<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29638?offset=630</link>
	<atom:link href="https://bioinformaticsonline.com/related/29638?offset=630" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34041/r-tuorial</guid>
	<pubDate>Mon, 31 Jul 2017 08:41:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34041/r-tuorial</link>
	<title><![CDATA[R tuorial]]></title>
	<description><![CDATA[<p>R learning resources</p>
<p>https://flowingdata.com/</p><p>Address of the bookmark: <a href="https://flowingdata.com/" rel="nofollow">https://flowingdata.com/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/9204/keep-your-important-ssh-session-running-when-you-disconnect-from-server</guid>
	<pubDate>Sat, 15 Mar 2014 21:39:17 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/9204/keep-your-important-ssh-session-running-when-you-disconnect-from-server</link>
	<title><![CDATA[Keep Your Important SSH Session Running when You Disconnect from Server !!!]]></title>
	<description><![CDATA[<p>As a Bioinformatician/ Computational biologist we swim in the ocean of genomic/proteomics data, and play with them with an ease. In our day to day simulation, analysis, comparative study we do need to run exhaustive programs, which might take more than a week. In such cases we do need to disconnect from sever in a way that our program/session should not get terminated. To do so there are lots of software, tools such as tmux ( <a href="http://tmux.sourceforge.net/">http://tmux.sourceforge.net/</a>, nohup (<a href="http://ss64.com/bash/nohup.html">http://ss64.com/bash/nohup.html</a>) , byobu (<a href="https://help.ubuntu.com/10.04/serverguide/byobu.html">https://help.ubuntu.com/10.04/serverguide/byobu.html</a>) and other commands (disown -a &amp;&amp; exit), but following are the ones I use the most.</p><p>Screen is like a window manager for your console. It will allow you to keep multiple terminal sessions running and easily switch between them. It also protects you from disconnection, because the screen session doesn&rsquo;t end when you get disconnected.<br /><br />You&rsquo;ll need to make sure that screen is installed on the server you are connecting to. If that server is Ubuntu or Debian, just use this command:<br /><br />sudo apt-get install screen<br /><br />Now you can start a new screen session by just typing screen at the command line. You&rsquo;ll be shown some information about screen. Hit enter, and you&rsquo;ll be at a normal prompt.<br /><br /><strong>To disconnect (but leave the session running)</strong><br /><br />Hit Ctrl + A and then Ctrl + D in immediate succession. You will see the message [detached]<br /><br /><strong>To reconnect to an already running session</strong><br /><br />screen -r<br /><br /><strong>To reconnect to an existing session, or create a new one if none exists</strong><br /><br />screen -D -r<br /><br /><strong>To create a new window inside of a running screen session</strong><br /><br />Hit Ctrl + A and then C in immediate succession. You will see a new prompt.<br /><br /><strong>To switch from one screen window to another</strong><br /><br />Hit Ctrl + A and then Ctrl + A in immediate succession.<br /><br /><strong>To list open screen windows</strong><br /><br />Hit Ctrl + A and then W in immediate succession</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35437/dupradar-package</guid>
	<pubDate>Sun, 04 Feb 2018 14:28:57 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35437/dupradar-package</link>
	<title><![CDATA[dupRadar package]]></title>
	<description><![CDATA[<p><span>The&nbsp;</span><em>dupRadar</em><span>&nbsp;package gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it. Thus, failed experiments can be easily identified at a glance</span></p><p>Address of the bookmark: <a href="https://bioconductor.org/packages/3.7/bioc/vignettes/dupRadar/inst/doc/dupRadar.html" rel="nofollow">https://bioconductor.org/packages/3.7/bioc/vignettes/dupRadar/inst/doc/dupRadar.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/9242/check-the-size-of-a-directory-free-disk-space</guid>
	<pubDate>Mon, 17 Mar 2014 02:35:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/9242/check-the-size-of-a-directory-free-disk-space</link>
	<title><![CDATA[Check the Size of a directory &amp; Free disk space.]]></title>
