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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/19636?offset=990</link>
	<atom:link href="https://bioinformaticsonline.com/related/19636?offset=990" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43046/postdoctoral-fellow-for-a-large-scale-microbial-comparative-genomics</guid>
  <pubDate>Thu, 29 Apr 2021 08:44:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[postdoctoral fellow for a large-scale microbial comparative genomics !]]></title>
  <description><![CDATA[
<p>Asaf Levy hiring a postdoctoral fellow for a large-scale microbial comparative genomics project at the Hebrew University of Jerusalem (Israel). <br />The project is a continuation of Levy Asaf et al. Nature Genetics 2018 paper.<br />Requirements: <br />1.Experience with programming in at least one programming language, preferably Python.<br />2.A PhD in bioinformatics/computational biology<br />3.At least one first authorship publication in a good journal, preferably more.<br />4.Good communication skills in English <br />5.Ability to enter and study in Israel (not applicable for Pakistani people, for example). <br />6.Ability to work in a team.<br />Please send CV to alevy@mail.huji.ac.il</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26587/last</guid>
	<pubDate>Wed, 09 Mar 2016 14:27:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26587/last</link>
	<title><![CDATA[LAST]]></title>
	<description><![CDATA[<p style="text-align: center;"><img src="http://last.cbrc.jp/lastwebfig.png" alt="sketch of  similar regions in sequences" style="border: 0px;"></p>
<p>LAST can:</p>
<ul>
<li>Handle <strong>big</strong> sequence data, e.g:
<ul>
<li>Compare two vertebrate genomes</li>
<li>Align billions of DNA reads to a genome</li>
</ul>
</li>
<li>Indicate the <a href="http://lastweb.cbrc.jp/about.html">reliability</a> of each aligned column.</li>
<li>Use sequence quality data <a href="http://nar.oxfordjournals.org/content/38/7/e100.abstract">properly</a>.</li>
<li>Compare DNA to proteins, with frameshifts.</li>
<li>Compare PSSMs to sequences</li>
<li>Calculate the likelihood of chance similarities between random sequences.</li>
<li>Do split and spliced alignment.</li>
<li><a href="http://last.cbrc.jp/doc/last-train.html">Train</a> alignment parameters for unusual kinds of sequence (e.g. nanopore).</li>
</ul><p>Address of the bookmark: <a href="http://last.cbrc.jp/" rel="nofollow">http://last.cbrc.jp/</a></p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44661/lovis4u-locus-visualisation-tool-for-comparative-genomics</guid>
	<pubDate>Tue, 17 Sep 2024 02:30:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44661/lovis4u-locus-visualisation-tool-for-comparative-genomics</link>
	<title><![CDATA[LoVis4u: Locus Visualisation tool for comparative genomics]]></title>
	<description><![CDATA[<p dir="auto"><a href="https://github.com/art-egorov/lovis4u/blob/main/docs/img/lovis4u_logo.png" target="_blank"><img src="https://github.com/art-egorov/lovis4u/raw/main/docs/img/lovis4u_logo.png" alt="image" width="300" style="border: 0px; border: 0px;"></a></p>
<div dir="auto">
<h2 dir="auto">Description</h2>
<a href="https://github.com/art-egorov/lovis4u#description"></a></div>
<p dir="auto"><span>LoVis4u</span>&nbsp;is a bioinformatics tool for&nbsp;<span>Lo</span>ci&nbsp;<span>Vis</span>ualisation.</p>
<p dir="auto"><span>LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.</span></p>
<p dir="auto">https://art-egorov.github.io/lovis4u/</p>
<p dir="auto">&nbsp;</p><p>Address of the bookmark: <a href="https://github.com/art-egorov/lovis4u" rel="nofollow">https://github.com/art-egorov/lovis4u</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34940/jpred4-a-protein-secondary-structure-prediction-server</guid>
	<pubDate>Fri, 29 Dec 2017 16:14:28 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34940/jpred4-a-protein-secondary-structure-prediction-server</link>
	<title><![CDATA[JPred4: A Protein Secondary Structure Prediction Server]]></title>
	<description><![CDATA[<p><span>JPred4 (</span><a href="http://www.compbio.dundee.ac.uk/jpred4" target="">http://www.compbio.dundee.ac.uk/jpred4</a><span>) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction.</span></p><p>Address of the bookmark: <a href="http://www.compbio.dundee.ac.uk/jpred4/" rel="nofollow">http://www.compbio.dundee.ac.uk/jpred4/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/43605/installing-elgg-on-ubuntu</guid>
