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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27430?offset=890</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11582/monitor-running-jobs-on-linux-server</guid>
	<pubDate>Fri, 06 Jun 2014 16:18:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11582/monitor-running-jobs-on-linux-server</link>
	<title><![CDATA[Monitor running jobs on Linux server]]></title>
	<description><![CDATA[<p>You as a bioinformatican run lots of program on your servers. Sometime the shared server is also used by your colleague. If server is busy you sometime need to check the running programs and want to monitor the running programs as well. The "top" command will come in handy when you need to find out if things are still running, how long they&rsquo;ve been running, or how much memory is being used.<br /><br />&lsquo;top&rsquo; is very simple to run: type<br /><br />%% top<br /><br />You&rsquo;ll get a screen that looks like this, and is updated regularly:<br /><br /><img src="http://bioinformaticsonline.com/mod/photo/top.png" width="659" height="582" alt="image" style="border: 0px;"><br />Simple, right? Heh.<br /><br />First! Note that you can use &lsquo;q&rsquo; or &lsquo;CTRL-C&rsquo; to exit from &lsquo;top&rsquo;.<br /><br />Now let&rsquo;s read and understand at each line independently.<br /><br />The first line:<br /><br />top - 23:00:48 up 39 days,&nbsp; 2 user,&nbsp; load average: 0.00, 0.00, 0.00<br /><br />The first line tells you the current time, how long the machine has been up, how many users are logged in, and the short/medium/long-term compute load on the machine. If you run something for a long time, you&rsquo;ll see these numbers go up. Right now, the machine is basically just sitting there, so these are all close to 0.<br /><br />The second line:</p><p>Tasks:&nbsp; 239 total,&nbsp;&nbsp; 1 running,&nbsp; 238 sleeping,&nbsp;&nbsp; 0 stopped,&nbsp;&nbsp; 0 zombie<br /><br />This line tells you how many processes are running. If you are using laptops machines it&rsquo;s not so interesting because you really are the only one using this machine.<br /><br />Cpu(s):&nbsp; 0.0%us,&nbsp; 0.0%sy,&nbsp; 0.0%ni,100.0%id,&nbsp; 0.0%wa,&nbsp; 0.0%hi,&nbsp; 0.0%si,&nbsp; 0.0%st<br /><br />This line contains the CPU load. The first two numbers are how busy the system is doing computation (&ldquo;us&rdquo; stands for &ldquo;user&rdquo;) and how busy the system is doing system-y things like accessing disks or network (&ldquo;sy&rdquo; stands for &ldquo;system&rdquo;). We&rsquo;ll talk more about this later.<br /><br />Mem:&nbsp;&nbsp; 49457320k total,&nbsp;&nbsp;&nbsp; 3492174k used,&nbsp; 14535596k free,&nbsp;&nbsp;&nbsp; 1435148k buffers<br /><br />This should be easy to understand &ndash; how much memory you&rsquo;re using! <br /><br />Swap:&nbsp;&nbsp; 539356k total,&nbsp;&nbsp; 28332k used,&nbsp;&nbsp; 836562k free,&nbsp;&nbsp;&nbsp; 29862014k cached<br /><br />Swap is just on-disk memory that can be used to &ldquo;swap&rdquo; out programs from main memory. Again, we&rsquo;ll talk about this later.:<br /><br />PID USER&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PR&nbsp; NI&nbsp; VIRT&nbsp; RES&nbsp; SHR S %CPU %MEM&nbsp;&nbsp;&nbsp; TIME+&nbsp; COMMAND<br />&nbsp; 1 root&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 39 &nbsp; 19&nbsp; 0&nbsp; 0&nbsp; 0 S&nbsp; 0.0&nbsp; 0.0&nbsp;&nbsp; 246:57.22 kipmi0<br />&nbsp; 2 root&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; RT&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp; 0 S&nbsp; 0.0&nbsp; 0.0&nbsp;&nbsp; 0:00.00 migration/0<br /><br />And... finally! What&rsquo;s actually running! The two most important numbers are the %CPU and %MEM towards the right, as well as the COMMAND. This tells you how compute- and memory-intensive your program is. Right now, nothing&rsquo;s running so the numbers aren&rsquo;t very interesting, but just wait until we run something...</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34088/sequence-evolution-function-computational-approaches-in-comparative-genomics</guid>
	<pubDate>Sun, 06 Aug 2017 06:58:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34088/sequence-evolution-function-computational-approaches-in-comparative-genomics</link>
	<title><![CDATA[Sequence - Evolution - Function; Computational Approaches in Comparative Genomics]]></title>
	<description><![CDATA[<p><em>Sequence - Evolution - Function</em><span>&nbsp;is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis.</span></p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/books/NBK20260/" rel="nofollow">https://www.ncbi.nlm.nih.gov/books/NBK20260/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/34929/shendurelab</guid>
  <pubDate>Thu, 28 Dec 2017 09:57:50 -0600</pubDate>
  <link></link>
  <title><![CDATA[ShendureLab]]></title>
  <description><![CDATA[
<p>The mission of our lab is to develop and apply new technologies and methods for genetics, genomics and molecular biology. Most of our work exploits next-generation DNA sequencing which is effectively emerging as a broadly enabling microscope for the measurement of biological phenomena. Our ongoing work generally falls into six areas. These are listed below as links to representative publications in each area.</p>

