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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41901?offset=10</link>
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	<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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41825/hnadock-a-nucleic-acid-docking-server-for-modeling-rnadna%E2%80%93rnadna-3d-complex-structures</guid>
	<pubDate>Thu, 04 Jun 2020 23:19:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41825/hnadock-a-nucleic-acid-docking-server-for-modeling-rnadna%E2%80%93rnadna-3d-complex-structures</link>
	<title><![CDATA[HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures]]></title>
	<description><![CDATA[<p><span>The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users are required to provide the three-dimensional (3D) structures of the two molecules to be docked.&nbsp;</span></p><p>Address of the bookmark: <a href="http://huanglab.phys.hust.edu.cn/hnadock/" rel="nofollow">http://huanglab.phys.hust.edu.cn/hnadock/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/9030/linux-ssh-client-commands-for-bioinformatics</guid>
	<pubDate>Thu, 13 Mar 2014 17:16:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/9030/linux-ssh-client-commands-for-bioinformatics</link>
	<title><![CDATA[Linux SSH Client Commands for Bioinformatics]]></title>
	<description><![CDATA[<p>Here come on let play with the following basic command line usage of the ssh client.<br /><br /><strong>1. Check your SSH Client Version:</strong><br /><br />Checking for your SSH client is very sare, but sometimes it may be necessary to identify the SSH client that you are currently running and it&rsquo;s corresponding version number. The SSh client can be identified as follows<br /><br />$ ssh -V<br />OpenSSH_3.9p1, OpenSSL 0.9.7a Feb 19 2013<br /><br />$ ssh -V<br />ssh: SSH Secure Shell 3.2.9.1 (non-commercial version) on i686-pc-linux-gnu<br /><br /><strong>2. Connect and login to remote host:</strong></p><p>The First time when you login to the remotehost from a localhost, it will display the host key not found message and you can give &ldquo;yes&rdquo; to continue. The host key of the remote host will be added under .ssh2/hostkeys directory of your home directory, as shown below.<br /><br />localhost$ ssh -l jit remotehost.example.com<br /><br />jit@remotehost.example.com password:</p><p>remotehost.example.com$</p><p>The Second time when you login to the remote host from the localhost, it will prompt only for the password as the remote host key is already added to the known hosts list of the ssh client.<br /><br />localhost$ ssh -l jit remotehost.example.com<br />jit@remotehost.example.com password: <br />remotehost.example.com$<br /><br />For some reason, if the host key of the remote host is changed after you logged in for the first time, you may get a warning message as shown below. This could be because of various reasons such as 1) Sysadmin upgraded/reinstalled the SSH server on the remote host 2) someone is doing malicious activity etc., The best possible action to take before saying &ldquo;yes&rdquo; to the message below, is to call your sysadmin and identify why you got the host key changed message and verify whether it is the correct host key or not.<br /><br />localhost$ ssh -l jit remotehost.example.com<br /><br />jit @remotehost.example.com's password: <br />remotehost$<br /><br /><strong>4. Debug SSH Client:</strong><br /><br />Sometimes it is necessary to view debug messages to troubleshoot any SSH connection issues. For this purpose, pass -v (lowercase v) option to the ssh as shown below.<br /><br />Example without debug message:<br /><br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; localhost$ ssh -l jit remotehost.example.com<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; warning: Connecting to remotehost.example.com failed: No address associated to the name<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; localhost$</p><p>Example with debug message:<br /><br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; locaclhost$ ssh -v -l jit remotehost.example.com<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; debug: SshConfig/sshconfig.c:2838/ssh2_parse_config_ext: Metaconfig parsing stopped at line 3.<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; debug: SshConfig/sshconfig.c:637/ssh_config_set_param_verbose: Setting variable 'VerboseMode' to 'FALSE'.<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; debug: SshConfig/sshconfig.c:3130/ssh_config_read_file_ext: Read 17 params from config file.