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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44213?offset=70</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly</guid>
	<pubDate>Tue, 17 Aug 2021 13:17:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly</link>
	<title><![CDATA[Bioinformatics tools for telomere to telomere assembly !]]></title>
	<description><![CDATA[<p>●&nbsp;<a href="https://github.com/arangrhie/merfin" target="_blank">Merfin</a>&nbsp;&ndash; k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)<br />●&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1" target="_blank">PanGenie</a>&nbsp;&ndash; algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)<br />●&nbsp;<a href="https://github.com/ConesaLab/SQANTI3" target="_blank">SQANTI3</a>&nbsp;&ndash; an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Roc&iacute;o Amor&iacute;n de Heged&uuml;s&nbsp;<a href="https://twitter.com/rocioadh" target="_blank">@rocioadh</a>)<br />●&nbsp;<a href="https://github.com/GenomeRIK/tama" target="_blank">tama</a>&nbsp;(Transcriptome Annotation by Modular Algorithms) &ndash; software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo&nbsp;<a href="https://twitter.com/GenomeRIK" target="_blank">@GenomeRIK</a>)<br />●&nbsp;<a href="https://github.com/PacificBiosciences/pbAA" target="_blank">pbaa</a>&nbsp;(PacBio Amplicon Analysis) &ndash; separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg&nbsp;<a href="https://twitter.com/zevkronenberg" target="_blank">@zevkronenberg</a>)<br />●&nbsp;<a href="https://github.com/yuanyuan929/bellerophon" target="_blank">bellerophon</a>&nbsp;&ndash; analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng&nbsp;<a href="https://twitter.com/Yuanyuan929" target="_blank">@Yuanyuan929</a>)<br />●&nbsp;<a href="https://github.com/amwenger/svpack" target="_blank">svpack</a>&nbsp;&ndash; tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)<br />●&nbsp;<a href="https://github.com/AntonBankevich/jumboDB" target="_blank">JumboDB</a>&nbsp;&ndash; tool for de Bruijn graph construction (Anton Bankevich&nbsp;<a href="https://twitter.com/AntonBankevich" target="_blank">@AntonBankevich</a>)<br />●&nbsp;<a href="https://github.com/ksahlin/ultra" target="_blank">uLTRA</a>&nbsp;&ndash; tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin&nbsp;<a href="https://twitter.com/krsahlin" target="_blank">@krsahlin</a>)<br />●&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2021.01.25.428044v1.full.pdf" target="_blank">LeafGo</a>&nbsp;&ndash; workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini&nbsp;<a href="https://twitter.com/ermini_luca" target="_blank">@ermini_luca</a>)</p><p>Reference:</p><p>https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/</p><p>&nbsp;</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools</guid>
	<pubDate>Thu, 17 Feb 2022 05:37:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools</link>
	<title><![CDATA[Comparative genomics visualisation tools !]]></title>
	<description><![CDATA[<p>Comparative genomics visualisation tools !</p><p>Address of the bookmark: <a href="https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&amp;selected=%23BRIG&amp;tag=Comparative" rel="nofollow">https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&amp;selected=%23BRIG&amp;tag=Comparative</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44551/bioinformatic-tools-for-pathogens-informatics-at-cvr</guid>
	<pubDate>Sat, 08 Jun 2024 15:59:46 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44551/bioinformatic-tools-for-pathogens-informatics-at-cvr</link>
	<title><![CDATA[Bioinformatic tools for pathogens informatics at CVR]]></title>
	<description><![CDATA[<div><div><div><div><div><p>Novel sequencing and analytical approaches focused on studying viruses and virus-host interactions. Below you will find summaries and links to a number of bioinformatic tools that have been developed @ CVR.</p></div><div><h3><a href="http://giffordlabcvr.github.io/DIGS-tool/" target="_blank" title="DIGS">DIGS</a></h3></div><div><p>The database-integrated genome-screening (DIGS) tool provides a framework for implementing automated in silico screening of sequence databases using BLAST in combination with a relational database (MySQL).</p></div><div><h3><a href="https://bioinformatics.cvr.ac.uk/software/discvr/" target="" title="DisCVR">DisCVR</a></h3></div><div><p>DisCVR is a Diagnostic tool for detecting known human viruses in clinical samples from Next-Generation Sequencing (NGS) data. The tool uses a simple and straightforward Graphical User Interface and is optimized on Windows OS without compromising speed and accuracy.