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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/3029?offset=750</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/870/6-phd-students-tu-dresden</guid>
  <pubDate>Sun, 14 Jul 2013 13:42:06 -0500</pubDate>
  <link></link>
  <title><![CDATA[6 PhD Students @ TU Dresden]]></title>
  <description><![CDATA[
<p>At TU Dresden, Faculty of Computer Science, the DFG Research Training Group GRK 1907 “Role-based Software Infrastructures for continuous-context-sensitive Systems” offers the positions of 6 PhD Students (E 13 TV-L)</p>

<p>for applicants interested in performing high-quality research on the connection between software engineering, database systems, and theoretical computer science as well as their applications in bioinformatics and business informatics. The research programme will start on October 1, 2013 until 30.09.2016. The period of employment is governed by the Fixed Term Research Contracts Act (Wissenschaftszeitvertragsgesetz – WissZeitVG).</p>

<p>This research programme is a joint activity of Professors Lehner, Assmann, Baader, Baier, Schill, Schlegel, Schroeder, and Strahringer at TU Dresden. Alongside their research, an individual mentoring and qualification approach are arranged with specialized courses that prepare them optimally for their research, a research seminar where they can meet internationally renowned researchers in the field, and soft skills and language courses.</p>

<p>Requirements: Applicants should have an excellent academic record, and hold a MSc (or an equivalent university degree) in computer science or related disciplines (such as mathematics, bioinformatics or business informatics). Fluency in spoken and written English is required. Applicants with a good knowledge of software engineering or one of the application areas mentioned above are preferred. TU Dresden is committed to increase the proportion of women in research.</p>

<p>Applications from women are particularly welcome. The same applies to disabled people.</p>

<p>Please send enquiries to: wolfgang.lehner@tu-dresden.de</p>

<p>Applications consist of a CV, the names of two referees, transcipts of documents summarizing their academic performance, and a statement of interest. Application by email in pdf format is preferred, and should be submitted to wolfgang.lehner@tu-dresden.de in an electronically signed and encrypted form by July 30, 2013 (stamped arrival date of the university central mail service applies). Alternatively, applications can be sent to: TU Dresden, Fakultät Informatik, Institut für Systemarchitektur, Prof.  Dr.-Ing.  Wolfgang Lehner, 01062 Dresden, Germany.</p>