<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; debug: Ssh2/ssh2.c:1707/main: User config file not found, using defaults. (Looked for '/home/jit/.ssh2/ssh2_config')<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; debug: Connecting to remotehost.example.com, port 22... (SOCKS not used)<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; warning: Connecting to remotehost.example.com failed: No address associated to</p><p><strong>5. Escape Character: (Toggle SSH session, SSH session statistics etc.)</strong><br /><br />Escape character ~ get&rsquo;s SSH clients attention and the character following the ~ determines the escape command.<br />Toggle SSH Session: When you&rsquo;ve logged on to the remotehost using ssh from the localhost, you may want to come back to the localhost to perform some activity and go back to remote host again. In this case, you don&rsquo;t need to disconnect the ssh session to the remote host. Instead follow the steps below.</p><p>i. Login to remotehost from localhost: localhost$ssh -l jit remotehost<br />ii. Now you are connected to the remotehost: remotehost$<br />iii. To come back to the localhost temporarily, type the escape character ~ and Control-Z. When you type ~ you will not see that immediately on the screen until you press and press enter. So, on the remotehost in a new line enter the following key strokes for the below to work: ~<br /><br />&nbsp;&nbsp;&nbsp; remotehost$ ~^Z<br />&nbsp;&nbsp;&nbsp; [1]+&nbsp; Stopped&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ssh -l jit remotehost<br />&nbsp;&nbsp;&nbsp; localhost$</p><p>iv. Now you are back to the localhost and the ssh remotehost client session runs as a typical unix background job, which you can check as shown below:<br /><br />&nbsp;&nbsp;&nbsp; localhost$ jobs<br />&nbsp;&nbsp;&nbsp; [1]+&nbsp; Stopped&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ssh -l jit remotehost<br /><br />v. You can go back to the remote host ssh without entering the password again by bringing the background ssh remotehost session job to foreground on the localhost<br /><br />&nbsp;&nbsp;&nbsp; localhost$ fg %1<br />&nbsp;&nbsp;&nbsp; ssh -l jit remotehost<br />&nbsp;&nbsp;&nbsp; remotehost$</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/42319/blast-2110-release-is-now-available-on-ftp-site</guid>
	<pubDate>Sat, 14 Nov 2020 21:37:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/42319/blast-2110-release-is-now-available-on-ftp-site</link>
	<title><![CDATA[BLAST+ 2.11.0 release is now available on FTP site !]]></title>
	<description><![CDATA[<p><span style="font-size: 12.8px;"></span><span style="font-size: 12.8px;">BLAST+ 2.11.0 release is now available from our FTP site. The main advance is the ability to provide usage reports to NCBI to help us improve BLAST. This information is limited to the name of the BLAST program, some basic database metadata, a few BLAST parameters, as well the number and total size of your queries. See the Privacy document for more details on the information we collect, how we will use it, and how you can opt-out of reporting.</span></p><div><div><div><div lang="EN-US"><div><p>Another new feature allows threading by query batch in rpsblast/rpstblastn. Enabling this option using -m t provides more efficient searching with large numbers of queries. &nbsp;See release notes for details on more improvements and bug fixes.</p><p>Useful Links<br />------------<br />NCBI Insights:&nbsp;<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2020/11/12/blast-2-11-0/" target="_blank">https://ncbiinsights.ncbi.nlm.nih.gov/2020/11/12/blast-2-11-0/</a></p><p>BLAST FTP:&nbsp;<a href="https://go.usa.gov/x7QQ3" target="_blank">https://go.usa.gov/x7QQ3</a><br />Privacy document:&nbsp;<a href="https://go.usa.gov/x7QQe" target="_blank">https://go.usa.gov/x7QQe</a><br />Release notes:&nbsp;<a href="https://go.usa.gov/x7Qnv" target="_blank">https://go.usa.gov/x7Qnv</a></p></div></div></div></div></div>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43374/reference-sequence-resource</guid>
	<pubDate>Wed, 15 Sep 2021 21:15:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43374/reference-sequence-resource</link>
	<title><![CDATA[Reference Sequence Resource!]]></title>
	<description><![CDATA[<p><span>The ENCODE project uses Reference Genomes from&nbsp;</span><a href="http://www.ncbi.nlm.nih.gov/genome/browse/reference/">NCBI</a><span>&nbsp;or&nbsp;</span><a href="http://hgdownload.cse.ucsc.edu/downloads.html">UCSC</a><span>&nbsp;to provide a consistent framework for mapping high-throughput sequencing data.&nbsp;In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse (mm9/mm10) genomes for historical comparability.&nbsp;</span><em>Drosophia melanogaster</em><span>&nbsp;experiments are mapped to either dm3 or dm6 and&nbsp;</span><em>Caenorhabdilis elegans&nbsp;</em><span>experiments are mapped to ce10 or ce11.&nbsp;T</span></p><p>Address of the bookmark: <a href="https://www.encodeproject.org/data-standards/reference-sequences/" rel="nofollow">https://www.encodeproject.org/data-standards/reference-sequences/</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<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" />