</p></div><div><h3><a href="http://josephhughes.github.io/DiversiTools/" target="_blank" title="DiversiTools">DiversiTools</a></h3></div><div><p>DiversiTools is a computational tool that is specifically tailored towards viral HTS data sets and the analysis of the underlying viral populations that they represent. It was initially developed in collaboration with a number of virologists interested in characterising the intra-host diversity of viral populations and studying their evolution across transmission chains at the micro-evolutionary scale.</p></div><div><h3><a href="http://glue-tools.cvr.gla.ac.uk/" target="_blank" title="GLUE">GLUE</a></h3></div><div><p>GLUE is a flexible data-centric bioinformatics environment for virus sequence data, with a focus on virus evolution and genomic variation. GLUE has been applied to a range of viruses. A GLUE-based resource focused on Hepatitis C virus is HCV-GLUE.</p></div><div><h3><a href="https://bioinformatics.cvr.ac.uk/tanoti/" target="_blank" title="Tanoti">Tanoti</a></h3></div><div><p>Tanoti is a BLAST guided reference based short read aligner. It is developed for maximising alignment in highly variable next generation sequence data sets (Illumina).</p></div><div><h3><a href="https://bioinformatics.cvr.ac.uk/victree/" target="_blank" title="VicTREE">ViCTree</a></h3></div><div><p>ViCTree is a bioinformatic framework that automatically selects new candidate virus sequences from GenBank, generates multiple sequence alignments, calculates a maximum likelihood phylogeny and integrates the sequences into the existing phylogenetic trees.&nbsp;<span>For more information click&nbsp;</span><a href="https://bioinformatics.cvr.ac.uk/victree_web/" target="_blank">here</a>.</p></div></div></div></div></div><div><div><div><div><div><h3><a href="https://bioinformatics.cvr.ac.uk/software/viral-host-predictor/" target="" title="Viral Host Predictor">Viral Host Predictor</a></h3></div><div><p>Viral Host Predictor provides a fast and simple way to predict the hosts and vectors of RNA viruses from viral sequences.</p></div><div><h3><a href="https://github.com/salvocamiolo/GRACy/releases/tag/v0.4.4" target="_blank" title="GRACy">GRACy</a></h3></div><div><p>GRACy is a bioinformatic tool designed for the analysis of Illumina data originated from Human cytomegalovirus samples. GRACy can be used to perform read quality filtering, genotyping, de novo assembly, variant detection, annotation and data submission to public database.</p></div><div><h3><a href="https://github.com/salvocamiolo/LoReTTA/releases/tag/v0.1" target="_blank" title="LoReTTA">LoReTTA</a></h3></div><div><p>LoReTTA (Long Read Template Targeted Assembler) is a reference assisted de novo assembler specifically designed to deal with PacBio reads generated from viral genomes.&nbsp;</p></div><div><h3><a href="https://bioinformatics.cvr.ac.uk/software/bingleseq/" target="" title="BingleSeq">BingleSeq</a></h3></div><div><p>BingleSeq is a R-package enables the user-friendly analysis of count tables obtained by both Bulk RNA-Seq and single-cell RNA-Seq protocols. The development of BingleSeq focused on providing a flexible and intuitive user experience.</p></div></div></div></div></div>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/10409/check-linux-server-configuration</guid>
	<pubDate>Tue, 06 May 2014 01:10:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/10409/check-linux-server-configuration</link>
	<title><![CDATA[Check Linux server configuration !!]]></title>
	<description><![CDATA[<p>Bioinformatician uses servers for computational analysis. Sometime we need to check the server details before running our programs or tools. Here I am showing some basic commands using them you can gather the system/server information.<br /><br />To check what version of Operating System is installed on the server you can use the following commands:-<br />&nbsp;=================================================================<br />1.cat /etc/issue<br />[root@localhost ~]# cat /etc/issue<br />Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br />Kernel \r on an \m<br /><br />2.cat /etc/redhat-release<br />[root@localhost ~]# cat /etc/redhat-release<br />Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br /><br /><br />3.lsb_release -a<br />[root@localhost ~]# lsb_release -a<br />LSB Version:&nbsp;&nbsp;&nbsp; :core-3.1-ia32:core-3.1-noarch:graphics-3.1-ia32:graphics-3.1-noarch<br />Distributor ID: RedHatEnterpriseServer<br />Description:&nbsp;&nbsp;&nbsp; Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br />Release:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5.5<br />Codename:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Tikanga<br /><br /><br /><br />To check whether the operating system is 32 or 64bit:-<br />================================<br /># uname -i<br />[root@localhost ~]# uname -i<br />i386<br />(i386 represents that server is having 32bit operating system)<br /><br />[root@localhost ~]# uname -i<br />x86_64<br />(x86_64 represents that server is having 64bit operating system)<br /><br />To see the processor/CPU information:-<br />=============================<br /># cat /proc/cpuinfo<br />[root@localhost ~] cat /proc/cpuinfo<br />processor&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />vendor_id&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : GenuineIntel<br />cpu family&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 6<br />model&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 15<br />model name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : Intel(R) Xeon(R) CPU&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5130&nbsp; @ 2.00GHz<br />stepping&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 6<br />cpu MHz&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 1995.087<br />cache size&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 4096 KB<br />physical id&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />siblings&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 2<br />core id&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />cpu cores&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 2<br />apicid&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />fdiv_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />hlt_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />f00f_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />coma_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />fpu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : yes<br />fpu_exception&nbsp;&nbsp; : yes<br />cpuid level&nbsp;&nbsp;&nbsp;&nbsp; : 10<br />wp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : yes<br />flags&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc pni monitor ds_cpl vmx tm2 ssse3 cx16 xtpr lahf_lm<br />bogomips&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 3990.17<br />(Here processor number 0 indicates that the system is having one process(processor number starts with zero))<br /><br /><br /><br /><br />To check memory information:-<br />===========================<br /># free -m<br />[root@localhost ~]# free -m<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; total&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; used&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; free&nbsp;&nbsp;&nbsp;&nbsp; shared&nbsp;&nbsp;&nbsp; buffers&nbsp;&nbsp;&nbsp;&nbsp; cached<br />Mem:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5066&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3513&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1552&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 612&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2319<br />-/+ buffers/cache:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 582&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4484<br />Swap:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1983&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1983<br /><br /><br /><br /># cat /proc/meminfo<br />[root@localhost ~]# cat /proc/meminfo<br />MemTotal:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5187752 kB<br />MemFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1639300 kB<br />Buffers:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 627024 kB<br />Cached:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2374944 kB<br />SwapCached:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />Active:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2458788 kB<br />Inactive:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 920964 kB<br />HighTotal:&nbsp;&nbsp;&nbsp;&nbsp; 4325164 kB<br />HighFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1561936 kB<br />LowTotal:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 862588 kB<br />LowFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 77364 kB<br />SwapTotal:&nbsp;&nbsp;&nbsp;&nbsp; 2031608 kB<br />SwapFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2031608 kB<br />Dirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 704 kB<br />Writeback:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />AnonPages:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 377892 kB<br />Mapped:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 