	<pubDate>Thu, 25 Nov 2021 01:45:59 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/43605/installing-elgg-on-ubuntu</link>
	<title><![CDATA[Installing ELGG on Ubuntu !]]></title>
	<description><![CDATA[<p>Follow this:</p><h3>Settings file</h3><ul>
<li>
<div>
<div>
<div>Error</div>
<div>
<p>Your web server does not have permission to create the settings.php file in your installation directory. You have two choices:</p>
<p>1. Change the permissions on the elgg-config directory of your Elgg installation</p>
<p>2. Copy the file elgg-config/settings.example.php to elgg-config/settings.php and follow the instructions in it for setting your database parameters.</p>
</div>
</div>
</div>
</li>
</ul><p>&nbsp;</p><p>To resolve this --&nbsp;</p><p>Change the permision&nbsp;</p><p>chmod 777 elgg-config</p><h3>Web server</h3><ul>
<li>
<div>
<div>
<div>Warning</div>
<div>
<p>Your server does not support automatic testing of the rewrite rules and your browser does not support checking via JavaScript. You can continue the installation, but you may experience problems with your site. You can manually test the rewrite rules by clicking this link:&nbsp;test. You will see the word success if the rules are working.</p>
</div>
</div>
</div>
</li>
</ul><p>create a .httaccess</p><p>and provide detail in it</p><p><span style="text-decoration: underline;">Installation of Elgg</span><span></span></p><p>&nbsp;</p><p>(Note: Elgg requires&nbsp;<a href="http://www.cs.oswego.edu/~odendahl/misc/howto/mysql/">installing an instance of MySQL</a>.)</p><p>&nbsp;</p><p><span style="text-decoration: underline;">Steps to make adjustment and disposal of trial installations easier</span>.</p><p>&nbsp;</p><p><span style="text-decoration: underline;">MySQL</span></p><p>At this point, we assume you've set up your&nbsp;<tt>MySQL</tt>&nbsp;database</p><div><ol>
<li>Start your&nbsp;<tt>mysqld</tt>&nbsp;server daemon.<br />(For the sake of this example, we'll assume we're running on port 9999; you shouldn't actually use this port because only one daemon can run on any port number.)</li>
<li>Login to the server as&nbsp;<tt>root</tt>&nbsp;user, using the&nbsp;<tt>mysql</tt>&nbsp;client.</li>
<li>Create a database to store Elgg's tables. We'll call the database&nbsp;<tt>elggalpha</tt>.<br /><tt>mysql&gt; create database elggalpha;</tt></li>
<li>Grant access to a user &mdash; for this example we'll call him/her&nbsp;<tt>elggalphauser</tt>.
<pre>mysql&gt; grant all privileges on elggalpha.* to 'elggalphauser'@'moxie'
    -&gt; identified by 'secretpassword';
</pre>
</li>
</ol></div><p>&nbsp;</p><p><span style="text-decoration: underline;">Elgg</span></p><p>&nbsp;</p><div><ol>
<li>Type&nbsp;<tt>umask 022</tt></li>
<li>Change into your&nbsp;<tt>public_html</tt>&nbsp;directory (<em>aka</em>&nbsp;folder).<br /><tt>cd public_html</tt></li>
<li>make a directory called&nbsp;<tt>elgg</tt><br /><tt>mkdir elgg</tt></li>
<li>Change into the&nbsp;<tt>elgg</tt>&nbsp;subdirectory of&nbsp;<tt>public_html</tt>.<br /><tt>cd elgg</tt></li>
<li>download elgg into this directory</li>
<li>you'll end up with a file named<br /><tt>/home/<em>your-user-id</em>/public_html/elgg/elgg-X.X.X.X.zip</tt><br />(It's not literally&nbsp;<tt>X.X.X.X</tt>, it might be&nbsp;<tt>elgg-1.8.0.1.zip</tt>, for example.)</li>
<li>unzip elgg<br /><tt>unzip -q elgg-1.8.0.1.zip</tt></li>
<li>you'll end up with a directory (folder) named<br /><tt>/home/<em>your-user-id</em>/public_html/elgg/elgg-X.X.X.X</tt></li>
<li>make a symbolic link (<em>aka</em>&nbsp;shortcut) to this<br /><tt>ln -s elgg-X.X.X.X alpha</tt><br />(For example,&nbsp;<tt>ln -s elgg-1.8.0.1 alpha</tt>)</li>
<li>Give user&nbsp;<tt>nobody</tt>&nbsp;access to this directory<br /><tt>/usr/misc/bin/acl.sh -r -u nobody elgg-1.8.0.1</tt></li>
<li>create a data directory for&nbsp;<tt>elgg</tt>&nbsp;(get into your home directory first):
<pre>cd
mkdir -p elgg/alpha/data
chmod -R 755 elgg/alpha/data
</pre>
</li>
<li>Change into the&nbsp;<tt>elgg/alpha</tt>&nbsp;directory.<br /><tt>cd elgg/alpha</tt></li>
<li>Give user&nbsp;<tt>nobody</tt>&nbsp;access to this subdirectory&nbsp;<tt>data</tt><br /><tt>/usr/misc/bin/acl.sh -u nobody data</tt></li>
<li>In your browser, navigate to your elgg installation<br /><tt>http://moxie.cs.oswego.edu/~<em>your-user-id</em>/elgg/alpha/</tt><br />You'll have a screen which includes this message:
<pre>Welcome

