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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44716?offset=300</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/17926/orange-bioinformatics-2534</guid>
	<pubDate>Mon, 06 Oct 2014 12:51:37 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/17926/orange-bioinformatics-2534</link>
	<title><![CDATA[Orange-Bioinformatics 2.5.34]]></title>
	<description><![CDATA[<p>Orange Bioinformatics extends <a href="http://orange.biolab.si/">Orange</a>, a data mining software package, with common functionality for bioinformatics. The provided functionality can be accessed as a Python library or through a visual programming interface (Orange Canvas). The latter is also suitable for non-programmers.</p>
<p>Orange Bioinformatics provides access to publicly available data, like GEO data sets, Biomart, GO, KEGG, Atlas, ArrayExpress, and PIPAx database. As for the analytics, there is gene selection, quality control, scoring distances between experiments with multiple factors. All features can be combined with powerful visualization, network exploration and data mining techniques from the Orange data mining framework.</p><p>Address of the bookmark: <a href="https://pypi.python.org/pypi/Orange-Bioinformatics/2.5.34" rel="nofollow">https://pypi.python.org/pypi/Orange-Bioinformatics/2.5.34</a></p>]]></description>
	<dc:creator>Robert M Willioms</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43546/introduction-to-phylogenies-in-r</guid>
	<pubDate>Wed, 13 Oct 2021 02:27:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43546/introduction-to-phylogenies-in-r</link>
	<title><![CDATA[Introduction to phylogenies in R]]></title>
	<description><![CDATA[<p><span>R phylogenetics is built on the contributed packages for phylogenetics in R, and there are many such packages. Let's begin today by installing a few critical packages, such as ape, phangorn, phytools, and geiger. To get the most recent CRAN version of these packages, you will need to have R 3.3.x installed on your computer!</span></p><p>Address of the bookmark: <a href="http://www.phytools.org/Cordoba2017/ex/2/Intro-to-phylogenies.html" rel="nofollow">http://www.phytools.org/Cordoba2017/ex/2/Intro-to-phylogenies.html</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18380/jrfsrf-at-university-of-hyderabad</guid>
  <pubDate>Fri, 17 Oct 2014 01:55:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF/SRF at University of Hyderabad]]></title>
  <description><![CDATA[
<p>Applications are invited for the following post of Junior Research Fellow (temporary position coterminous with the project) under DBT funded research project on ““Understanding the functions of α1β1γ1/α2β1γ1 selective AMPK Modulators in dissecting the pharmacological role of these isozymes in metabolic diseases”</p>

<p>Qualified and interested candidates can send their curriculum vitae by e-mail to hr@drils.org on or before 27th October 2014 mention in the subject line of the mail the following code: AMPK-Biology.</p>

<p>Selected candidates will be called for a personal interview to Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad. The selected candidate is expected to report within two weeks from the date of selection to start work on the project.</p>

<p>Junior Research Fellowship (Molecular Modeling/Biology) for two years and Senior Research fellowship for one year</p>

<p>Junior Research Fellowship: Rs. 15,600/- (consolidated) per month for first two years.<br />Senior Research Fellowship: Rs. 18,200/-(consolidated) per month for the 3rd year.</p>

<p>Duration: The duration of the fellowship is for three years. However, the performance of the candidate will be reviewed after the completion of every year and the fellowship will be renewed only upon satisfactory performance.</p>

<p>Responsibilities:</p>

<p>1) Literature search.<br />2) Design, plan and execute experiments under the supervision of the scientist.<br />3) Provide scientific support to the scientist in his/her research activities.<br />4) Book keeping and maintenance of stocks and consumables.</p>

<p>Essential Qualifications:</p>

<p>Required: M.Sc. in Microbiology/Biotechnology/Bioinformatics or any other related branch of basic Sciences from a recognized university/institute with a consistent academic record of minimum 60% aggregate in all qualifying examinations. The candidate should be NET qualified for lectureship. The candidate should be motivated to work with dedication.</p>

<p>Desirable: expertise/experience in both Molecular Modeling and Molecular Biology.</p>

<p>Experience: 0-2 years in the areas of Molecular Modeling and/or Molecular Biology and cell biology and Biochemistry.</p>

<p>Preferable: Relevant research experience as evident from thesis/dissertation/project work.</p>