35328 kB<br />Slab:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 153036 kB<br />PageTables:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6316 kB<br />NFS_Unstable:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />Bounce:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />CommitLimit:&nbsp;&nbsp; 4625484 kB<br />Committed_AS:&nbsp;&nbsp; 977132 kB<br />VmallocTotal:&nbsp;&nbsp; 116728 kB<br />VmallocUsed:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4492 kB<br />VmallocChunk:&nbsp;&nbsp; 112124 kB<br />HugePages_Total:&nbsp;&nbsp;&nbsp;&nbsp; 0<br />HugePages_Free:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br />HugePages_Rsvd:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br />Hugepagesize:&nbsp;&nbsp;&nbsp;&nbsp; 2048 kB<br /><br /><br />To check the model and serial name of the server:-<br />=======================================<br />[root@localhost ~]#&nbsp; dmidecode | egrep -i "product name|Serial number"<br />Product Name: PowerEdge R710<br />Serial Number: AB8CDE1<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<br /><br />To check the host name:-<br />=====================<br />[root@localhost ~]# uname -n<br />localhost<br /><br />[root@localhost ~]# hostname<br />localhost<br /><br />To check the kernel version:-<br />========================<br />[root@localhost ~]# uname -r<br />2.6.18-238.9.1.el5PAE</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/14868/bioinformaticians-summer-vacation</guid>
	<pubDate>Wed, 03 Sep 2014 13:11:50 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/14868/bioinformaticians-summer-vacation</link>
	<title><![CDATA[Bioinformatician&#039;s summer vacation !!!]]></title>
	<description><![CDATA[<p>Yes, the bioinformatician do spend their summer vacation like this. They spend more time on cheking the JOBS running on various servers.</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/14868" length="638462" type="image/png" />
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27238/slurm</guid>
	<pubDate>Wed, 04 May 2016 05:13:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27238/slurm</link>
	<title><![CDATA[SLURM]]></title>
	<description><![CDATA[<p><a href="http://www.schedmd.com/">SLURM</a> workload manager software, a free open-source workload manager designed specifically to satisfy the demanding needs of high performance computing.</p>
<p>This page is a <em>HOWTO</em> guide for setting up a <a href="http://www.schedmd.com/">SLURM</a> installation, currently focused on a CentOS 7 Linux OS. Please send feedback to Ole.H.Nielsen /at/ fysik.dtu.dk.</p>
<p>See the <a href="http://www.schedmd.com/">SLURM</a> homepage (also <a href="https://computing.llnl.gov/linux/slurm/">https://computing.llnl.gov/linux/slurm/</a>).</p><p>Address of the bookmark: <a href="https://wiki.fysik.dtu.dk/niflheim/SLURM" rel="nofollow">https://wiki.fysik.dtu.dk/niflheim/SLURM</a></p>]]></description>
	<dc:creator>Jit</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>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41504/quartataweb-user-friendly-server-developed-for-polypharmacological-and-chemogenomics-analyses</guid>
	<pubDate>Wed, 01 Apr 2020 10:30:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41504/quartataweb-user-friendly-server-developed-for-polypharmacological-and-chemogenomics-analyses</link>
	<title><![CDATA[QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.]]></title>
	<description><![CDATA[<p><span>Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as&nbsp;</span><a href="http://www.drugbank.ca/" target="_blank">DrugBank</a><span>&nbsp;and&nbsp;</span><a href="http://stitch.embl.de/" target="_blank">STITCH</a><span>. These data usually reflect observed interactions, while the lack of data for a given protein-drug/chemical pair does not necessarily mean the lack of interaction. Indeed, recent studies, both computational and experimental, highlighted the promiscuity of both proteins and small molecules: many drugs have side effects i.e. they target proteins other than those known in public databases; and many proteins bind chemicals other than those known, opening the way to design repurposable drugs, new chemicals, or polypharmacological treatments.</span></p>
<p><span><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa210/5813333">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa210/5813333</a></span></p><p>Address of the bookmark: <a href="http://quartata.csb.pitt.edu/" rel="nofollow">http://quartata.csb.pitt.edu/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

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