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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41565?offset=20</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43587/fix-rewritable-error-of-elgg</guid>
	<pubDate>Mon, 15 Nov 2021 06:23:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43587/fix-rewritable-error-of-elgg</link>
	<title><![CDATA[Fix rewritable error of ELGG !]]></title>
	<description><![CDATA[<p>The&nbsp;<code><a href="https://httpd.apache.org/docs/2.4/mod/mod_rewrite.html">mod_rewrite</a></code>&nbsp;module uses a rule-based rewriting engine, based on a PCRE regular-expression parser, to rewrite requested URLs on the fly. By default,&nbsp;<code><a href="https://httpd.apache.org/docs/2.4/mod/mod_rewrite.html">mod_rewrite</a></code>&nbsp;maps a URL to a filesystem path. However, it can also be used to redirect one URL to another URL, or to invoke an internal proxy fetch.</p>
<p><code><a href="https://httpd.apache.org/docs/2.4/mod/mod_rewrite.html">mod_rewrite</a></code>&nbsp;provides a flexible and powerful way to manipulate URLs using an unlimited number of rules. Each rule can have an unlimited number of attached rule conditions, to allow you to rewrite URL based on server variables, environment variables, HTTP headers, or time stamps.</p>
<p><code><a href="https://httpd.apache.org/docs/2.4/mod/mod_rewrite.html">mod_rewrite</a></code>&nbsp;operates on the full URL path, including the path-info section. A rewrite rule can be invoked in&nbsp;<code>httpd.conf</code>&nbsp;or in&nbsp;<code>.htaccess</code>. The path generated by a rewrite rule can include a query string, or can lead to internal sub-processing, external request redirection, or internal proxy throughput.</p>
<p>Further details, discussion, and examples, are provided in the&nbsp;<a href="https://httpd.apache.org/docs/2.4/rewrite/">detailed mod_rewrite documentation</a>.</p>
<p>&nbsp;</p>
<ul>
<li>sudo a2enmod rewrite</li>
</ul>
<ul>
<li>sudo systemctl restart apache2</li>
</ul>
<ul>
<li>sudo nano /etc/apache2/sites-available/000-default.conf</li>
</ul>
<p>Write this</p>
<div title="/etc/apache2/sites-available/000-default.conf">/etc/apache2/sites-available/000-default.conf</div>
<div>
<div>
<pre><code><span>&lt;</span>VirtualHost *:8<span><span>0</span>&gt;</span>
    <span></span><span><span>&lt;</span>Directory /var/www/html<span>&gt;</span></span><span></span>
        <span>Options Indexes FollowSymLinks MultiViews</span>
        <span>AllowOverride All</span>
        <span>Require all granted</span>
    <span></span><span><span>&lt;</span>/Directory<span>&gt;</span></span><span></span>

