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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44742?offset=70</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation</guid>
	<pubDate>Tue, 18 Jun 2024 02:04:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation</link>
	<title><![CDATA[BioKit: a set of tools dedicated to bioinformatics, data visualisation]]></title>
	<description><![CDATA[<p><span>BioKit is a set of tools dedicated to bioinformatics, data visualisation (</span><a href="https://biokit.readthedocs.io/en/latest/references.html#module-biokit.viz" title="biokit.viz"><code><span>biokit.viz</span></code></a><span>), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g.,&nbsp;</span><a href="https://biokit.readthedocs.io/en/latest/references.html#module-biokit.stats" title="biokit.stats"><code><span>biokit.stats</span></code></a><span>). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).</span></p><p>Address of the bookmark: <a href="https://biokit.readthedocs.io/en/latest/index.html" rel="nofollow">https://biokit.readthedocs.io/en/latest/index.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26729/ga4gh-data-working-group</guid>
	<pubDate>Sun, 20 Mar 2016 23:13:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26729/ga4gh-data-working-group</link>
	<title><![CDATA[GA4GH Data Working Group]]></title>
	<description><![CDATA[<p>GA4GH Data Working Group</p>
<p>Led by David Haussler (UCSC) and Richard Durbin (Sanger Institute), the Data Working Group (DWG) of the Global Alliance brings together the leading Genome Institutes and Centers with IT industry leaders to create global standards and tools for the secure, privacy respecting and interoperable sharing of Genomic data.</p>
<p>More at&nbsp;http://ga4gh.org/#/</p><p>Address of the bookmark: <a href="http://ga4gh.org/#/" rel="nofollow">http://ga4gh.org/#/</a></p>]]></description>
	<dc:creator>Jitendra Prajapati</dc:creator>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37993/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data</guid>
	<pubDate>Thu, 25 Oct 2018 06:14:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37993/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data</link>
	<title><![CDATA[Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data]]></title>
	<description><![CDATA[<p><strong>Platypus</strong><span>&nbsp;is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on&nbsp;</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=24463883">whole-genome</a><span>,&nbsp;</span><a href="http://www.nature.com/ng/journal/v45/n1/abs/ng.2492.html">exon-capture</a><span>, and&nbsp;</span><a href="http://www.nature.com/nature/journal/v493/n7432/abs/nature11725.html">targeted capture</a><span>&nbsp;data, it has been run on very large datasets as part of the&nbsp;</span><a href="http://www.1000genomes.org/">Thousand Genomes</a><span>&nbsp;and WGS500 projects, and is being used in clinical sequencing trials in the&nbsp;</span><a href="http://www.mcgprogramme.com/">Mainstreaming Cancer Genetics</a><span>&nbsp;programme.&nbsp;</span></p>
<p><span>Tutorial&nbsp;https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt</span></p><p>Address of the bookmark: <a href="http://www.well.ox.ac.uk/platypus" rel="nofollow">http://www.well.ox.ac.uk/platypus</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39875/lrsday-long-read-sequencing-data-analysis-for-yeasts</guid>
	<pubDate>Mon, 26 Aug 2019 18:07:33 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39875/lrsday-long-read-sequencing-data-analysis-for-yeasts</link>
	<title><![CDATA[LRSDAY: Long-read Sequencing Data Analysis for Yeasts]]></title>
	<description><![CDATA[<p><span>Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast,&nbsp;</span><em>Saccharomyces cerevisiae</em><span>, has many isolates currently being sequenced with long reads.&nbsp;</span></p><p>Address of the bookmark: <a href="https://github.com/yjx1217/LRSDAY" rel="nofollow">https://github.com/yjx1217/LRSDAY</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/42324/comparative-genomics-data-set-including-240-mammals-released</guid>
	<pubDate>Thu, 19 Nov 2020 06:45:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/42324/comparative-genomics-data-set-including-240-mammals-released</link>
	<title><![CDATA[Comparative Genomics Data Set Including 240 Mammals Released !]]></title>
	<description><![CDATA[<p>The genome of 130 mammals was sequenced by a large international consortium and the data was analyzed together with 110 existing genomes to allow scientists to identify the important positions in the DNA. This report, published in Nature today will help advance research on human disease mutations and inform how best to protect endangered species.</p><p>In addition to the knowledge of the human genome, all these genomes, widely sampled across mammals, can be used to research how particular organisms respond to different conditions. Some otters, for example, have a thick, water-resistant shell, and some rodents, but not all, have adapted to hibernation. These animal traits will help us to understand human traits, such as metabolic diseases.</p><p><img src="https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fs41586-020-2876-6/MediaObjects/41586_2020_2876_Fig1_HTML.png?as=webp" alt="image" style="border: 0px; border: 0px;"></p><p>With climate change and more animal ecosystems being threatened by human activity, the protection of endangered species is becoming increasingly important. Scientists have historically researched several people in various populations of a species to understand the genetic variation that occurs in that species. This is important for understanding how particular species can be protected. In this study, animals on the Red List of Endangered Species of the International Union for Conservation of Nature had fewer differences in their genomes, which is consistent with their endangered status.</p><p>Ref @&nbsp;A comparative genomics multitool for scientific discovery and conservation&nbsp;https://www.nature.com/articles/s41586-020-2876-6</p><p>&nbsp;Data at&nbsp;http://zoonomiaproject.org/</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44545/amr-database</guid>