<p>Shortlisted candidates will be invited to Dresden in the middle of August to give a presentation on their Master’s thesis and discuss their research interest with the participating professors. Candidates that have not yet finished their degree when they send in their application should send preliminary transcripts of their academic records as well as a letter by the thesis adviser that comments on their progress so far and on the expected date of completion of their MSc or equivalent degree.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2</guid>
	<pubDate>Mon, 10 Apr 2017 04:45:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2</link>
	<title><![CDATA[WGS Celera Assembler version 8.3rc2]]></title>
	<description><![CDATA[<p>These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.<br><br>This distribution package provides a stable, tested, documented version of the software.&nbsp; The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.<br><br>The source code package includes full source code (revision 4627), Makefiles, and scripts.&nbsp; A subset of the kmer package (http://kmer.sourceforge.net/, version r1994), used by some modules of Celera Assembler, is included.&nbsp; This distribution includes [http://samtools.sourceforge.net/ SAMtools], [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish 2.0], [https://github.com/pbjd/pbutgcns PBUTGCNS], [https://github.com/PacificBiosciences/pbdagcon PBDAGCON], [https://github.com/PacificBiosciences/BLASR BLASR], and parts of the [https://github.com/PacificBiosciences/FALCON/tree/v0.1.3 Falcon assembler].<br><br>Full documentation can be found online at http://wgs-assembler.sourceforge.net/.</p>
<p>Interesting scripts within it</p>
<p>urbe@urbo214b[bin] ls&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; []<br>-rwxrwxr-x 1 urbe urbe&nbsp; 11K Apr 10 11:41 addCNSToStore<br>-rwxrwxr-x 1 urbe urbe 575K Apr 10 11:41 addReadsToUnitigs<br>-rwxrwxr-x 1 urbe urbe 128K Apr 10 11:41 analyzeBest<br>-rwxrwxr-x 1 urbe urbe 257K Apr 10 11:41 analyzePosMap<br>-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 analyzeScaffolds<br>-rwxrwxr-x 1 urbe urbe 224K Apr 10 11:41 asmOutputFasta<br>-rwxrwxr-x 1 urbe urbe 448K Apr 10 11:41 asmOutputStatistics<br>-rwxrwxr-x 1 urbe urbe 2,4K Apr 10 11:41 asmToAGP.pl<br>-rwxrwxr-x 1 urbe urbe 7,6M Apr 10 11:41 blasr<br>-rwxrwxr-x 1 urbe urbe 1,6M Apr 10 11:41 bogart<br>-rwxrwxr-x 1 urbe urbe 183K Apr 10 11:41 bogus<br>-rwxrwxr-x 1 urbe urbe 272K Apr 10 11:41 bogusness<br>-rwxrwxr-x 1 urbe urbe 247K Apr 10 11:41 buildPosMap<br>-rwxrwxr-x 1 urbe urbe 213K Apr 10 11:41 buildRefContigs<br>-rwxrwxr-x 1 urbe urbe 990K Apr 10 11:41 buildUnitigs<br>-rwxrwxr-x 1 urbe urbe&nbsp; 18K Apr 10 11:41 ca2ace.pl<br>-rwxrwxr-x 1 urbe urbe&nbsp; 12K Apr 10 11:41 caqc_help.ini<br>-rwxrwxr-x 1 urbe urbe&nbsp; 61K Apr 10 11:41 caqc.pl<br>-rwxrwxr-x 1 urbe urbe&nbsp; 23K Apr 10 11:41 cat-corrects<br>-rwxrwxr-x 1 urbe urbe&nbsp; 24K Apr 10 11:41 cat-erates<br>-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 cgw<br>-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 cgwDump<br>-rwxrwxr-x 1 urbe urbe 204K Apr 10 11:41 chimChe<br>-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 chimera<br>-rwxrwxr-x 1 urbe urbe 220K Apr 10 11:41 classifyMates<br>-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:41 