	<description><![CDATA[<p>The amount of databases we bioinformatician deal are just HUGE &hellip; In such cases, we always need to check our server for free spaces etc. I planned this article to explains 2 simple commands that most bioinformatician want to know when they start using Linux / BioLinux. First: Size of a directory (du) and and second: free disk space that exists on your machine (df).</p><p><br /><strong>'du' &ndash; Check the size of a directory</strong></p><p><br />$ du<br />This command ( du) gives you a list of directories that exist in the current working directory along with their sizes in kilobytes (default). The last line of the output gives you the total size of the current directory including its subdirectories. <br /><br />$ du /home/jin1<br />The above command would give you the directory size of the directory /home/david<br /><br />$ du -h<br />The same &ldquo;du&rdquo;command with some flag gives you a better output than the default one. The option '-h' stands for human readable format. Therefore, in order to print the sizes of the files / directories in your desire notation use this time suffixed with a 'k' if its kilobytes and 'M' if its Megabytes and 'G' if its Gigabytes.<br /><br />$ du -ah<br />If you are interested in checking everything present in a folder use above mentioned command. It gives us not only the directories but also all the files that are present in the current directory. The &ldquo;-a&rdquo; flag displays the filenames along with the directory names in the output. <br /><br />$ du -c<br />This gives you a grand total as the last line of the output. So if your directory occupies 30MB the last 2 lines of the output would be 30M.<br /><br />$ du -s<br />Use this command to displays a summary of the directory size. It is the simplest way to know the total size of the current directory.<br /><br />$ du -S<br />This would display the size of the current directory excluding the size of the subdirectories that exist within that directory. So it basically shows you the total size of all the files that exist in the current directory.<br /><br />$ du --exculde=mp3<br />Several times it required to exclude some directory in our size calculation. In such cases the above command would display the size of the current directory along with all its subdirectories, but it would exclude all the files having the given pattern present in their filenames.</p><p><br /><strong>'df' - finding the disk free space / disk usage</strong><br /><br />$ df<br />Hmmm &hellip; now &ldquo;df&rdquo; command is really useful, and I guess you are going to use it over time. Typing the above command, outputs a table consisting of 6 columns. All the columns are very easy to understand. Remember that the 'Size', 'Used' and 'Avail' columns use kilobytes as the unit. The 'Use%' column shows the usage as a percentage which is also very useful.<br /><br />$ df -h<br />Displays the same output as the previous command but the '-h' indicates human readable format. Hence instead of kilobytes as the unit the output would have 'M' for Megabytes and 'G' for Gigabytes.<br /><br />Example: Linux installed on /dev/hda1<br />$ df -h | grep /dev/hda1</p><p><br />All right, this is not the only option to check the sizes and free spaces but there are a few more options that can be used with 'du' and 'df' . I will discuss it later.<br /><br /></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/37049/chromomap-an-r-package-for-interactive-visualization-and-mapping-of-human-chromosomes</guid>
	<pubDate>Mon, 25 Jun 2018 17:22:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/37049/chromomap-an-r-package-for-interactive-visualization-and-mapping-of-human-chromosomes</link>
	<title><![CDATA[chromoMap-An R package for Interactive visualization and mapping of human chromosomes]]></title>
	<description><![CDATA[
<p>chromoMap is an R package that provides interactive, configurable and elegant graphics visualization of the human chromosomes allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the enormous size of the chromosomes, it is impractical to visualize each element on the same plot. But chromoMap plots provide a magnified view for each of chromosome location to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order (You will see in the demos below). Not ony that, the plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.</p>

