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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27080?offset=1290</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32048/json</guid>
	<pubDate>Tue, 04 Apr 2017 08:02:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32048/json</link>
	<title><![CDATA[JSON]]></title>
	<description><![CDATA[<p><strong>JSON</strong>&nbsp;(JavaScript Object Notation) is a lightweight data-interchange format. It is easy for humans to read and write. It is easy for machines to parse and generate. It is based on a subset of the&nbsp;<a href="http://javascript.crockford.com/">JavaScript Programming Language</a>,&nbsp;<a href="http://www.ecma-international.org/publications/files/ecma-st/ECMA-262.pdf">Standard ECMA-262 3rd Edition - December 1999</a>. JSON is a text format that is completely language independent but uses conventions that are familiar to programmers of the C-family of languages, including C, C++, C#, Java, JavaScript, Perl, Python, and many others. These properties make JSON an ideal data-interchange language.</p>
<p>JSON is built on two structures:</p>
<ul>
<li>A collection of name/value pairs. In various languages, this is realized as an&nbsp;<em>object</em>, record, struct, dictionary, hash table, keyed list, or associative array.</li>
<li>An ordered list of values. In most languages, this is realized as an&nbsp;<em>array</em>, vector, list, or sequence.</li>
</ul>
<p>These are universal data structures. Virtually all modern programming languages support them in one form or another. It makes sense that a data format that is interchangeable with programming languages also be based on these structures.</p><p>Address of the bookmark: <a href="http://json.org/" rel="nofollow">http://json.org/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection</guid>
	<pubDate>Wed, 08 May 2024 07:02:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection</link>
	<title><![CDATA[Alvis: a tool for contig and read ALignment VISualisation and chimera detection]]></title>
	<description><![CDATA[<p><span>Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.</span></p>
<p>More at&nbsp;https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0</p><p>Address of the bookmark: <a href="https://github.com/SR-Martin/alvis" rel="nofollow">https://github.com/SR-Martin/alvis</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32134/lifemap</guid>
	<pubDate>Mon, 10 Apr 2017 05:42:37 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32134/lifemap</link>
	<title><![CDATA[Lifemap]]></title>
	<description><![CDATA[<p><strong>Lifemap</strong> is an interactive tool to explore the WHOLE NCBI TAXONOMY. The concept used in <strong>Lifemap</strong> is similar to the one used in cartography with tools like Google Maps&copy; or Open Street Maps: exploring is done by zooming and panning.</p>
<div>
<p>&nbsp;The current tree contains ALL species present in NCBI taxonomy as of <span style="text-decoration: underline;">October 18th, 2016</span>: 1,135,169 species including 10,545 Archaea, 418,777 Bacteria and 705,847 Eukaryotes. The Lifemap tree is updated every two weeks.</p>
</div>
<p>&nbsp;All the nodes in the tree are clickable. This displays various information and options:</p>
<ul>
<li>The species name (and the associated common name if there is one)</li>
<li>The rank (kingdom, family, class, species...)</li>
<li>Ability to go to the corresponding node/species on NCBI web site (displayed in a new window)</li>
<li>Possibility to download the corresponding subtree in newick extended format</li>
<li>Possibilty to get the whole lineage from the current node/tip to the root of the tree.</li>
</ul><p>Address of the bookmark: <a href="http://lifemap-ncbi.univ-lyon1.fr/" rel="nofollow">http://lifemap-ncbi.univ-lyon1.fr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/view/459</guid>
	<pubDate>Thu, 11 Jul 2013 14:39:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/view/459</link>
	<title><![CDATA[Python vs Perl]]></title>
	<description><![CDATA[<p>Why bioinformatician still using Perl when Python is easy to code, good in ReXp and faster than perl?</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32187/chromhmm-chromatin-state-discovery-and-characterization</guid>
	<pubDate>Wed, 19 Apr 2017 04:06:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32187/chromhmm-chromatin-state-discovery-and-characterization</link>
	<title><![CDATA[ChromHMM: Chromatin state discovery and characterization]]></title>
	<description><![CDATA[<p><span>ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization of each state. ChromHMM also produces files with genome-wide maps of chromatin state annotations that can be directly visualized in a genome browser.&nbsp;</span><br><br></p>
<ul>
<li><a href="http://compbio.mit.edu/ChromHMM/ChromHMM.zip">ChromHMM software v1.12</a>&nbsp;(<a href="http://compbio.mit.edu/ChromHMM/versionlog.txt">version log</a>)</li>
<li><a href="http://compbio.mit.edu/ChromHMM/ChromHMM_manual.pdf">ChromHMM manual</a></li>
</ul><p>Address of the bookmark: <a href="http://compbio.mit.edu/ChromHMM/" rel="nofollow">http://compbio.mit.edu/ChromHMM/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/840/junior-research-fellow-jrf</guid>
  <pubDate>Sat, 13 Jul 2013 11:17:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[Junior Research Fellow (JRF)]]></title>
  <description><![CDATA[
<p>School of Biotechnology<br />Gautam Buddha University<br />Greater Noida, UP - 201310</p>