classifyMatesApply<br>-rwxrwxr-x 1 urbe urbe 215K Apr 10 11:41 classifyMatesPairwise<br>-rwxrwxr-x 1 urbe urbe 366K Apr 10 11:41 computeCoverageStat<br>-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 convert-fasta-to-v2.pl<br>-rwxrwxr-x 1 urbe urbe&nbsp; 48K Apr 10 11:41 convertOverlap<br>-rwxrwxr-x 1 urbe urbe 119K Apr 10 11:41 convertSamToCA<br>-rwxrwxr-x 1 urbe urbe&nbsp; 20K Apr 10 11:41 convertToPBCNS<br>-rwxrwxr-x 1 urbe urbe 197K Apr 10 11:41 correct-frags<br>-rwxrwxr-x 1 urbe urbe 259K Apr 10 11:41 correct-olaps<br>-rwxrwxr-x 1 urbe urbe 520K Apr 10 11:41 correctPacBio<br>-rwxrwxr-x 1 urbe urbe 540K Apr 10 11:41 ctgcns<br>-rwxrwxr-x 1 urbe urbe 162K Apr 10 11:40 deduplicate<br>-rwxrwxr-x 1 urbe urbe&nbsp; 37K Apr 10 11:41 demotePosMap<br>-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 dumpCloneMiddles<br>-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:41 dumpPBRLayoutStore<br>-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 dumpSingletons<br>-rwxrwxr-x 1 urbe urbe 171K Apr 10 11:41 erate-estimate<br>-rwxrwxr-x 1 urbe urbe 221K Apr 10 11:40 estimate-mer-threshold<br>-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 extendClearRanges<br>-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 extendClearRangesPartition<br>-rwxrwxr-x 1 urbe urbe 205K Apr 10 11:40 extractmessages<br>-rwxrwxr-x 1 urbe urbe 7,2M Apr 10 11:41 falcon_sense<br>-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 fastaToCA<br>-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:40 fastqAnalyze<br>-rwxrwxr-x 1 urbe urbe 137K Apr 10 11:40 fastqSample<br>-rwxrwxr-x 1 urbe urbe&nbsp; 62K Apr 10 11:40 fastqSimulate<br>-rwxrwxr-x 1 urbe urbe 121K Apr 10 11:40 fastqSimulate-sort<br>-rwxrwxr-x 1 urbe urbe 246K Apr 10 11:40 fastqToCA<br>-rwxrwxr-x 1 urbe urbe 140K Apr 10 11:41 filterOverlap<br>-rwxrwxr-x 1 urbe urbe 341K Apr 10 11:40 finalTrim<br>-rwxrwxr-x 1 urbe urbe 228K Apr 10 11:41 fixUnitigs<br>-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 fragmentDepth<br>-rwxrwxr-x 1 urbe urbe&nbsp; 29K Apr 10 11:41 fragsInVars<br>-rwxrwxr-x 1 urbe urbe 545K Apr 10 11:41 frgs2clones<br>-rwxrwxr-x 1 urbe urbe 398K Apr 10 11:40 gatekeeper<br>-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:40 gatekeeperbench<br>-rwxrwxr-x 1 urbe urbe 167K Apr 10 11:40 gkpStoreCreate<br>-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 gkpStoreDumpFASTQ<br>-rwxrwxr-x 1 urbe urbe 184K Apr 10 11:41 greedyFragmentTiling<br>-rwxrwxr-x 1 urbe urbe 1,6K Apr 10 11:41 greedy_layout_to_IUM<br>-rwxrwxr-x 1 urbe urbe 142K Apr 10 11:40 initialTrim<br>-rwxrwxr-x 1 urbe urbe 967K Apr 10 11:41 jellyfish<br>-rwxrwxr-x 1 urbe urbe 219K Apr 10 11:41 markRepeatUnique<br>-rwxrwxr-x 1 urbe urbe 273K Apr 10 11:40 markUniqueUnique<br>-rwxrwxr-x 1 urbe urbe 114K Apr 10 11:40 mercy<br>-rwxrwxr-x 1 urbe urbe 3,8K Apr 10 11:41 mergeqc.pl<br>-rwxrwxr-x 1 urbe urbe 422K Apr 10 11:40 merTrim<br>-rwxrwxr-x 1 urbe urbe 125K Apr 10 11:40 merTrimApply<br>-rwxrwxr-x 1 urbe urbe 376K Apr 10 11:40 meryl<br>-rwxrwxr-x 1 urbe urbe 176K Apr 10 11:41 metagenomics_ovl_analyses<br>-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:41 olap-from-seeds<br>-rwxrwxr-x 1 urbe urbe 275K Apr 10 11:41 outputLayout<br>-rwxrwxr-x 1 urbe urbe 229K Apr 10 11:41 overlapInCore<br>-rwxrwxr-x 1 urbe urbe 144K Apr 10 11:40 