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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44414?offset=30</link>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/9429/srf-vacancy-at-nipgr</guid>
  <pubDate>Tue, 25 Mar 2014 19:20:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[SRF Vacancy at NIPGR]]></title>
  <description><![CDATA[
<p>Applications are invited from suitable candidates for filling up the purely temporary position of one Senior Research Fellow in DST’s Indo-Australian Joint project (with ICRISAT) entitled “Genomic Approach for Stress Tolerant Chickpea” under the guidance of Dr. Mukesh Jain, Scientist, NIPGR.</p>

<p>(A) Senior Research Fellow (One Post):    Emoluments as per DST/DBT norms.</p>

<p>Candidates having M.Sc. degree (with minimum of 55% marks) or equivalent in Life Sciences/Biotechnology/Bioinformatics/ Molecular Biology or any other related field with minimum of two years of post M.Sc. research experience are eligible to apply. The candidate having computer skill (Linux, Perl, Java, MySQL) and/or experience in advanced molecular biology, next generation sequencing data analysis and molecular markers analysis will be preferred.</p>

<p>The position is completely on temporary basis and co-terminus with the project. The initial appointment will be for one year, which can be curtailed/extended on the basis of assessment of the candidate’s performance and discretion of the Competent Authority. NIPGR reserves the right to select the candidate against the above posts depending upon the qualifications and experience of the candidates. Reservation of posts shall be as per Govt. of India norms.</p>

<p>Eligible candidates may apply by sending hard copy of completed application in the given format with a cover letter showing interest and attested copies of the certificates and proof of research experience. The applications should reach at the address given below within 15 days from the date of the advertisement. The subject line on envelope must be superscribed by “Application for the Post of SRF in DST - AISRF project”.</p>

<p>Note: ONLY hard copy of the application in the given format will be accepted.</p>

<p>Last date April 03, 2014</p>

<p>Dr. Mukesh Jain<br />Staff Scientist<br />National Institute of Plant Genome Research<br />Aruna Asaf Ali Marg, P.O. Box NO. 10531,<br />New Delhi - 110067</p>

<p>Advertisement: http://www.nipgr.res.in/careers/vacancies_latest.php#</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44934/genomic-basis-of-evolutionary-innovations-gevol</guid>
	<pubDate>Sat, 06 Dec 2025 06:11:00 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44934/genomic-basis-of-evolutionary-innovations-gevol</link>
	<title><![CDATA[Genomic Basis of Evolutionary Innovations (GEvol)]]></title>
	<description><![CDATA[<p>The Priority Programme (SPP 2349) funded by German Science Foundation (DFG) started 2022: &bdquo;Genomic Basis of Evolutionary Innovations (GEvol)&ldquo;</p>
<p>GEvol is unique as it will use, for the first time, a large taxonomic group to focus on one goal: to characterise the dynamics and mechanisms of genomic innovations underlying novel traits using comparative evolutionary genomics (and related data).<br>Thus, projects participating in GEvol we will ask fundamental evolutionary questions such as:<br>1. At what level is evolution repeatable?<br>2. How does genomic plasticity interfere with phenotypic plasticity during evolution?<br>3. How do inter- and intra-specific interactions influence genomic architectures?<br>4. How predictable is phenotypic variation given some knowledge about the dynamics and mechanisms of underlying genome evolution?</p><p>Address of the bookmark: <a href="https://g-evol.uni-muenster.de/open-positions/" rel="nofollow">https://g-evol.uni-muenster.de/open-positions/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34391/taxoblast-taxoblast-is-a-pipeline-to-identify-contamination-in-genomic-sequence</guid>
	<pubDate>Thu, 23 Nov 2017 08:37:15 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34391/taxoblast-taxoblast-is-a-pipeline-to-identify-contamination-in-genomic-sequence</link>
	<title><![CDATA[Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence]]></title>
	<description><![CDATA[<p><span>Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp&nbsp;</span><em>Saccharina japonica</em><span>. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at&nbsp;</span><a href="http://sdittami.altervista.org/taxoblast" title="">http://sdittami.altervista.org/taxoblast</a><span>&nbsp;and via SourceForge (</span><a href="https://sourceforge.net/projects/taxoblast" title="">https://sourceforge.net/projects/taxoblast</a><span>).</span></p><p>Address of the bookmark: <a href="https://sourceforge.net/projects/taxoblast/files/" rel="nofollow">https://sourceforge.net/projects/taxoblast/files/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</guid>
	<pubDate>Mon, 30 Apr 2018 04:38:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</link>
	<title><![CDATA[ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.]]></title>
	<description><![CDATA[<p><span>ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.&nbsp;</span></p>
<p><span>Detail paper at&nbsp;https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8</span></p><p>Address of the bookmark: <a href="https://github.com/VicugnaPacos/ALPACA" rel="nofollow">https://github.com/VicugnaPacos/ALPACA</a></p>]]></description>
	<dc:creator>Seema Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36927/restrictiondigest-a-powerful-perl-module-for-simulating-genomic-restriction-digests</guid>
	<pubDate>Tue, 12 Jun 2018 13:17:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36927/restrictiondigest-a-powerful-perl-module-for-simulating-genomic-restriction-digests</link>
	<title><![CDATA[RestrictionDigest: A powerful Perl module for simulating genomic restriction digests]]></title>
	<description><![CDATA[RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes at one run and generates concise comparison of enzyme(s) performance across the genomes.