	<pubDate>Tue, 04 Jun 2024 13:37:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44545/amr-database</link>
	<title><![CDATA[AMR Database !]]></title>
	<description><![CDATA[<ul>
<li><a href="http://en.mediterranee-infection.com/article.php?laref=283%26titre=arg-annot">ARG-ANNOT</a>. PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/24145532">24145532</a></li>
<li><a href="https://card.mcmaster.ca/">CARD</a>. PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/23650175">23650175</a></li>
<li><a href="https://megares.meglab.org/">MEGARes</a>&nbsp;PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/27899569">27899569</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/pathogens/isolates#/refgene/">NCBI</a>&nbsp;BioProject:&nbsp;<a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA313047">PRJNA313047</a></li>
<li><a href="https://cge.cbs.dtu.dk/services/PlasmidFinder/">plasmidfinder</a>&nbsp;PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/24777092">24777092</a></li>
<li><a href="https://cge.cbs.dtu.dk//services/ResFinder/">resfinder</a>. PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/22782487">22782487</a></li>
<li><a href="http://www.mgc.ac.cn/VFs/">VFDB</a>. PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/26578559">26578559</a></li>
<li><a href="https://github.com/katholt/srst2">SRST2</a>'s version of ARG-ANNOT. PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/25422674">25422674</a>.</li>
<li><a href="https://cge.cbs.dtu.dk/services/VirulenceFinder/">VirulenceFinder</a>&nbsp;PMID:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/24574290">24574290</a>.</li>
</ul><p>Address of the bookmark: <a href="https://github.com/sanger-pathogens/ariba/wiki/Task%3A-getref" rel="nofollow">https://github.com/sanger-pathogens/ariba/wiki/Task%3A-getref</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/45253/brava-browser</guid>
	<pubDate>Sun, 23 Aug 2026 10:32:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/45253/brava-browser</link>
	<title><![CDATA[BRaVa Browser]]></title>
	<description><![CDATA[<p>BRaVa Browser is an interactive web tool for exploring rare genetic variant associations. It allows users to search and visualize rare variant association results across genes and traits, making it easier to investigate potential relationships between genetic variation and disease or other phenotypes.</p>
<p>More at&nbsp;https://nikbaya.github.io/brava_browser/#/</p><p>Address of the bookmark: <a href="https://nikbaya.github.io/brava_browser/#/" rel="nofollow">https://nikbaya.github.io/brava_browser/#/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42570/breeding-insight</guid>
	<pubDate>Wed, 06 Jan 2021 19:49:21 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42570/breeding-insight</link>
	<title><![CDATA[Breeding Insight]]></title>
	<description><![CDATA[<p><span><span>Breeding Insight&nbsp;at Cornell University will leverage recent improvements in genomics and open source informatics components, and in&nbsp;partnership with small breeding programs, will enable these programs to harness&nbsp;&nbsp;powerful digital tools to accelerate their genetic gains</span></span></p>
<p><span>Breeding Insight is funded by&nbsp;the&nbsp;</span><span><a href="https://www.ars.usda.gov/about-ars/" target="_blank">U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS)</a></span><span>&nbsp;through Cornell University. The USDA ARS delivers scientific solutions to national and global agricultural challenges. As a global leader&nbsp;in agricultural discovery through scientific excellence, ARS is committed to delivering cutting-edge, scientific tools and innovative solutions for American farmers, producers, industry, and communities to support the nourishment and well-being of all people; sustaining our nation&rsquo;s agroecosystems and natural resources; and ensuring the economic competitiveness and excellence of our agriculture.</span></p><p>Address of the bookmark: <a href="https://www.breedinginsight.org/" rel="nofollow">https://www.breedinginsight.org/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43768/summer-school-open-to-phd-students</guid>
  <pubDate>Wed, 02 Feb 2022 06:08:35 -0600</pubDate>
  <link></link>
  <title><![CDATA[Summer school open to PhD students]]></title>
  <description><![CDATA[
<p>Some PhD students are organizing a summer school open to PhD students with different backgrounds and interests.</p>

<p>Several sessions and workshops will be held within five focus groups, and one common theme: mountain research.</p>

<p>The summer school will take place in Obergurgl, in the middle of the Austrian Alps, September 5-9.</p>

<p>Abstract submission is now open, until February 16th: https://www.imc2022.info/summerschool/</p>

<p>The summer school takes place in the context of the International Mountain Conference 2022, Innsbruck, Austria: https://www.imc2022.info/</p>

<p>Please feel free to spread the word among potentially interested colleagues and PhD students.</p>

<p>"Capponi, Lisa"</p>
]]></description>
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<item>
  <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>
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