overlap_partition<br>-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStats<br>-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStore<br>-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:41 overlapStoreBucketizer<br>-rwxrwxr-x 1 urbe urbe 175K Apr 10 11:41 overlapStoreBuild<br>-rwxrwxr-x 1 urbe urbe&nbsp; 33K Apr 10 11:41 overlapStoreIndexer<br>-rwxrwxr-x 1 urbe urbe&nbsp; 48K Apr 10 11:41 overlapStoreSorter<br>-rwxrwxr-x 1 urbe urbe 604K Apr 10 11:40 overmerry<br>lrwxrwxrwx 1 urbe urbe&nbsp;&nbsp;&nbsp; 4 Apr 10 11:41 pacBioToCA -&gt; PBcR<br>-rwxrwxr-x 1 urbe urbe 131K Apr 10 11:41 PBcR<br>-rwxrwxr-x 1 urbe urbe 2,9M Apr 10 11:41 pbdagcon<br>-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 pbutgcns<br>-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 remove_fragment<br>-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:40 removeMateOverlap<br>-rwxrwxr-x 1 urbe urbe 2,5K Apr 10 11:41 replaceUIDwithName-fastq<br>-rwxrwxr-x 1 urbe urbe 1,2K Apr 10 11:41 replaceUIDwithName-posmap<br>-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 resolveSurrogates<br>-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:41 rewriteCache<br>-rwxrwxr-x 1 urbe urbe 232K Apr 10 11:41 runCA<br>-rwxrwxr-x 1 urbe urbe&nbsp; 88K Apr 10 11:41 runCA-dedupe<br>-rwxrwxr-x 1 urbe urbe&nbsp; 14K Apr 10 11:41 runCA-overlapStoreBuild<br>-rwxrwxr-x 1 urbe urbe 3,6K Apr 10 11:41 run_greedy.csh<br>-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:40 sffToCA<br>-rwxrwxr-x 1 urbe urbe&nbsp; 13K Apr 10 11:40 show-corrects<br>-rwxrwxr-x 1 urbe urbe 557K Apr 10 11:41 splitUnitigs<br>-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 terminator<br>drwxrwxr-x 2 urbe urbe 4,0K Apr 10 11:41 TIGR<br>-rwxrwxr-x 1 urbe urbe 526K Apr 10 11:41 tigStore<br>-rwxrwxr-x 1 urbe urbe&nbsp; 35K Apr 10 11:41 tracearchiveToCA<br>-rwxrwxr-x 1 urbe urbe&nbsp; 35K Apr 10 11:41 tracedb-to-frg.pl<br>-rwxrwxr-x 1 urbe urbe&nbsp; 44K Apr 10 11:41 trimFastqByQVWindow<br>-rwxrwxr-x 1 urbe urbe&nbsp; 18K Apr 10 11:40 uidclient<br>-rwxrwxr-x 1 urbe urbe 589K Apr 10 11:41 unitigger<br>-rwxrwxr-x 1 urbe urbe&nbsp; 42K Apr 10 11:40 upgrade-v8-to-v9<br>-rwxrwxr-x 1 urbe urbe&nbsp; 42K Apr 10 11:40 upgrade-v9-to-v10<br>-rwxrwxr-x 1 urbe urbe&nbsp; 854 Apr 10 11:41 utg2fasta<br>-rwxrwxr-x 1 urbe urbe 731K Apr 10 11:41 utgcns<br>-rwxrwxr-x 1 urbe urbe 561K Apr 10 11:41 utgcnsfix<br><br><br></p><p>Address of the bookmark: <a href="http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page" rel="nofollow">http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/864/the-laboratoire-de-genomique-fonctionelle</guid>
  <pubDate>Sun, 14 Jul 2013 13:03:18 -0500</pubDate>
  <link></link>
  <title><![CDATA[The Laboratoire de genomique fonctionelle]]></title>
  <description><![CDATA[
<p>One persistent challenge of post genome biology remains the determination of the functions of all potential genes. In mammals this task is formidable given that a single gene can produce numerous protein isoforms through alternative pre-mRNA splicing. Protein isoforms from a single gene can have diverse, and in some cases antagonistic, functions. AS plays a pivotal biological role in protein diversity and developmental regulation. It is now believed that AS occurs in up to 74% of human genes, making it more of a rule than an exception.</p>

