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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/23892?offset=1320</link>
	<atom:link href="https://bioinformaticsonline.com/related/23892?offset=1320" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/2422/bioinformatics-codes-search</guid>
	<pubDate>Thu, 15 Aug 2013 11:08:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/2422/bioinformatics-codes-search</link>
	<title><![CDATA[Bioinformatics Codes Search]]></title>
	<description><![CDATA[<p>I bet, this website will be your best friend in near future. This helps us to explore the existing open source codes and learn from it.</p>
<p>You can find some useful open source bioinformatics codes for your analysis work. You can use the left bar options to filtere out or narrow down your search result. This webpage can be an useful resource for a beginners bioinformatician as it contain several bioinformatics basics script that are commonly used by biological programmers and biologist.</p>
<p>Stand on the slumped, dandruff-covered shoulders of millions of computer nerds. _/\_</p>
<p>Enjoy the code and research work.</p>
<p>http://code.ohloh.net/search?s=bioinformatics</p><p>Address of the bookmark: <a href="http://code.ohloh.net/search?s=bioinformatics" rel="nofollow">http://code.ohloh.net/search?s=bioinformatics</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/5191/programming-language-to-build-synthetic-dna</guid>
	<pubDate>Mon, 30 Sep 2013 16:37:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/5191/programming-language-to-build-synthetic-dna</link>
	<title><![CDATA[Programming language to build synthetic DNA]]></title>
	<description><![CDATA[<p style="color: #333333; font-size: 13px; font-style: normal; font-weight: normal; text-align: start;">A team led by <a href="http://homes.cs.washington.edu/~seelig/index.html">Georg Seelig</a>&nbsp;(<a href="http://homes.cs.washington.edu/~seelig/index.html">http://homes.cs.washington.edu/~seelig/index.html</a>) at&nbsp;University of Washington has developed a programming language for chemistry that it hopes will streamline efforts to design a network that can guide the behavior of chemical-reaction mixtures in the same way that embedded electronic controllers guide cars, robots and other devices. In medicine, such networks could serve as &ldquo;smart&rdquo; drug deliverers or disease detectors at the cellular level.</p><p style="color: #333333; font-size: 13px; font-style: normal; font-weight: normal; text-align: start;">Reference &amp; More @</p><p style="color: #333333; font-size: 13px; font-style: normal; font-weight: normal; text-align: start;"><a href="http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2013.189.html">http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2013.189.html</a></p><p style="color: #333333; font-size: 13px; font-style: normal; font-weight: normal; text-align: start;"><a href="http://www.washington.edu/news/2013/09/30/uw-engineers-invent-programming-language-to-build-synthetic-dna/">http://www.washington.edu/news/2013/09/30/uw-engineers-invent-programming-language-to-build-synthetic-dna/</a></p><p style="color: #333333; font-size: 13px; font-style: normal; font-weight: normal; text-align: start;">Image source:&nbsp;washington.edu</p><p style="color: #333333; font-size: 13px; font-style: normal; font-weight: normal; text-align: start;"><img src="http://www.washington.edu/news/files/2013/09/Programmable-chemistry-2.jpg" alt="image" style="border: 0px; border: 0px;"></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/12943/a-history-of-bioinformatics-in-the-year-2039</guid>
	<pubDate>Wed, 23 Jul 2014 06:37:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/12943/a-history-of-bioinformatics-in-the-year-2039</link>
	<title><![CDATA[A History of Bioinformatics (in the Year 2039)]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/uwsjwMO-TEA" frameborder="0" allowfullscreen></iframe><p>C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039</p>]]></description>
	
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22938/research-assistant-in-computational-biology</guid>
  <pubDate>Wed, 24 Jun 2015 07:55:16 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research assistant in computational biology]]></title>
  <description><![CDATA[
<p>http://www.au.dk/en/about/vacant-positions/scientific-positions/stillinger/Vacancy/show/743161/5283/</p>

<p>Qualifications:<br />MSc degree in computer science, engineering, genetics or similar field with a strong emphasis on computational methods.</p>