Installing Elgg has 6 simple steps and reading this welcome is the first one!

If you haven't already, read through the installation instructions included with Elgg (or click the instructions link at the bottom of the page).

If you are ready to proceed, click the Next button.
</pre>
</li>
<li>Follow configuration process:
<ul>
<li>The first screen probably will contain a success message in green and a failure message in pink:
<pre><span>Requirements check</span>

Your server failed the requirements check. After you have fixed the below issues, refresh this
page. Check the troubleshooting links at the bottom of this page if you need further assistance.
<span>PHP</span></pre>
<div>Your server's PHP satisfies all of Elgg's requirements.</div>
<pre>
<span>Web server</span></pre>
<div>We think your server is running the Apache web server. The rewrite test failed and the most likely cause is that AllowOverride is not set to All for Elgg's directory. This prevents Apache from processing the .htaccess file which contains the rewrite rules. A less likely cause is Apache is configured with an alias for your Elgg directory and you need to set the RewriteBase in your .htaccess. There are further instructions in the .htaccess file in your Elgg directory.</div>
<pre>
<span>Database</span></pre>
<div>The database requirements are checked when Elgg loads its database.</div>
</li>
<li>To correct this, replace the&nbsp;<tt>.htaccess</tt>&nbsp;file that Elgg created with one that you can edit:
<pre>cp -ip .htaccess temp-htaccess
rm .htaccess
mv temp-htaccess .htaccess
</pre>
</li>
<li>Edit the&nbsp;<tt>.htaccess</tt>&nbsp;file: Go to approximately line 101 (where it says&nbsp;<tt>#RewriteBase /</tt>) and add the line:<br /><tt>RewriteBase /~<em>your-user-id</em>/elgg/alpha/</tt></li>
<li>Be sure to save the edited file.
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>Click the&nbsp;<span>Refresh</span>&nbsp;button.
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>If this hasn't fixed things, seek professional help.
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>Click the&nbsp;<span>Next</span>&nbsp;button.
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>Fill in the parameters appropriate to your MySQL installation.
<pre><span>Database installation</span>

If you haven't already created a database for Elgg, do that now. Then fill in the values below to
initialize the Elgg database.

