<?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/36994?offset=80</link>
	<atom:link href="https://bioinformaticsonline.com/related/36994?offset=80" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41875/virtualflow-a-versatile-parallel-workflow-platform-for-carrying-out-virtual-screening</guid>
	<pubDate>Sat, 13 Jun 2020 13:03:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41875/virtualflow-a-versatile-parallel-workflow-platform-for-carrying-out-virtual-screening</link>
	<title><![CDATA[VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening]]></title>
	<description><![CDATA[<p>&nbsp;related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem&nbsp;(such as SLURM).&nbsp;</p>
<p>Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks:</p>
<ul>
<li><strong><a href="https://virtual-flow.org/#vflp">VFLP: VirtualFlow for Ligand Preparation</a></strong></li>
<li><strong><a href="https://virtual-flow.org/#vfvs"><strong>VFVS</strong><strong>&nbsp;:</strong>&nbsp;VirtualFlow for Virtual Screenings</a></strong></li>
</ul>
<p>They use the same core technology regarding the workflow management and parallelization, and they can be used individually&nbsp;or in concert with each other.&nbsp;Additional versions are expected to arrive in the future.&nbsp;</p>
<p><a href="https://github.com/VirtualFlow">https://github.com/VirtualFlow</a></p>
<p><a href="https://www.nature.com/articles/s41586-020-2117-z">https://www.nature.com/articles/s41586-020-2117-z?</a></p><p>Address of the bookmark: <a href="https://virtual-flow.org/" rel="nofollow">https://virtual-flow.org/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <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/40351/repeatmodeler2-automated-genomic-discovery-of-transposable-element-families</guid>
	<pubDate>Mon, 02 Dec 2019 06:52:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40351/repeatmodeler2-automated-genomic-discovery-of-transposable-element-families</link>
	<title><![CDATA[RepeatModeler2: automated genomic discovery of transposable element families]]></title>
	<description><![CDATA[<p><span>RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (</span><a href="https://github.com/Dfam-consortium/RepeatModeler">https://github.com/Dfam-consortium/RepeatModeler</a><span>,&nbsp;</span><a href="https://github.com/Dfam-consortium/TETools">https://github.com/Dfam-consortium/TETools</a><span>).</span></p><p>Address of the bookmark: <a href="https://github.com/Dfam-consortium/TETools" rel="nofollow">https://github.com/Dfam-consortium/TETools</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44292/gget</guid>
	<pubDate>Sat, 01 Apr 2023 09:42:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44292/gget</link>
	<title><![CDATA[gget]]></title>
	<description><![CDATA[<p><code>gget</code><span>&nbsp;is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases.&nbsp;</span><code>gget</code><span>&nbsp;consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.</span></p>
<p><span><img src="https://github.com/pachterlab/gget/raw/main/figures/gget_overview.png?raw=true" alt="image" style="border: 0px;"></span></p><p>Address of the bookmark: <a href="https://github.com/pachterlab/gget" rel="nofollow">https://github.com/pachterlab/gget</a></p>]]></description>
	<dc:creator>BioStar</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/file/view/18653/genetic-code-amino-acid</guid>
	<pubDate>Sun, 26 Oct 2014 07:45:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/18653/genetic-code-amino-acid</link>
	<title><![CDATA[Genetic code - Amino Acid]]></title>
	<description><![CDATA[<p>The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon.</p><p>The image summarise all in one.</p><p>More at http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html</p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/18653" length="226605" type="image/jpeg" />
</item>

</channel>
</rss>