<p>Deadline<br />01.08.2015</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/fun/view/14036/introduction-to-programming-write-short-programs-that-generate-graphics-and-animation</guid>
	<pubDate>Thu, 14 Aug 2014 23:29:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/fun/view/14036/introduction-to-programming-write-short-programs-that-generate-graphics-and-animation</link>
	<title><![CDATA[Introduction to programming. Write short programs that generate graphics and animation.]]></title>
	<description><![CDATA[<p>Introduction to programming. Write short programs that generate graphics and animation.</p><p>http://funprogramming.org/</p>]]></description>
	<dc:creator>Ram Yash Pal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34546/comparative-genomics-scripts</guid>
	<pubDate>Wed, 06 Dec 2017 15:20:45 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34546/comparative-genomics-scripts</link>
	<title><![CDATA[Comparative genomics scripts]]></title>
	<description><![CDATA[<p>Comparative genomics educational material and papers bookmarks</p>
<p>https://github.com/iansealy/coursera-comparinggenomes</p><p>Address of the bookmark: <a href="https://github.com/iansealy/coursera-comparinggenomes" rel="nofollow">https://github.com/iansealy/coursera-comparinggenomes</a></p>]]></description>
	<dc:creator>Jit</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/33219/dbcan-a-web-server-and-database-for-automated-carbohydrate-active-enzyme-annotation</guid>
	<pubDate>Mon, 29 May 2017 05:39:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33219/dbcan-a-web-server-and-database-for-automated-carbohydrate-active-enzyme-annotation</link>
	<title><![CDATA[dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation]]></title>
	<description><![CDATA[<p><a href="http://csbl.bmb.uga.edu/dbCAN/index.php">dbCAN</a>&nbsp;is a web server and&nbsp;<span style="text-decoration: underline;">D</span>ata<span style="text-decoration: underline;">B</span>ase for&nbsp;<a href="http://csbl.bmb.uga.edu/dbCAN/annotate.php"><strong>automated&nbsp;<span style="text-decoration: underline;">C</span>arbohydrate-active enzyme&nbsp;<span style="text-decoration: underline;">AN</span>notation</strong></a>, funded by the&nbsp;<a href="http://bioenergycenter.org/">BioEnergy Science Center of the DOE</a>. Similar resources on the web include&nbsp;<a href="http://www.cazy.org/" target="_blank">CAZy database</a>&nbsp;and&nbsp;<a href="http://cricket.ornl.gov/cgi-bin/cat.cgi" target="_blank">CAT</a>. All data in dbCAN are generated based on the family classification from&nbsp;<a href="http://www.cazy.org/" target="_blank">CAZy database</a>&nbsp;while it has the following&nbsp;<strong><span style="text-decoration: underline;">unique features</span></strong>&nbsp;compared with CAZy database and CAT:</p>
<ul>
<li>dbCAN provides the capability of&nbsp;<a href="http://csbl.bmb.uga.edu/dbCAN/annotate.php">automated and comprehensive CAZyme annotation</a>&nbsp;of a given genome submitted by the user;</li>
<li>dbCAN provides an explicitly defined&nbsp;<span style="text-decoration: underline;">signature domain</span>&nbsp;for each and every CAZyme family along with its location in all the relevant full-length CAZyme proteins in all sequenced&nbsp;<a href="http://csbl.bmb.uga.edu/dbCAN/genome.php">genomes</a>;</li>
<li>dbCAN provides the most complete set of&nbsp;<span style="text-decoration: underline;">metagenomic CAZyme</span>&nbsp;genes published so far and represents the first step towards discovering novel CAZyme catalysts in metagenomes;</li>
<li>dbCAN provides a&nbsp;<span style="text-decoration: underline;">subfamily classification</span>&nbsp;of the existing CAZyme families based on sequence similarities;</li>
<li>dbCAN make all pre-computed data freely available to the public, including sequence alignments,&nbsp;<a href="http://csbl.bmb.uga.edu/dbCAN/download/">hidden markov models (HMMs)</a>&nbsp;and phylogenies of the signature domain regions in each and every CAZyme family and subfamily.</li>
</ul>
<p><a href="http://csbl.bmb.uga.edu/dbCAN/help.php">dbCAN</a>&nbsp;is updated regularly when&nbsp;<a href="http://www.cazy.org/" target="_blank">CAZy database</a>&nbsp;created new families based on latest literature.</p><p>Address of the bookmark: <a href="http://csbl.bmb.uga.edu/dbCAN/index.php" rel="nofollow">http://csbl.bmb.uga.edu/dbCAN/index.php</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38908/busca-an-integrative-web-server-to-predict-subcellular-localization-of-proteins</guid>
	<pubDate>Thu, 07 Feb 2019 14:08:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38908/busca-an-integrative-web-server-to-predict-subcellular-localization-of-proteins</link>
	<title><![CDATA[BUSCA: an integrative web server to predict subcellular localization of proteins]]></title>
	<description><![CDATA[<p><span>BUSCA (Bologna Unified Subcellular Component Annotator) is a web-server for predicting protein subcellular localization. BUSCA integrates different tools to predict localization-related protein features (DeepSig, TPpred3, PredGPI and ENSEMBLE3.0) as well as tools for discriminating subcellular localization of both globular and membrane proteins (BaCelLo, MemLoci and SChloro).</span></p><p>Address of the bookmark: <a href="http://busca.biocomp.unibo.it/" rel="nofollow">http://busca.biocomp.unibo.it/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

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