<span>Database Username</span></pre>
<div>elggalphauser</div>
<pre>User that has full priviledges to the MySQL database that you created for Elgg

<span>Database Password</span></pre>
<div>secretpassword</div>
<pre>Password for the above database user account

<span>Database Name</span></pre>
<div>elggalpha</div>
<pre>Name of the Elgg database

<span>Database Host</span></pre><sup>&Dagger;</sup>
<div>moxie:9999</div>
<pre>Hostname of the MySQL server (usually localhost)
<strong>&Dagger;You might need to use <tt>127.0.0.1:9999</tt> for the host
    if you haven't set up MySQL as we've done.</strong>



<span>Database Table Prefix</span></pre>
<div>elgg_</div>
<pre>The prefix given to all of Elgg's tables (usually elgg_)
</pre>
<div><span>Next</span></div>
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>Continue filling in forms as requested.
<pre>Configure site</pre>
<div>Database has been installed.</div>
<pre>
We need some information about the site as we configure Elgg. If you haven't created a data directory for Elgg, you need to do so now.

<span>Site Name</span></pre>
<div>My Elgg Site version Alpha</div>
<pre>The name of your new Elgg site

<span>Site Email Address</span></pre>
<div><em>your-user-id</em>@oswego.edu</div>
<pre>Email address used by Elgg for communication with users

<span>Site URL</span></pre>
<div>http://moxie.cs.oswego.edu/~<em>your-user-id</em>/elgg/alpha/</div>
<pre>The address of the site (Elgg usually guesses this correctly)

<span>Elgg Install Directory</span></pre>
<div>/home/<em>your-user-id</em>/public_html/elgg/elgg.1.8.0.1/</div>
<pre>The directory where you put the Elgg code (Elgg usually guesses this correctly)

<span>Data Directory</span></pre>
<div>/home/<em>your-user-id</em>/elgg/alpha/data</div>
<pre>The directory that you created for Elgg to save files (the permissions on this directory are checked
when you click Next)

<span>Default Site Access</span></pre>
<div>Public</div>
<pre>The default access level for new user created content
</pre>
</li>
<li>
<pre><span>Create admin account</span></pre>
<div>Site settings have been saved.</div>
<pre>
It is now time to create an administrator's account.

<span>Display Name</span></pre>
<div>&nbsp;</div>
<pre>The name that is displayed on the site for this account

<span>Email Address</span></pre>
<div>&nbsp;</div>
<pre>
<span>Username</span></pre>
<div>&nbsp;</div>
<pre>Account username used for logging in

<span>Password</span></pre>
<div>&nbsp;</div>
<pre>Account password must be at least 6 characters long

<span>Password Again</span></pre>
<div>&nbsp;</div>
<pre>Retype password to confirm</pre>
</li>
</ul>
</li>
</ol></div>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37937/frodock-20-fast-protein%E2%80%93protein-docking-server</guid>
	<pubDate>Wed, 17 Oct 2018 04:31:30 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37937/frodock-20-fast-protein%E2%80%93protein-docking-server</link>
	<title><![CDATA[FRODOCK 2.0: fast protein–protein docking server]]></title>
	<description><![CDATA[<p><span>frodock: a&nbsp;user-friendly protein&ndash;protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein&ndash;protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein&ndash;protein binding conformations that can be further refined with more computationally demanding strategies.</span></p><p>Address of the bookmark: <a href="http://frodock.chaconlab.org/" rel="nofollow">http://frodock.chaconlab.org/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40865/dminda2-an-integrated-web-server-for-dna-motif-identification-and-analyses</guid>
	<pubDate>Sun, 02 Feb 2020 14:26:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40865/dminda2-an-integrated-web-server-for-dna-motif-identification-and-analyses</link>
	<title><![CDATA[DMINDA2: an integrated web server for DNA motif identification and analyses]]></title>
	<description><![CDATA[<p><span>DMINDA (</span><strong>D</strong><span>NA&nbsp;</span><strong>m</strong><span>otif&nbsp;</span><strong>i</strong><span>dentification a</span><strong>nd a</strong><span>nalyses) is an integrated web server for DNA motif identification and analyses</span></p>
<p><span>More at&nbsp;http://bmbl.sdstate.edu/DMINDA2/</span></p>
<p><span><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/</a></span></p><p>Address of the bookmark: <a href="http://bmbl.sdstate.edu/DMINDA2/" rel="nofollow">http://bmbl.sdstate.edu/DMINDA2/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/26435/bioinformatics-centre-bose-institute-vacancy-of-research-associate-senior-research-fellow</guid>
  <pubDate>Mon, 22 Feb 2016 03:27:17 -0600</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Centre, Bose Institute vacancy of Research Associate / Senior Research Fellow]]></title>
  <description><![CDATA[
<p>Bioinformatics Centre, Bose Institute vacancy of Research Associate / Senior Research Fellow</p>