<p>Advertisement: http://www.ilsresearch.org/userfiles/Junior%20REsearch%20Fellowship%20-%20AMPK(Biology).pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44401/bioinformatics-tools-for-phylogeny</guid>
	<pubDate>Mon, 06 Nov 2023 03:09:59 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44401/bioinformatics-tools-for-phylogeny</link>
	<title><![CDATA[Bioinformatics Tools for Phylogeny !]]></title>
	<description><![CDATA[<p><span>Direct access to the individual tools available on this server.</span></p><table summary="list of individual tools">
<thead>
<tr><th>Multiple Alignment:</th><th>Phylogeny:</th><th>Tree viewers:</th><th>Utilities:</th></tr>
</thead>
<tbody>
<tr>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=muscle">MUSCLE</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=phyml">PhyML</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=treedyn">TreeDyn</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks">Gblocks</a></td>
</tr>
<tr>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=tcoffee">T-Coffee</a>&nbsp;/&nbsp;<a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=expresso">3DCoffee</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=tnt">TNT</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=drawgram">Drawgram</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=jalview">Jalview</a></td>
</tr>
<tr>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=clustalw">ClustalW</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=bionj">BioNJ</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=drawtree">Drawtree</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=readseq">Readseq</a></td>
</tr>
<tr>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=probcons">ProbCons</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=mrbayes">MrBayes</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=atv">ATV (A Tree Viewer)</a></td>
<td><a href="http://phylogeny.lirmm.fr/phylo_cgi/data_converter.cgi">Built-in converter</a></td>
</tr>
</tbody>
</table>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18385/biinformamatics-lead-at-google-life-sciences</guid>
  <pubDate>Fri, 17 Oct 2014 02:24:55 -0500</pubDate>
  <link></link>
  <title><![CDATA[Biinformamatics Lead at Google Life Sciences]]></title>
  <description><![CDATA[
<p>Google Life Sciences is recruiting a technical lead with experience in bioinformatics and clinical bioinformatics, including for biomarker discovery projects such as the Baseline study.</p>

<p>Responsibilities</p>

<p>Lead teams of scientists in structuring, prototyping, and executing large-scale bioinformatic and other analysis.<br />Develop novel bioinformatics, statistical, data processing, pathway, data mining and other algorithms to identify biological signals and their clinical correlates in broad kinds of individual and population data.<br />Develop novel platform-level analytical tools for sequence-based assays (assembly, annotation, variant calling and interpretation, phasing, genome structure, etc.), expression assays (RNAseq and microarray), proteomics, and metabolomics.<br />Develop statistical models that robustly correlate complex laboratory-derived information with phenotypic and clinical information.<br />Create scientifically rigorous visualizations, communications, and presentations of results.</p>

<p>Reference @ https://www.google.com/about/careers/search#!t=jo&amp;jid=62095001</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34400/ioniser-tools-for-the-quality-assessment-of-data-produced-by-oxford-nanopore%E2%80%99s-minion-sequencer</guid>
	<pubDate>Thu, 23 Nov 2017 10:24:19 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34400/ioniser-tools-for-the-quality-assessment-of-data-produced-by-oxford-nanopore%E2%80%99s-minion-sequencer</link>
	<title><![CDATA[IONiseR:  tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer]]></title>
	<description><![CDATA[<p>This package is intended to provide tools for the quality assessment of data produced by Oxford Nanopore&rsquo;s MinION sequencer. It includes a functions to generate a number plots for examining the statistics that we think will be useful for this task.</p>
<p>However, nanopore sequencing is an emerging and rapidly developing technology. It is not clear what will be most informative. We hope that&nbsp;<code>IONiseR</code>&nbsp;will provide a framework for visualisation of metrics that we haven&rsquo;t thought of, and welcome feedback at&nbsp;<a href="mailto:mike.smith@embl.de" target="_blank">mike.smith@embl.de</a>.</p>
<p>If you&rsquo;re not interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the final section of this document.</p><p>Address of the bookmark: <a href="https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html" rel="nofollow">https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18580/faculty-positions-at-central-university-of-punjab-bathinda</guid>
  <pubDate>Wed, 22 Oct 2014 10:45:37 -0500</pubDate>
  <link></link>
  <title><![CDATA[Faculty Positions at CENTRAL UNIVERSITY OF PUNJAB, BATHINDA]]></title>
  <description><![CDATA[
<p>Advertisement No. T/NT-01 (2014)</p>