<p>Developing New Molecular Methods</p>

<p>Genomic Approaches to Developmental Biology</p>

<p>Massively Parallel Functional Genomics</p>

<p>Translating Genomics to the Clinic</p>

<p>Genetic Basis of Human Disease</p>

<p>Genome Sequencing Technologies</p>

<p>http://krishna.gs.washington.edu/index.html<br />http://www.gs.washington.edu/faculty/shendure.htm</p>
]]></description>
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  <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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40955/the-global-alliance-for-genomics-and-health-ga4gh</guid>
	<pubDate>Sat, 08 Feb 2020 07:37:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40955/the-global-alliance-for-genomics-and-health-ga4gh</link>
	<title><![CDATA[The Global Alliance for Genomics and Health (GA4GH)]]></title>
	<description><![CDATA[<p>The Global Alliance for Genomics and Health (GA4GH) is a policy-framing and technical standards-setting organization, seeking to enable responsible genomic data sharing within a <a href="https://www.ga4gh.org/genomic-data-toolkit/regulatory-ethics-toolkit/framework-for-responsible-sharing-of-genomic-and-health-related-data/">human rights framework</a>.</p>
<p>GA4GH core funders and sponsors enable our work and allow us to convene the international genomic data sharing community.</p>
<p>https://www.ga4gh.org/</p><p>Address of the bookmark: <a href="https://www.ga4gh.org/" rel="nofollow">https://www.ga4gh.org/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/42470/the-new-corona-variant-has-23-mutations-in-all-which-is-unusually-huge</guid>
	<pubDate>Wed, 23 Dec 2020 03:50:50 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/42470/the-new-corona-variant-has-23-mutations-in-all-which-is-unusually-huge</link>
	<title><![CDATA[The new corona variant has 23 mutations in all, which is unusually huge !]]></title>
	<description><![CDATA[<p>The new SARS-CoV-2 version, B.1.1.7, which was first seen in the third week of September in Kent and Greater London, has since spread to other locations in the UK. According to the COVID-19 Genomics UK Consortium (COG-UK Consortium) that analysed the genome data of the virus and identified the variant, the new variant has been spreading "rapidly" over the last four weeks and has now been detected in other locations in the UK, suggesting further spread of the variant in the region.</p><p><span>According to a<span>&nbsp;</span></span><a href="https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563"><strong><span>preliminary report</span></strong></a><span><span>&nbsp;</span>posted on December 19 by the COG-UK Consortium scientists, as of December 15, 1,623 variant genomes have been sequenced. In a<span>&nbsp;</span></span><a href="https://twitter.com/TheCGPS/status/1340749351803629569"><strong><span>December 21 tweet</span></strong></a><span>, COG-UK Consortium said that it added 2,963 more genome sequences of SARS-CoV-2, of which 942 (32%) belong to the new variant. The Consortium<span>&nbsp;</span></span><a href="https://twitter.com/CovidGenomicsUK/status/1341073233420955654"><strong><span>intends to sequence</span></strong></a><span><span>&nbsp;</span>20,000 more SARS-CoV-2 genomes in the next two weeks to further ascertain the spread of the variant.</span></p><p><span>There is no clear proof, at least not yet, that it does cause severe pandemic. But there is a justification for seriously taking the possibility. Another coronavirus lineage in South Africa has acquired one specific mutation that is also present in B.1.1.7. This variant is increasingly spreading across South Africa's coastal regions. And doctors have observed in preliminary research that individuals infected with this variant bear a higher viral load-a higher concentration of the virus in their upper respiratory tract. In many viral diseases, this is associated with more severe symptoms.</span></p><p>&nbsp;</p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43362/machine-learning-for-genomics</guid>
	<pubDate>Thu, 09 Sep 2021 11:26:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43362/machine-learning-for-genomics</link>