<p>Link @ http://lgfus.ca/public/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32184/metagenomics-assembly-workshop</guid>
	<pubDate>Tue, 18 Apr 2017 04:28:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32184/metagenomics-assembly-workshop</link>
	<title><![CDATA[Metagenomics assembly workshop !!]]></title>
	<description><![CDATA[<div>
<div>
<div id="welcome-to-metagenomics-workshop">
<p>Welcome to the one-day metagenomics assembly workshop. This tutorial will guide you through the typical steps of metagenome assembly and binning.</p>
<div>
<ul>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/data.html">The Tutorial Data Set</a></li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/qc/index.html">FastQC Quality Control</a></li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/assembly/index.html">Assembly</a>
<ul>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/assembly/velvet.html">Velvet Assembly</a></li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/assembly/megahit.html">MEGAHIT Assembly</a></li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/assembly/idba_ud.html">IDBA-UD Assembly</a></li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/assembly/ray.html">Ray Assembly</a></li>
</ul>
</li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/geneprediction/index.html">Gene Prediction</a></li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/evaluation/index.html">Assembly Evaluation</a>
<ul>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/evaluation/mapping.html">Read Mapping</a></li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/evaluation/metaquast.html">MetaQUAST</a></li>
</ul>
</li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/binning/index.html">Binning</a>
<ul>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/binning/maxbin.html">MaxBin Binning</a></li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/binning/metabat.html">MetaBAT Binning</a></li>
</ul>
</li>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/classification/index.html">Classification</a>
<ul>
<li><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/classification/kraken.html">Kraken Taxonomic Sequence Classification System</a></li>
</ul>
</li>
</ul>
</div>
</div>
</div>
</div>
<div><a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/data.html" title="The Tutorial Data Set">Next&nbsp;<span></span></a>
<p>&nbsp;</p>
</div><p>Address of the bookmark: <a href="http://denbi-metagenomics-workshop.readthedocs.io/en/latest/index.html" rel="nofollow">http://denbi-metagenomics-workshop.readthedocs.io/en/latest/index.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32420/fastq-format</guid>
	<pubDate>Wed, 03 May 2017 04:23:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32420/fastq-format</link>
	<title><![CDATA[Fastq format]]></title>
	<description><![CDATA[<p><strong>FASTQ format</strong>&nbsp;is a text-based&nbsp;<a href="https://en.wikipedia.org/wiki/File_format" title="File format">format</a>&nbsp;for storing both a biological sequence (usually&nbsp;<a href="https://en.wikipedia.org/wiki/Nucleotide_sequence" title="Nucleotide sequence">nucleotide sequence</a>) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single&nbsp;<a href="https://en.wikipedia.org/wiki/ASCII" title="ASCII">ASCII</a>&nbsp;character for brevity.</p>
<p>It was originally developed at the&nbsp;<a href="https://en.wikipedia.org/wiki/Wellcome_Trust_Sanger_Institute" title="Wellcome Trust Sanger Institute">Wellcome Trust Sanger Institute</a>&nbsp;to bundle a&nbsp;<a href="https://en.wikipedia.org/wiki/FASTA_format" title="FASTA format">FASTA</a>&nbsp;sequence and its quality data, but has recently become the&nbsp;<em>de facto</em>&nbsp;standard for storing the output of high-throughput sequencing instruments such as the&nbsp;<a href="https://en.wikipedia.org/wiki/Illumina_(company)" title="Illumina (company)">Illumina</a>&nbsp;Genome Analyzer.<sup id="cite_ref-Cock2009_1-0"><a href="https://en.wikipedia.org/wiki/FASTQ_format#cite_note-Cock2009-1">[1]</a></sup></p><p>Address of the bookmark: <a href="https://en.wikipedia.org/wiki/FASTQ_format" rel="nofollow">https://en.wikipedia.org/wiki/FASTQ_format</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32485/bacterial-genome-assembly</guid>
	<pubDate>Fri, 05 May 2017 06:11:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32485/bacterial-genome-assembly</link>
	<title><![CDATA[Bacterial genome assembly !!]]></title>
	<description><![CDATA[<p>This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of&nbsp;bacterial sequence data. The bacterial sample used in this tutorial will be referred&nbsp;to simply&nbsp;as &ldquo;Species&rdquo; since it is&nbsp;live data. This data is paired-end data, meaning that there are forward and reverse reads, which we will designate as Sample_R1.fastq and Sample_R2.fastq, respectively.</p>
<p>https://github.com/jennomics/WorkflowPaper/blob/master/Genome%20Assembly%20and%20Annotation.md</p><p>Address of the bookmark: <a href="http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/" rel="nofollow">http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1217/studentship-at-bioinformatics-infrastructure-facility-bif-department-of-biotechnology-alagappa-university</guid>
  <pubDate>Fri, 02 Aug 2013 10:33:54 -0500</pubDate>
  <link></link>
  <title><![CDATA[Studentship at Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University]]></title>
  <description><![CDATA[
<p>WALK IN INTERVIEW</p>