    <span>.</span> <span>.</span> <span>.</span>
<span>&lt;</span>/VirtualHost<span>&gt;</span></code></pre>
</div>
</div><p>Address of the bookmark: <a href="https://www.digitalocean.com/community/tutorials/how-to-rewrite-urls-with-mod_rewrite-for-apache-on-ubuntu-18-04" rel="nofollow">https://www.digitalocean.com/community/tutorials/how-to-rewrite-urls-with-mod_rewrite-for-apache-on-ubuntu-18-04</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44213/bioinformatics-tools-to-explore-ssrs-in-genomes</guid>
	<pubDate>Tue, 07 Mar 2023 13:06:15 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44213/bioinformatics-tools-to-explore-ssrs-in-genomes</link>
	<title><![CDATA[Bioinformatics tools to explore SSRs in genomes !]]></title>
	<description><![CDATA[<p>There are several bioinformatics tools that can be used to explore Simple Sequence Repeats (SSRs), which are also known as microsatellites. Here are a few examples:</p><ol>
<li>
<p>MISA: MISA (MIcroSAtellite) is a web-based tool that can identify SSRs in DNA sequences. It can be used to analyze nucleotide sequences from various organisms and can identify perfect, compound, and imperfect SSRs.</p>
</li>
<li>
<p>SSR Locator: SSR Locator is a web-based tool that identifies SSRs in both DNA and RNA sequences. It can identify perfect, compound, and imperfect SSRs, and can also filter out low complexity regions.</p>
</li>
<li>
<p>SciRoKo: SciRoKo is a software tool that can identify SSRs in DNA sequences. It can be used to analyze genomic and transcriptomic sequences from various organisms and can identify perfect, compound, and imperfect SSRs.</p>
</li>
<li>
<p>Primer3: Primer3 is a web-based tool that designs PCR primers for SSRs. It can design primers for perfect and imperfect SSRs, and can be used to design primers for SSRs in various organisms.</p>
</li>
<li>
<p>QDD: QDD (Quick Detection of Duplication) is a software tool that can identify SSRs in DNA sequences and can also identify duplicate loci. It can be used to analyze genomic and transcriptomic sequences from various organisms.</p>
</li>
</ol><p>These are just a few examples of the many bioinformatics tools available for exploring SSRs. Depending on your specific needs and research questions, you may find that other tools are more appropriate for your analysis.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/10810/uk-executive-accused-in-glaxosmithkline-china-probe</guid>
	<pubDate>Wed, 14 May 2014 04:55:42 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/10810/uk-executive-accused-in-glaxosmithkline-china-probe</link>
	<title><![CDATA[UK executive accused in GlaxoSmithKline China probe]]></title>
	<description><![CDATA[<p>Mark Reilly and two other colleagues are also suspected of bribing government officials in Beijing and Shanghai, they said.</p><p>Police have handed the case over to prosecutors, officials said.</p><p>GSK said it took the allegations "very seriously" and would co-operate with the authorities over the matter.</p><p>Chinese authorities announced in July last year that they were investigating GSK, detaining four Chinese GSK executives.</p><p>http://www.bbc.com/news/world-asia-china-27403914</p>]]></description>
	<dc:creator>phu</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37529/bokeh-an-interactive-visualization-library-that-targets-modern-web-browsers-for-presentation</guid>
	<pubDate>Fri, 10 Aug 2018 18:43:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37529/bokeh-an-interactive-visualization-library-that-targets-modern-web-browsers-for-presentation</link>
	<title><![CDATA[Bokeh: An interactive visualization library that targets modern web browsers for presentation]]></title>
	<description><![CDATA[<p id="about">Bokeh is an interactive visualization library that targets modern web browsers for presentation. Its goal is to provide elegant, concise construction of versatile graphics, and to extend this capability with high-performance interactivity over very large or streaming datasets. Bokeh can help anyone who would like to quickly and easily create interactive plots, dashboards, and data applications.</p>
<p>To get started using Bokeh to make your visualizations, see the&nbsp;<a href="https://bokeh.pydata.org/en/latest/docs/user_guide.html#userguide">User Guide</a>.</p>
<p>To see examples of how you might use Bokeh with your own data, check out the&nbsp;<a href="https://bokeh.pydata.org/en/latest/docs/gallery.html#gallery">Gallery</a>.</p>
<p>A complete API reference of Bokeh is at&nbsp;<a href="https://bokeh.pydata.org/en/latest/docs/reference.html#refguide">Reference Guide</a>.</p>
<p>If you are interested in contributing to Bokeh, or extending the library, see the&nbsp;<a href="https://bokeh.pydata.org/en/latest/docs/dev_guide.html#devguide">Developer Guide</a>.</p><p>Address of the bookmark: <a href="https://bokeh.pydata.org/en/latest/" rel="nofollow">https://bokeh.pydata.org/en/latest/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39114/plumberan-r-package-that-converts-your-existing-r-code-to-a-web-api</guid>
	<pubDate>Wed, 13 Mar 2019 19:20:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39114/plumberan-r-package-that-converts-your-existing-r-code-to-a-web-api</link>
	<title><![CDATA[plumber:An R package that converts your existing R code to a web API]]></title>
	<description><![CDATA[<p>plumber allows you to create a REST API by merely decorating your existing R source code with special comments. Take a look at an example.</p>
<pre><code><span># plumber.R
</span><span>
</span><span>#* Echo back the input
#* @param msg The message to echo
#* @get /echo
</span><span>function</span><span>(</span><span>msg</span><span>=</span><span>""</span><span>){</span><span>
  </span><span>list</span><span>(</span><span>msg</span><span> </span><span>=</span><span> </span><span>paste0</span><span>(</span><span>"The message is: '"</span><span>,</span><span> </span><span>msg</span><span>,</span><span> </span><span>"'"</span><span>))</span><span>
</span><span>}</span><span>

</span><span>#* Plot a histogram
#* @png
#* @get /plot
</span><span>function</span><span>(){</span><span>
  </span><span>rand</span><span> </span><span>&lt;-</span><span> </span><span>rnorm</span><span>(</span><span>100</span><span>)</span><span>
  </span><span>hist</span><span>(</span><span>rand</span><span>)</span><span>
</span><span>}</span><span>