	<title><![CDATA[Machine Learning for Genomics]]></title>
	<description><![CDATA[<h3>Module 1: Statistics for genomics (2-8 August 2021)</h3>
<ul>
<li>A simple intro to statistical distributions</li>
<li>hypothesis testing</li>
<li>linear models.</li>
</ul>
<p>reading:&nbsp;<a href="http://compgenomr.github.io/book/stats.html">http://compgenomr.github.io/book/stats.html</a></p>
<p>slides:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week1/compgen2021_stats.pdf">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week1/compgen2021_stats.pdf</a></p>
<p>exercises+code:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week1/">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week1/</a></p>
<h3><a href="https://github.com/BIMSBbioinfo/compgen2021#module-2-unsupervised-learning-for-genomics-9-15-august-2021"></a>Module 2: Unsupervised learning for genomics (9-15 August 2021)</h3>
<ul>
<li>Understanding basic intuition behind machine learning approaches.</li>
<li>Using unsupervised learning to cluster and visualise data points</li>
<li>Dimension reduction techniques for visualisation and as input to clustering methods</li>
</ul>
<p>reading:&nbsp;<a href="http://compgenomr.github.io/book/unsupervisedLearning.html">http://compgenomr.github.io/book/unsupervisedLearning.html</a></p>
<p>slides:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week2/compgen2021_unsupervisedLearning.pdf">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week2/compgen2021_unsupervisedLearning.pdf</a></p>
<p>exercises+code:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week2/">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week2/</a></p>
<h3><a href="https://github.com/BIMSBbioinfo/compgen2021#module-3-supervised-learning-for-genomics-16-22-august-2021"></a>Module 3: Supervised learning for genomics (16-22 August 2021)</h3>
<ul>
<li>Understanding and using supervised learning methods for predictive purposes</li>
<li>How to measure prediction performance</li>
<li>Understand and use cross-validation and related concepts</li>
</ul>
<p>reading:&nbsp;<a href="http://compgenomr.github.io/book/supervisedLearning.html">http://compgenomr.github.io/book/supervisedLearning.html</a></p>
<p>slides:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week3/compgen2021_supervisedLearning.pdf">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week3/compgen2021_supervisedLearning.pdf</a></p>
<p>exercises+code:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week3/">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week3/</a></p>
<p>https://github.com/BIMSBbioinfo/compgen2021</p><p>Address of the bookmark: <a href="https://github.com/BIMSBbioinfo/compgen2021" rel="nofollow">https://github.com/BIMSBbioinfo/compgen2021</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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<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/opportunity/view/44412/scientist-positions-csir-institute-of-genomics-integrative-biology-igib</guid>
  <pubDate>Sat, 02 Dec 2023 00:51:08 -0600</pubDate>
  <link></link>
  <title><![CDATA[Scientist positions @ CSIR-Institute of Genomics &amp; Integrative Biology (IGIB)]]></title>
  <description><![CDATA[
<p>CSIR-Institute of Genomics &amp; Integrative Biology (IGIB) is a premier Institute of Council of Scientific<br />and Industrial Research (CSIR), engaged in research of national importance in the areas of genomics,<br />molecular medicine, bioinformatics and proteomics. For more details, kindly refer to website<br />https://igib.res.in.<br />The Institute is looking for dynamic and creative Indian researchers having excellent academic record<br />and interested in Product Development / Technology Innovation / Applied Technology / Translational<br />Research in the above broad areas. The eligible candidates may apply for the following positions<br />through the CSIR-IGIB website.</p>

<p>More at https://www.igib.res.in/bdmg/ScientistRecruitmentAdvt2023.pdf</p>
]]></description>
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