<p>A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 004 on 03.08.2013 (Saturday) at 12:30 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.</p>

<p>1. Studentship (One Post):</p>

<p>Stipend : Rs. 5000 p.m. (consolidated)</p>

<p>Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/<br />Life Sciences</p>

<p>Interested candidates are encouraged to send their Curriculum Vitae by email to alagappauniv.btisnet@nic.in in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&amp;DA will be given for attending the interview.</p>

<p>Advertisement: http://www.alagappabiotech.org/Notification.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32631/barrnap-bacterial-ribosomal-rna-predictor</guid>
	<pubDate>Fri, 12 May 2017 09:24:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32631/barrnap-bacterial-ribosomal-rna-predictor</link>
	<title><![CDATA[Barrnap: Bacterial ribosomal RNA predictor]]></title>
	<description><![CDATA[<p>Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).</p>
<p>It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs.&nbsp;</p><p>Address of the bookmark: <a href="https://github.com/tseemann/barrnap" rel="nofollow">https://github.com/tseemann/barrnap</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/2042/ngs-course-medical-genomics-scheduled-for-17-20-september-2013-in-uz-leuven-belgium</guid>
	<pubDate>Mon, 12 Aug 2013 12:08:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/2042/ngs-course-medical-genomics-scheduled-for-17-20-september-2013-in-uz-leuven-belgium</link>
	<title><![CDATA[NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).]]></title>
	<description><![CDATA[<p>This course is open to all students and postdocs and registration for all academic participants is free of charge. To help us in organizing the course, please register online via http://gc.uzleuven.be where the preliminary program is also available.</p><p>This course is organized with support from the IAP &ldquo;Belgian Medical Genomics Initiative&rdquo;, SymBioSys and the Genomics Core.</p><p>For inquiries, please email Ms Narcisse Opdekamp ( narcisse.opdekamp@uzleuven.be ).</p><p>More at &gt;&gt;&nbsp;<a href="http://gc.uzleuven.be/">http://gc.uzleuven.be/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/1332/bioinformatics-companies-in-india</guid>
	<pubDate>Mon, 05 Aug 2013 20:20:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/1332/bioinformatics-companies-in-india</link>
	<title><![CDATA[Bioinformatics Companies in India]]></title>
	<description><![CDATA[<p>Following are the list of top 30 bioinformatics companies in India. The companies name order does not follow any specific pattern.</p><p>1. Accelrys Software Solution Pvt Ltd.<br />12th Floor, Discover, ITPL, White Field, Bangalore-65.<br /><a href="http://www.accelrys.com/">www.accelrys.com</a></p><p>2. Apticraft Systems (P) Ltd.<br />142, Electronics Complex, Pardeshipura, Indore &ndash; 452010 (M.P.), India<br /><a href="http://www.apticraft.com/">www.apticraft.com</a></p><p>3. Aptuit Informatics<br />Plot No. 100-103, Export Promotion Industrial Park, White Field, Bangalore-560066<br /><a href="http://www.aptiuit.com/">www.aptiuit.com</a></p><p>4. Bigtec<br />J. K. Towers, 8th Block, Sangam Circle,46th Cross, Bangalore-560082.<br /><a href="http://www.bigtec.org/">www.bigtec.org</a></p><p>5. Bijam Biosciences Private Limited<br />Nagarjuna Hills, Hyderabad 500 082, India<br /><a href="http://www.nagarjunagroup.com/">www.nagarjunagroup.com</a></p><p>6. Bio Base Databases India Pvt Ltd.<br />Crescent Towers, 4th Floor, No : 32/1, Crescent Road, Bnagalore &ndash; 560 001<br /><a href="http://www.biobase-international.com/">www.biobase-international.com</a></p><p>7. BioImagene India Pvt. Ltd.<br />4th floor, C-Wing, Godrej Eternia, Shivajinagar, Pune-411005<br /><a href="http://www.bioimagene.com/">www.bioimagene.com</a></p><p>8. BioInformatics Institute Of India &ndash; Noida<br />C-56 A/28, Sector -62, Noida &ndash; 201 301<br /><a href="http://www.bii.in/">www.bii.in</a></p><p>9. CLC bio India Pvt Ltd<br />#Plot No. 51, H.No. 8-3-214/51, Srinivasa Nagar (West) Ameerpet Hyderabad &ndash; 500 038<br /><a href="http://www.clcbio.com/india">www.clcbio.com/india</a></p><p>10. CytoGenomics India (P) Ltd.