<p>https://cran.r-project.org/web/packages/chromoMap/index.html</p>
]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/9441/jrf-at-gautam-buddha-university</guid>
  <pubDate>Thu, 27 Mar 2014 03:53:57 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF at Gautam Buddha University]]></title>
  <description><![CDATA[
<p>Gautam Buddha University (GBU) Noida invites applications for the follow posts<br />2014 March Advertisement from Gautam Buddha University (GBU)<br />Junior Research Fellow (JRF)<br />No. of Positions:  01<br />Educational Qualifications:<br />Master degree in any discipline of Life Science with NET qualified or valid GATE score. Desirable Qualification: Preference will be given to candidates having research experience in Bioinformatics<br />Experience:</p>

<p>(details of experience required)<br />Pay Scale:<br />INR Rs.12000/-P.M. + HRA<br />Category:<br />Science and Research Jobs<br />How To Apply:<br />The interested candidates should report for the Interview on 31st<br />March, 2014 at 10:00 am in the Conference Room of Dean, School of Biotechnology, First floor, Gautam Buddha University, Greater<br />Noida. Interested candidates may also send their resume to undersigned by post-mail/e-mail shaktis@gbu.ac.in or shaktisahi@gmail.com. No TA and DA will be paid for appearing for the interview<br />Download Official Notification:</p>

<p>http://www.gbu.ac.in/Recruitment/JRF_advertisement_DSTProject_Shakti_24March14.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library</guid>
	<pubDate>Wed, 09 Jan 2019 11:00:32 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library</link>
	<title><![CDATA[visNetwork: an R package for network visualization, using vis.js javascript library]]></title>
	<description><![CDATA[<div id="introduction">
<p><strong>visNetwork</strong>&nbsp;is an R package for network visualization, using&nbsp;<strong>vis.js</strong>&nbsp;javascript library (<a href="http://visjs.org/">http://visjs.org/</a>). All remarks and bugs are welcome on github :&nbsp;<a href="https://github.com/datastorm-open/visNetwork">https://github.com/datastorm-open/visNetwork</a>.</p>
</div>
<div id="features">
<h2>Features</h2>
<p>Based on&nbsp;<a href="http://www.htmlwidgets.org/">htmlwidgets</a>, so :</p>
<ul>
<li>compatible with&nbsp;<a href="http://shiny.rstudio.com/">shiny</a>, R Markdown documents, and RStudio viewer</li>
</ul>
<p>The package proposes all the features available in&nbsp;<strong>vis.js</strong>&nbsp;API, and even more with special features for R :</p>
<ul>
<li>easy to use</li>
<li>custom shapes, styles, colors, sizes, &hellip;</li>
<li>works smooth on any modern browser for up to a few thousand nodes and edges</li>
<li>interactivity controls (highlight, collapsed nodes, selection, zoom, physics, movement of nodes, tooltip, events, &hellip;)</li>
<li>visualize&nbsp;<code>rpart</code>&nbsp;tree</li>
<li></li>
</ul>
</div><p>Address of the bookmark: <a href="https://datastorm-open.github.io/visNetwork/" rel="nofollow">https://datastorm-open.github.io/visNetwork/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/9598/junior-research-fellowship-at-gb-pant-university</guid>
  <pubDate>Thu, 03 Apr 2014 12:29:46 -0500</pubDate>
  <link></link>
  <title><![CDATA[Junior Research Fellowship at G.B. PANT UNIVERSITY]]></title>
  <description><![CDATA[
<p>DEPARTMENT OF MOLECULAR BIOLOGY &amp; GENETIC ENGINEERING<br />COLLEGE OF BASIC SCIENCE AND HUMANITIES<br />G.B. PANT UNIVERSITY OF AGRICULTURE AND TECHNOLOGY<br />PANTNAGAR -263145, UTTARAKHAND</p>

<p>No. CBSH/MBGE/356</p>

<p>Subject: Advertisement for the award of Junior Research Fellowship.</p>

<p>Applications are invited for award of one Junior Research Fellowship on a consolidated fellowship of Rs. 12,000/- pm in the project “Bioinformatics Sub-DIC ”, under the Coordinatorship Dr. Anil Kumar. The fellowship is purely temporary and may continue till the duration of the project or maximum three years which ever is earlier. The appointment shall be given on six monthly review basis.</p>

<p>ESSENTIAL QUALIFICATION</p>

<p>M.Sc. Bioinformatics having research experience on In silico experimentation.</p>