<p>Location where with post of Research Associate / Senior Research Fellow is available:<br />Bioinformatics Centre, Bose Institute in Kolkata, West Bengal</p>

<p>Title of the Project: "Setting up of National Facility on Interactive Graphics Computer System".</p>

<p>No. of the Post: 01 One</p>

<p>Salary: Rs. 22000/- per month plus admissible HRA and Medical Benefits for RA and Rs. 20000/- per month plus admissible HRA and Medical Benefits for SRF (Extended).</p>

<p>Age Limit: Max. 35 years for RA and Max. 33 years for SRF (Extended)</p>

<p>Required Job Profile:</p>

<p>Candidate must possess PhD degree in biological or chemical sciences with in depth understanding of protein structure and function; experience on protein crystallization and various modeling software will be advantages and candidate who have submitted PhD thesis can be considered as extended SRF.</p>

<p>The project would involve cloning, expression, crustallization of vibrio cholera toxin, Ace and modeling of its admissible HRA and medical benefits for SRF (Extended).</p>

<p>How to apply:</p>

<p>Eligible and interested candidates should need to appear before the selection committee along with typed application addressed to the above mentioned address along with biodata with complete details and attested copies of certificates on 02.03.2016 at 11:30 am. No TA or DA will be paid for attending the interview. No TA or DA will be paid for attending the interview.</p>

<p>Refer to http://www.boseinst.ernet.in/ADVT/15/p_30.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41901/far-manager-commands-and-links</guid>
	<pubDate>Tue, 23 Jun 2020 06:24:36 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41901/far-manager-commands-and-links</link>
	<title><![CDATA[Far Manager Commands and Links !]]></title>
	<description><![CDATA[<p>Far Manager is a program for managing files and archives in&nbsp;<acronym title="2000/XP/2003/Vista/2008/7">Windows operating systems</acronym>. Far Manager works in text mode and provides a simple and intuitive interface for performing most of the necessary actions:</p>
<ul>
<li>viewing files and directories;</li>
<li>editing, copying and renaming files;</li>
<li>and many other actions.</li>
</ul>
<p><a href="https://www.farmanager.com/">https://www.farmanager.com/</a></p>
<p>Basic instruction at</p>
<p><a href="https://conemu.github.io/en/FarManager.html">https://conemu.github.io/en/FarManager.html</a></p>
<p>Plugins at&nbsp;</p>
<p><a href="https://plugring.farmanager.com/">https://plugring.farmanager.com/</a></p><p>Address of the bookmark: <a href="https://www.farmanager.com/" rel="nofollow">https://www.farmanager.com/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25781/bioinformatics-trainee-at-university-of-kalyani</guid>
  <pubDate>Tue, 22 Dec 2015 01:51:42 -0600</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Trainee at University of Kalyani]]></title>
  <description><![CDATA[
<p>Bioinformatics Trainee<br />Eligibility : MSc<br />Location : Kolkata<br />Last Date : 28 Dec 2015<br />Hiring Process : Walk - In<br />University of Kalyani </p>

<p>Bioinformatics Trainee Job position in University of Kalyani<br />Number of Posts :  02 <br />Qualification : M.Sc. in any branch of life science with prior knowledge of Bioinformatics <br />Fellowship / Stipend / Salary : As per DBT rules <br />Duration of the Post :  Six months starting from January, 2016 <br />How to apply<br />Walk-in-interview will be held on 28.12.2015 at Department of Biochemistry and Biophysics, University of Kalyani.</p>

<p>More at http://www.klyuniv.ac.in/index.php/recruitments</p>
]]></description>
</item>

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