<br />#3004, 12A Main HAL 2nd Stage, Bangalore 560008<br /><a href="http://www.silicocyte.com/">www.silicocyte.com</a></p><p>11. Genotypic Technology<br />211, 6th Cross, 80ft Road, RMV II Stage, Bangalore 560094<br /><a href="http://www.genotypic.co.in/">www.genotypic.co.in</a></p><p>12. Genvea Biosciences<br />Dr. D. T. Singh, CSO, 53, Craig Rd. #04-01, Singapore-089691<br /><a href="http://www.genvea.com/">www.genvea.com</a></p><p>13. Helix Info Systems<br />132 A, II Floor, Sterling Towers, IV Cross Street, Sterling Road, Nungambakkam, Chennai.<br /><a href="http://www.helixinfosystems.com/">www.helixinfosystems.com</a></p><p>14. Jalaja Technologies Pvt. Ltd.,<br />21/1,Victoria Layout, Victoria Road, Bangalore-47<br /><a href="http://www.jalaja.com/">www.jalaja.com</a></p><p>15. Jubilant Biosys Ltd<br />#96, Industrial Subrub, 2nd Stage, Yeshwanthpur, Bangalore- 560022<br />Jubilant Organosys Ltd.<br />1A, Sector 16A, Noida &ndash; 201 301 (India)<br /><a href="http://www.jubl.com/">www.jubl.com</a></p><p>16. Kshema Technologies<br />#1, Global Village, Mylasandra, Mysore Road, Bangalore-560 059.<br /><a href="http://www.mphasis.com/">www.mphasis.com</a></p><p>17. LabNetworx<br />B-704, Gitanjali Apartments, Vikas Marg Extension, New Delhi &ndash; 110 092<br /><a href="http://www.labnetworx.com/">www.labnetworx.com</a></p><p>18. LabVantage Solutions Pvt. Ltd.<br />Bengal Intelligent Park, Building C, 2nd Floor, Sector V, Salt Lake Electronics Complex, Kolkata &ndash; 700 091<br /><a href="http://www.labvantage.com/">www.labvantage.com</a></p><p>19. LeadInvent,&nbsp;<br />2nd Floor, Biotech Centre, University of Delhi, South Campus, Benito Juarez Road, New Delhi 110021, India<br />Contact no: +91 11 24119241<br />Email: contact@leadinvent.com<br /><a href="http://www.leadinvent.com">www.leadinvent.com</a></p><p>20. Mascon Life Sciences<br />B &ndash; 8/ 10, Vasant Vihar, New Delhi 110057, India<br /><a href="http://www.masconlifesciences.com/">www.masconlifesciences.com</a></p><p>21. Molecular Connections P Ltd<br />Kandala Mansion, 2/2 Kariappa Road, Near Krishna Rao Park, Basavangudi, Bangalore &ndash; 4<br /><a href="http://www.molecularconnections.com/">www.molecularconnections.com</a></p><p>22.Novo Informatics Pvt. Ltd.<br />TBIU, 2nd Floor, Synergy Building, Indian Institute of Technology,&nbsp;Hauz Khas, New Delhi-16.<br />Contact: 91-11-26581524, 91-11-26581766(Extension: 28)<br />Email: info@novoinformatics.com<br /><a href="http://www.novoinformatics.com">www.novoinformatics.com</a></p><p>23. Ocimum Biosolutions (India) Ltd<br />6th Floor, Reliance Classic, Road No.1 Banjara Hills, Hyderabad 500 034, India.<br /><a href="http://www.ocimumbio.com/">www.ocimumbio.com</a></p><p>24. Scube Scientific Software Solutions<br />613, Hemkunt Chambers, 89, Nehru Place, New Delhi -110 019<br /><a href="http://www.scribeindia.com/">www.scribeindia.com</a></p><p>25. Siri Technologies Pvt Ltd.<br />38/C -23, South End Road, Basavanagudi, Bangalore-56004.<br /><a href="http://www.siritech.com/">www.siritech.com</a></p><p>26. Strand Life Sciences Pvt. Ltd.<br />#237, Sir C. V. Raman Avenue, Raj Mahal Vilas, Bangalore 560 080 INDIA<br /><a href="http://www.strandls.com/">www.strandls.com<br /></a><br />27. SooryaKiran Bioinformatics (P) Ltd<br />TBIC-13, Tejaswini Building, Technopark, Thriruvananthapuram- 695 584, Keralam, India</p><p>Ph: +91 471 4060979,+91 9895404104<br />Email:&nbsp;<a href="mailto:reachus@sooryakiran.com">reachus@sooryakiran.com</a><br /><a href="http://www.sooryakiran.com/">http://www.sooryakiran.com</a></p><p>28. Systat Software Asia Pacific<br />4th Floor, Block 1, Shankar Narayan Building, No.25, MG Road, Bangalore &ndash; 560001<br /><a href="http://www.systat.com/">www.systat.com</a></p><p>29. ABC Genomics (India) Pvt. Ltd.<br />Biotech Park, Sector G, Jankipuram, Kursi Road, Lucknow-226021, U.P., INDIA<br />Tel +91-522-4068579, Email: director@abcgenomics.com<br /><a href="http://www.abcgenomics.com/">www.abcgenomics.com</a></p><p>30. en-GENE-ier's Core Technology Services,<br />1/340, Virat Khand, Gomtinagar,&nbsp;<br />(Near Maharaja Agrasen Public School)<br />lucknow-226010, U.P., India.<br /><a href="http://www.bio.egicore.com/"></a><a href="http://www.bio.egicore.com/">http://www.bio.egicore.com/</a></p><p>&nbsp;</p><p>Best of luck for your job hunts :).</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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