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	<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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/36384/binding-site-prediction-in-protein</guid>
	<pubDate>Wed, 25 Apr 2018 04:35:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/36384/binding-site-prediction-in-protein</link>
	<title><![CDATA[Binding Site Prediction in Protein !]]></title>
	<description><![CDATA[<p><span>The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the intermolecular complex formed between two or more molecules (docking).</span></p><h4>Pockets Identification</h4><p><a href="http://sts.bioengr.uic.edu/castp/" target="_blank">CASTp</a></p><div style="text-align: justify;">Automatic Identification of pockets and cavities in proteins structure, and quantitation of their volumes using Delaunay triangulation. Available also as PyMOL plugin</div><p><a href="http://www.bioinformatics.leeds.ac.uk/pocketfinder/" target="_blank">Pocket-Finder</a></p><div style="text-align: justify;">Automatic identification of pockets and cavities in proteins structure, and quantitation of their volumes.</div><p><a href="http://gecco.org.chemie.uni-frankfurt.de/pocketpicker/index.html" target="_blank">PocketPicker</a></p><div style="text-align: justify;">Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for&nbsp;<a href="https://bip.weizmann.ac.il/toolbox/structure/pymol.htm">PyMOL</a></div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;"><h4>Binding Site Prediction</h4>
<p><a href="http://consurf.tau.ac.il/" target="_blank">ConSurf</a></p>
</div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;">Identification of functional regions in proteins by surface-mapping of phylogenetic information</div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;"><a href="http://www-cryst.bioc.cam.ac.uk/~crescendo/crescendo.php" target="_blank">CRESCENDO</a></div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;">Identification protein interaction sites. It uses sequence conservation patterns in homologous proteins to distinguish between residues that are conserved due to structural restraints from those due to functional restraints.&nbsp;&nbsp;</div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;"><strong>Ligand Binding Sites</strong></div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;"><a href="http://www.sbg.bio.ic.ac.uk/~3dligandsite/" target="_blank">3DLigandSite</a></div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;">The server utilizes protein-structure prediction to provide structural models of the binding site. Ligands bound to structures are superimposed onto the model and use to predict the binding site.</div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;">F<a href="http://cssb.biology.gatech.edu/skolnick/files/FINDSITE/" target="_blank">INDSITE</a></div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;">A threading-based method for ligand-binding site prediction and functional annotation based on binding-site similarity across superimposed groups of threading templates.</div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;">
<p><a href="http://scoppi.biotec.tu-dresden.de/pocket/" target="_blank">LIGSITE<sup>csc</sup></a></p>
<div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;">Prediction of binding site by pocket identification using the Connolly surface and degree of conservation</div>
<p><a href="http://metapocket.eml.org/" target="_blank"></a></p>
</div><div style="text-align: justify;">&nbsp;</div><div style="text-align: justify;"><a href="http://metapocket.eml.org/" target="_blank">metaPocket</a>A meta server for ligand-binding site prediction. metaPocket use&nbsp;<a href="https://bip.weizmann.ac.il/toolbox/structure/binding.htm#ligsite">LIGSITE<sup>csc</sup></a>,&nbsp;<a href="https://bip.weizmann.ac.il/toolbox/structure/binding.htm#pass">PASS</a>,&nbsp;<a href="https://bip.weizmann.ac.il/toolbox/structure/binding.htm#qsite">Q-SiteFinder</a>&nbsp;and&nbsp;<a href="http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html" target="_blank">SURFNET</a></div>]]></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>

</channel>
</rss>