest/</a></p>]]></description>
	<dc:creator>Jit</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>

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