<p>Applications are invited for one position of Junior Research Fellow (JRF) in a Department of Biotechnology (DBT) sponsored research project entitled “Design, synthesis and evaluation of potent aminopeptidase inhibitors for malarial therapy” under the supervision of Dr. Shakti Sahi.</p>

<p>The monthly fellowship of JRF will be Rs 12,000/- plus HRA as per the University rules.</p>

<p>Essential Qualification: Master degree in any discipline of Life Science with NET qualified.</p>

<p>Desirable Qualification: Preference will be given to candidates having research experience in in silico drug designing/Bioinformatics.</p>

<p>Interested candidates may send their resume to undersigned on or before 14th July 2013 by post-mail/e-mail shaktis@gbu.ac.in or shaktisahi@gmail.com. No TA and DA will be paid for appearing for the interview. Dr. Shakti Sahi (Principle Investigator)</p>

<p>Advertisement:<br />www.gbu.ac.in/Recruitment/JRF_Advt_DBTProject_Shakt</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32379/enrichr-a-comprehensive-gene-set-enrichment-analysis</guid>
	<pubDate>Thu, 27 Apr 2017 05:42:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32379/enrichr-a-comprehensive-gene-set-enrichment-analysis</link>
	<title><![CDATA[Enrichr: a comprehensive gene set enrichment analysis]]></title>
	<description><![CDATA[<p><span>Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at:&nbsp;</span><a href="http://amp.pharm.mssm.edu/Enrichr" target="">http://amp.pharm.mssm.edu/Enrichr</a><span>.</span></p>
<p>https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377</p><p>Address of the bookmark: <a href="http://amp.pharm.mssm.edu/Enrichr/" rel="nofollow">http://amp.pharm.mssm.edu/Enrichr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/847/nedelec-lab</guid>
  <pubDate>Sat, 13 Jul 2013 17:38:55 -0500</pubDate>
  <link></link>
  <title><![CDATA[Nedelec Lab]]></title>
  <description><![CDATA[
<p>Location :European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.</p>

<p>Our long-term research objective is to understand microtubule organization in living cells, with an emphasis on mitosis. We develop in-vitro assays, quantitative image analysis and cytosim, a computer simulation to study cellular architecture from a mechanistic angle, modeling the interactions of microtubules and related proteins such as molecular motors. In the past, we combined simulations and experiments to study microtubule self-organization, and the mechanical stability of two interacting asters. More recently, we looked at the focusing of mitotic fibers, the formation of antiparallel arrays of microtubules in fission yeast and the spindle positionning in C. elegans.<br />We are supported by BioMS, an initiative in Systems Biology, and involved in Cell networks.</p>

<p>Link: http://www.cytosim.org</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32483/cla-contig-layout-authenticator</guid>
	<pubDate>Fri, 05 May 2017 05:58:36 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32483/cla-contig-layout-authenticator</link>
	<title><![CDATA[CLA: Contig-Layout-Authenticator]]></title>
	<description><![CDATA[<p><span>To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.</span></p>
<p><span>Script&nbsp;https://sourceforge.net/projects/c-l-authenticator/files/</span></p><p>Address of the bookmark: <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155459" rel="nofollow">http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155459</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/855/bahlo-lab</guid>
  <pubDate>Sun, 14 Jul 2013 12:17:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bahlo Lab]]></title>
  <description><![CDATA[
<p>Melanie Bahlo is an applied statistician working in the areas of statistical genetics, bioinformatics and population genetics. Her main area of research is linkage mapping, in humans and mice.</p>

<p>Research Area:<br />Mapping loci in ENU mutants in mice in complex pedigrees<br />Investigation of DNA sharing in distantly related individuals<br />CNV analysis in pedigrees and connections to linkage studies<br />Statistical Genetics</p>

<p>Link @ http://www.wehi.edu.au/faculty_members/dr_melanie_bahlo</p>
]]></description>
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