For more information, please see the academic paper published online (http://www.sciencedirect.com/science/article/pii/S071734581630001X).<p>Address of the bookmark: <a href="https://github.com/JINPENG-WANG/RestrictionDigest" rel="nofollow">https://github.com/JINPENG-WANG/RestrictionDigest</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web</guid>
	<pubDate>Fri, 31 May 2019 19:55:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web</link>
	<title><![CDATA[Apollo: First instantaneous, collaborative genomic annotation editor available on the Web]]></title>
	<description><![CDATA[<ul>
<li>Apollo is a plug-in for the&nbsp;<a href="http://jbrowse.org/">JBrowse</a>&nbsp;Genome Viewer.</li>
<li>In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the &lsquo;Information Editor&rsquo;.</li>
<li>History tracking with undo/redo functions is available.</li>
<li>Users are able to directly set an annotation to a specific state, choosing from the &lsquo;History&rsquo; display.</li>
<li>Adding and updating PubMed IDs will prompt users with a publication title to confirm their submission.</li>
<li>Gene Ontology (GO) terms are supported and GO ID auto-completion has been incorporated.</li>
<li>Users may access a &lsquo;Recent Changes&rsquo; page.</li>
<li>Help page with Apollo specific content is available.</li>
</ul><p>Address of the bookmark: <a href="http://genomearchitect.github.io/" rel="nofollow">http://genomearchitect.github.io/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41464/phytozome-v121-plant-science-community-hub-for-accessing-palnts-genomic-data</guid>
	<pubDate>Tue, 17 Mar 2020 07:30:17 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41464/phytozome-v121-plant-science-community-hub-for-accessing-palnts-genomic-data</link>
	<title><![CDATA[Phytozome  v12.1: plant science community hub for accessing palnts genomic data]]></title>
	<description><![CDATA[<p>Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. As of release v12.1.6, Phytozome hosts 93 assembled and annotated genomes, from 82 Viridiplantae species. More than half of these genomes have been sequenced, assembled and/or annotated with JGI Plant Science program resources. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.</p><p>Address of the bookmark: <a href="https://phytozome.jgi.doe.gov/pz/portal.html" rel="nofollow">https://phytozome.jgi.doe.gov/pz/portal.html</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44659/figeno-tool-for-plotting-sequencing-data-along-genomic-coordinates</guid>
	<pubDate>Tue, 17 Sep 2024 02:28:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44659/figeno-tool-for-plotting-sequencing-data-along-genomic-coordinates</link>
	<title><![CDATA[Figeno: Tool for plotting sequencing data along genomic coordinates.]]></title>
	<description><![CDATA[<p><span>Tool for plotting sequencing data along genomic coordinates.</span></p>
<div>
<pre><code>FIGENO is a
  FIGure
    GENerator
for GENOmics</code></pre>
</div>
<p dir="auto">With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview:&nbsp;<a href="https://www.youtube.com/watch?v=h1cBeXoSYTA">https://www.youtube.com/watch?v=h1cBeXoSYTA</a>.</p>
<p dir="auto"><a href="https://github.com/CompEpigen/figeno/blob/main/docs/content/images/figeno.png" target="_blank"><img src="https://github.com/CompEpigen/figeno/raw/main/docs/content/images/figeno.png" alt="figeno" style="border: 0px;"></a></p><p>Address of the bookmark: <a href="https://github.com/CompEpigen/figeno" rel="nofollow">https://github.com/CompEpigen/figeno</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35800/scikit-bio%E2%84%A2-is-an-open-source-bsd-licensed-python-package-providing-data-structures-algorithms-and-educational-resources-for-bioinformatics</guid>
	<pubDate>Fri, 02 Mar 2018 04:29:47 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35800/scikit-bio%E2%84%A2-is-an-open-source-bsd-licensed-python-package-providing-data-structures-algorithms-and-educational-resources-for-bioinformatics</link>
	<title><![CDATA[scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.]]></title>
	<description><![CDATA[<p><span>scikit-bio is currently in beta. We are very actively developing it, and&nbsp;</span><strong>backward-incompatible interface changes can and will arise</strong><span>. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the&nbsp;</span><a href="https://github.com/biocore/scikit-bio/blob/master/doc/source/user/api_stability.rst">API stability docs</a><span>&nbsp;for more details, including what we mean by&nbsp;</span><em>stable</em><span>&nbsp;and&nbsp;</span><em>experimental</em><span>&nbsp;in this context.</span></p><p>Address of the bookmark: <a href="http://scikit-bio.org/" rel="nofollow">http://scikit-bio.org/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40591/modelstudio-a-package-automates-the-explanation-of-machine-learning-predictive-models</guid>
	<pubDate>Wed, 22 Jan 2020 23:58:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40591/modelstudio-a-package-automates-the-explanation-of-machine-learning-predictive-models</link>
	<title><![CDATA[modelStudio: a package automates the explanation of machine learning predictive models]]></title>
	<description><![CDATA[<p>The&nbsp;<code>modelStudio</code>&nbsp;package automates the explanation of machine learning predictive models. This package generates advanced interactive and animated model explanations in the form of a serverless HTML site.</p>
<p>It combines&nbsp;<strong>R</strong>&nbsp;with&nbsp;<strong>D3.js</strong>&nbsp;to produce plots and descriptions for various local and global explanations. Tools for model exploration unite with tools for EDA (Exploratory Data Analysis) to give a broad overview of the model behavior.&nbsp;<code>modelStudio</code>&nbsp;is a fast and condensed way to get all the answers without much effort. Break down your model and look into its ingredients with only a few lines of code.</p><p>Address of the bookmark: <a href="https://modeloriented.github.io/modelStudio/index.html" rel="nofollow">https://modeloriented.github.io/modelStudio/index.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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