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	<link>https://bioinformaticsonline.com/related/44204?offset=1290</link>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43329/postdoc-position-at-kiel-university-germany</guid>
  <pubDate>Sat, 28 Aug 2021 01:16:55 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoc position at Kiel University, Germany]]></title>
  <description><![CDATA[
<p>In the Genomic Microbiology Group of Prof. Tal Dagan at the Institute<br />of Microbiology at Kiel University, Germany, a</p>

<p>Postdoc position (m/w/d)</p>

<p>in the field of computational evolutionary microbiology is available<br />for an initially limited period of 36 months at the earliest possible<br />date. The weekly working time corresponds to 100% of full employment<br />(If the legal requirements under collective bargaining law are met, the<br />tariff grouping is carried out up to pay scale 13 TV-L. The obligation<br />to teach amounts to 4 hours.</p>

<p>The Genomic Microbiology Group research interests are focused on<br />microbial genome evolution with an emphasis on the study of lateral gene<br />transfer. In our research we use both computational and experimental<br />approaches (see www.uni-kiel.de/genomik). The position offers the<br />opportunity to develop an independent research profile within the group<br />research focus. The successful applicant is expected to be involved<br />in teaching of bioinformatics and molecular evolution, including the<br />development of teaching materials (lectures/exercises/short videos).</p>

<p>Your profile:<br />· Doctoral or PhD degree in Molecular Evolution, Bioinformatics or<br />related fields.<br />· Knowledge and experience in programming (e.g., Python) and<br />biostatistical analysis (e.g., with R or MatLab).<br />· Any of the following expertise is an advantage: the analysis of<br />genomic or transcriptomic data, phylogenetic reconstruction,<br />comparative genomics.<br />· Good oral and written communication skills in English.<br />· Ability to teach in German is an advantage (alternatively, an<br />indication to do so from the 2nd year on).<br />· Skills and motivation to communicate and interact with other<br />scientists.<br /> <br />The Christian-Albrechts-University sees itself as a modern and<br />cosmopolitan employer. We welcome your application regardless of your age,<br />gender, cultural and social background, religion, ideology, disability<br />or sexual identity. We promote equality of the sexes.</p>

<p>The Christian-Albrechts-University is committed to the employment of<br />people with disabilities. Preference will be given to applications from<br />severely handicapped persons and persons of equal standing, provided<br />they are suitable.</p>

<p>We expressly welcome applications from people with a migration background.</p>

<p>For enquiries regarding the position, teaching obligations and research<br />topic please contact Prof. Tal Dagan: tdagan@ifam.uni-kiel.de.</p>

<p>Applications should be submitted by email to Mrs. Haacks<br />(dhaacks@ifam.uni-kiel.de) as a single PDF and include: (1) a letter of<br />motivation (max 1 page, Arial 11, line spacing 1.15), (2) CV, (3) PhD<br />certificate. Please use 'GMG postdoc application - [your name]'<br />as a subject.</p>

<p>Please, refrain from sending us application photos.</p>

<p>Application deadline:  August 31 2021 or until the position is<br />filled. Interviews will take place during September/October 2021. The<br />planned starting date for the position is flexible (but in 2021).</p>
]]></description>
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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/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction</guid>
	<pubDate>Wed, 21 Feb 2024 06:19:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction</link>
	<title><![CDATA[pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction]]></title>
	<description><![CDATA[<p dir="auto"><span>ausarg/pipesnake</span>&nbsp;is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.</p>
<p dir="auto">The pipeline is built using&nbsp;<a href="https://www.nextflow.io/">Nextflow</a>, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The&nbsp;<a href="https://www.nextflow.io/docs/latest/dsl2.html">Nextflow DSL2</a>&nbsp;implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.</p><p>Address of the bookmark: <a href="https://github.com/AusARG/pipesnake" rel="nofollow">https://github.com/AusARG/pipesnake</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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