<p>Candidates possessing the above qualifications may submit their application on<br />plain paper in the following format to the undersigned latest 18 April, 2014 the interviews will be held on 19 April, 2014 at 11.00 AM in the office of the undersigned. No separate letter for interview will be issued or any TA/DA will be paid for attending the interview.</p>

<p>Advertisement: http://www.gbpuat.ac.in/01042014_18april14_Advertisement%20for%20JRF%20Position,%20BI.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38541/geneoverlap-an-r-package-to-test-and-visualize-gene-overlaps</guid>
	<pubDate>Thu, 27 Dec 2018 19:45:52 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38541/geneoverlap-an-r-package-to-test-and-visualize-gene-overlaps</link>
	<title><![CDATA[GeneOverlap: An R package to test and visualize gene overlaps]]></title>
	<description><![CDATA[<p>Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose, the gene expression can be turned on or off. Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its activating role, if we overlap the genes that are bound by H3K4me3 with the genes that are highly expressed, we should expect a positive association. Similary, we can perform such kind of overlapping between the gene lists of different histone modifications with that of various expression groups and establish each histone modification&rsquo;s role in gene regulation.</p><p>Address of the bookmark: <a href="https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf" rel="nofollow">https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/9859/bioinformatics-jrfsrf-position-at-university-of-hyderabad</guid>
  <pubDate>Tue, 15 Apr 2014 20:07:52 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics JRF/SRF position at University of Hyderabad]]></title>
  <description><![CDATA[
<p>UNIVERSITY OF HYDERABAD SCHOOL OF LIFE SCIENCES </p>

<p>Applications are invited from qualified individuals for a JRF/SRF position (sponsored by DBT/DST) at Prof. Jagan Pongubala’s laboratory, University of Hyderabad. Dr. Pongubala’s laboratory is investigating the molecular pathways that control the development of innate and adaptive immune cell types utilizing a combination of genetic, molecular and computational approaches.</p>

<p>JRF/SRF</p>

<p>Masters degree in Bioinformatics  (M.Sc./M.Tech.)</p>

<p>Rs. 12,000+HRA<br />Rs. 16,000+HRA</p>

<p>Initial appointment is for one year and  subjected to renewal up to 2 years</p>

<p>Candidates selected for the above position would have a choice to work on computational biology or experimental  biology. Candidates interested to work on computational biology are expected to perform high-throughput sequencing  (NGS) data analysis and should have a strong background in Bioinformatics &amp; Computational Biology, good  programming skills particularly Perl, Python, R and work experience in Linux environment.</p>

<p>Candidates interested to work on experimental biology should have work experience in techniques that are routinely  used in molecular biology and mammalian cell culture. A basic knowledge of bioinformatics is also desired. </p>

<p>Applicants for the above positions should have a Masters degree (M.Tech/M.Sc) with an aggregate marks greater  than 70% or a 7.5 CGPA. Candidates having JRF-fellowship through CSIR/UGC/ICMR/DBT will be encouraged  to enroll into Ph.D. program. The interested candidates having excellent organizational skills and the ability to work  in a team environment with an aspiration to learn new techniques and explore new scientific areas are requested to generate their resume using the link https://cvmkr.com/CV/new#0 and forward to pongubalajagan@gmail.com</p>

<p>Review of applications will begin immediately and continue until the position is filled. Eligible candidates will be called for an interview. No TA/ DA will be paid for attending the interview or at the time of joining the post. Applicants should note that the appointment is purely temporary and subjected to renewal up to three years and there is no Right to Claim for any regular appointment with the University.</p>

<p>Corresponding address: Jagan Pongubala, Ph.D.<br />Department of Animal Sciences<br />School of Life Sciences, Room:S44<br />University of Hyderabad<br />Gachibowli, Hyderabad 500046</p>

<p>Advertisement: https://www.uohyd.ac.in/images/recruitment/jrf-srf_130414.pdf</p>
]]></description>
</item>

</channel>
</rss>