</span><span>#* Return the sum of two numbers
#* @param a The first number to add
#* @param b The second number to add
#* @post /sum
</span><span>function</span><span>(</span><span>a</span><span>,</span><span> </span><span>b</span><span>){</span><span>
  </span><span>as.numeric</span><span>(</span><span>a</span><span>)</span><span> </span><span>+</span><span> </span><span>as.numeric</span><span>(</span><span>b</span><span>)</span><span>
</span><span>}</span></code></pre><p>Address of the bookmark: <a href="https://www.rplumber.io/" rel="nofollow">https://www.rplumber.io/</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/42370/ncbi-blast-have-added-new-columns-to-the-descriptions</guid>
	<pubDate>Tue, 01 Dec 2020 09:56:07 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/42370/ncbi-blast-have-added-new-columns-to-the-descriptions</link>
	<title><![CDATA[NCBI BLAST have added new columns to the Descriptions]]></title>
	<description><![CDATA[<p><span>NCBI BLAST have added new columns to the Descriptions Table for web BLAST output. The new columns are&nbsp; Scientific Name, Common Name, Taxid, and Accession Length. Common Name and Accession Length are now part of the default display. You can click 'Select columns' or 'Manage columns' to add or remove columns from the display Your preferences will be saved for your next visit to BLAST, and when you download your results, whatever columns you have displayed will be saved. See the NCBI Insights post (</span><a href="https://go.usa.gov/x7fPE" target="_blank">https://go.usa.gov/x7fPE</a><span>) for more details.</span></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl</guid>
	<pubDate>Tue, 26 Dec 2017 18:06:57 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34812/building-web-uis-with-mojolicious-perl</link>
	<title><![CDATA[Building Web UIs With Mojolicious Perl]]></title>
	<description><![CDATA[<p>Mojolicious is one of 3 leading web frameworks available in the perl ecosystem (along with Dancer and Catalyst) and by far my favorite.</p>
<p>Mojolicious aims to provide a complete web development experience. It thus has no hard dependencies, comes with a built-in development and production server and many other features one needs to build a web application. It's easy to install, has an applciation generator script and many plugins and extensions.</p>
<p><em>Libraries for developing Web applications</em></p>
<ul>
<li><a href="https://metacpan.org/pod/Amon2">Amon2</a></li>
<li><a href="https://metacpan.org/pod/Catalyst">Catalyst</a>&nbsp;- Overflowing with features. Very popular.</li>
<li><a href="https://metacpan.org/pod/Dancer">Dancer</a>&nbsp;(<a href="http://perldancer.org/">Official site</a>)</li>
<li><a href="https://metacpan.org/pod/Dancer2">Dancer2</a></li>
<li><a href="https://metacpan.org/pod/Gantry">Gantry</a>&nbsp;- Web application framework for mod_perl, cgi, etc.</li>
<li><a href="https://metacpan.org/pod/Kossy">Kossy</a>&nbsp;- A Web framework with simple interface.</li>
<li><a href="https://metacpan.org/pod/Mojolicious">Mojolicious</a>&nbsp;- An all in one framework.</li>
<li><a href="https://metacpan.org/pod/Poet">Poet</a>&nbsp;- a modern Perl web framework for Mason developers</li>
</ul><p>Address of the bookmark: <a href="https://www.ynonperek.com/2017/09/28/perl-mojolicious-web-development/" rel="nofollow">https://www.ynonperek.com/2017/09/28/perl-mojolicious-web-development/</a></p>]]></description>
	<dc:creator>Jit</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/36897/gmcloser-closing-gaps-in-assemblies-accurately-with-a-likelihood-based-selection-of-contig-or-long-read-alignments</guid>
	<pubDate>Mon, 11 Jun 2018 05:43:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36897/gmcloser-closing-gaps-in-assemblies-accurately-with-a-likelihood-based-selection-of-contig-or-long-read-alignments</link>
	<title><![CDATA[GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments]]></title>
	<description><![CDATA[GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from various organisms that the gap-closing accuracy of GMcloser is 3–100-fold higher than those of other available tools, with similar efficiency.

https://academic.oup.com/bioinformatics/article/31/23/3733/209212<p>Address of the bookmark: <a href="https://academic.oup.com/bioinformatics/article/31/23/3733/209212" rel="nofollow">https://academic.oup.com/bioinformatics/article/31/23/3733/209212</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43888/syri-compares-alignments-between-two-chromosome-level-assemblies-and-identifies-synteny-and-structural-rearrangements</guid>
	<pubDate>Wed, 01 Jun 2022 02:01:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43888/syri-compares-alignments-between-two-chromosome-level-assemblies-and-identifies-synteny-and-structural-rearrangements</link>
	<title><![CDATA[Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.]]></title>
	<description><![CDATA[<p><span>Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.</span></p>
<p><span><img src="https://github.com/schneebergerlab/syri/raw/master/example/ampril_col0_chr3_6600000_10000000.png" alt="image" style="border: 0px;"></span></p><p>Address of the bookmark: <a href="https://github.com/schneebergerlab/syri" rel="nofollow">https://github.com/schneebergerlab/syri</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>

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