<p>Faculty Positions<br />The Central University of Punjab (CUP), Bathinda will be having the Schools and Departments as given in Table-I. The University invites applications from eligible candidates for the posts of Professors (Pay Band Rs. 37400-67000 with AGP of Rs. 10, 000/-), Associate Professors (Pay Band Rs.37400-67000 with AGP of Rs. 9,000/-) and Assistant Professors (Pay Band Rs.15600-39100 with AGP of Rs. 6,000/-)</p>

<p>POSITION AVAILABLE IN THE AREA OF SPECIALIZTION</p>

<p>3. Bioinformatics,</p>

<p>Procedure to apply: Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 750/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:</p>

<p>Registrar (Officiating)<br />Central University of Punjab<br />City Campus, Mansa Road<br />Bathinda-151 001</p>

<p>Application forms from the prospective candidates are accepted upto November 10, 2014.</p>

<p>Based on the qualification of the candidates and the need of the university, the applications received will be processed through appropriately constituted selection committees shortly. Minimum qualification can be relaxed in case of exceptionally outstanding candidate. For further details visit www.cup.ac.in; www.centralunipunjab.com; www.cup.edu.in</p>

<p>The candidate should download the application form available at website www.cup.ac.in;<br />www.centralunipunjab.com; and submit it complete in all respects on or before 10th November 2014.</p>

<p>Those who have applied earlier need to submit Academic Performance Index (API) form, 5 copies of Summary of the Application Form (available at: www.cup.ac.in; www.centralunipunjab.com and Updated CV if not updated recently (without application fee).</p>

<p>http://cup.edu.in/Faculty_details_and_general_instructions.pdf</p>

<p>http://cup.edu.in/Final%20Application%20and%20summary%20Sheet%20and%20Api%20form.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</guid>
	<pubDate>Tue, 08 May 2018 04:27:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</link>
	<title><![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]></title>
	<description><![CDATA[<p><strong>HISAT2</strong><span>&nbsp;is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs&nbsp;</span><a href="http://dl.acm.org/citation.cfm?id=2674828">[Sir&eacute;n et al. 2014]</a><span>, we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).&nbsp;</span></p>
<p><span>more at&nbsp;https://ccb.jhu.edu/software/hisat2/index.shtml</span></p><p>Address of the bookmark: <a href="https://github.com/infphilo/hisat2" rel="nofollow">https://github.com/infphilo/hisat2</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19020/jrf-in-bioinformatics-bioinformatics-centre-north-eastern-hill-university</guid>
  <pubDate>Thu, 06 Nov 2014 10:24:05 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF in Bioinformatics @ Bioinformatics Centre, North-Eastern Hill University]]></title>
  <description><![CDATA[
<p>Applications with complete bio-data are invited for JRF (3) and Project Assistant (1) in a DBT project "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" sanctioned for a period of 3 years.</p>

<p>Details are available at www.nehu.ac.in and www.bicnehu.ac.in.</p>

<p>Applications must reach the undersigned within 15 days from the date of publication of this advertisement.</p>

<p>Prof. Pramod Tandon. PI/Mr. Devendra Kumar Biswal (Co-PI)</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter</guid>
	<pubDate>Fri, 12 Oct 2018 04:37:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter</link>
	<title><![CDATA[DNA Nucleotide Counter]]></title>
	<description><![CDATA[<p style="margin: 2px 5px 4px 6px; color: #000011; font-size: 12px; font-style: normal; font-weight: 400; text-align: justify;">DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools.<span>&nbsp;</span><a href="http://www.dnabaser.com/download/biology-tools-package-download-count.html">Download</a><span>&nbsp;</span>the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder&nbsp;and double click the program you want to use.</p>
<p style="margin: 2px 5px 4px 6px; color: #000011; font-size: 12px; font-style: normal; font-weight: 400; text-align: justify;">It<span>&nbsp;</span><a href="http://www.dnabaser.com/download/install-anywhere.html">installs in any computer</a><span>&nbsp;</span>even if you don't have administrator rights!</p><p>Address of the bookmark: <a href="http://www.dnabaser.com/download/DNA-Counter/index.html" rel="nofollow">http://www.dnabaser.com/download/DNA-Counter/index.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

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