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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/37590?offset=40</link>
	<atom:link href="https://bioinformaticsonline.com/related/37590?offset=40" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/842/ngs-bioinformatics-summit-europe</guid>
  <pubDate>Sat, 13 Jul 2013 17:02:34 -0500</pubDate>
  <link></link>
  <title><![CDATA[NGS &amp; Bioinformatics Summit Europe]]></title>
  <description><![CDATA[
<p>NGS &amp; Bioinformatics Summit Europe </p>

<p>Conference </p>

<p>7th   to  8th October 2013 <br />Berlin, Germany </p>

<p>Website: https://www.gtcbio.com/conference/ngseurope-overview <br />Contact person: Kristen Starkey </p>

<p>We welcome you to join us at GTC’s NGS &amp; Bioinformatics Summit Europe on October 7-8, 2013 in Berlin, Germany. </p>

<p>Organized by: GTC <br />Deadline for abstracts/proposals: 7th September 2013</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31714/krona</guid>
	<pubDate>Wed, 22 Mar 2017 04:47:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31714/krona</link>
	<title><![CDATA[Krona]]></title>
	<description><![CDATA[<p>Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an <a href="https://github.com/marbl/Krona/wiki/ExcelTemplate">Excel template</a> or <a href="https://github.com/marbl/Krona/wiki/KronaTools">KronaTools</a>, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser (see <a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).</p>
<p><a href="http://marbl.github.io/Krona/img/screen_mgrast.png"><img src="https://camo.githubusercontent.com/27b71b1f1832523723c3d14dec764e7ad098438c/687474703a2f2f6d6172626c2e6769746875622e696f2f4b726f6e612f696d672f7468756d625f6d67726173742e706e67" width="210" height="167" alt="image" style="border: 0px;"></a></p><p>Address of the bookmark: <a href="https://github.com/marbl/Krona/wiki" rel="nofollow">https://github.com/marbl/Krona/wiki</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/859/boku-chair-of-bioinformatics</guid>
  <pubDate>Sun, 14 Jul 2013 12:37:23 -0500</pubDate>
  <link></link>
  <title><![CDATA[Boku Chair of Bioinformatics]]></title>
  <description><![CDATA[
<p>The Bioinformatics group at Boku University has two main areas of interest, underpinning a common goal, the study of complex systems in living organisms. To overcome the engineered redundancies and combinatorial effects prevalent in higher eukaryotes, novel views augmenting the classical gene by gene approaches are required. We combine<br />Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and<br />Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)</p>

<p>Link @ http://bioinf.boku.ac.at/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32018/tmap-torrent-mapping-alignment-program-general-notes</guid>
	<pubDate>Sun, 02 Apr 2017 15:53:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32018/tmap-torrent-mapping-alignment-program-general-notes</link>
	<title><![CDATA[TMAP - torrent mapping alignment program General Notes]]></title>
	<description><![CDATA[<p>TMAP - torrent mapping alignment program <a href="https://github.com/iontorrent/TS/tree/master/Analysis/TMAP#general-notes"></a>General Notes</p>
<p>TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.</p>
<ul>
<li>
<p>The latest TMAP is unsupported. To use a supported version, please see the TMAP version associated with a Torrent Suite release below.</p>
</li>
<li>
<p>Get the latest source code:</p>
<div>
<pre>git clone git://github.com/iontorrent/TMAP.git
 <span>cd</span> TMAP
 git submodule init
 git submodule update</pre>
</div>
</li>
</ul>
<p>https://github.com/iontorrent/TS/tree/master/Analysis/TMAP</p><p>Address of the bookmark: <a href="https://github.com/iontorrent/TS/tree/master/Analysis/TMAP" rel="nofollow">https://github.com/iontorrent/TS/tree/master/Analysis/TMAP</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>

<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/researchlabs/view/872/jayaram-lab</guid>
  <pubDate>Sun, 14 Jul 2013 14:04:37 -0500</pubDate>
  <link></link>
  <title><![CDATA[Jayaram Lab]]></title>
  <description><![CDATA[
<p>Responsible (a) for developing Chemgenome, Bhageerath &amp; Sanjeevini methods &amp; softwares for genome annotation, protein tertiary structure prediction &amp; computer aided drug design respectively, (b) for setting up a multi-teraflop supercomputing facility for Bioinformatics &amp; Computational Biology at IIT Delhi, and (c) for making the hardware and software freely accessible at (www.scfbio-iitd.res.in) to the global scientific user community.</p>

<p>Faculty facilitator/Founder Director for two start-up companies (Leadinvent incubated at IIT, Delhi from 2006-2009 &amp; Novoinformatics, under incubation at IIT Delhi since 2011).</p>

<p>Research Interest <br />Genome Analysis, Protein Structure Prediction and Drug Design.</p>

<p>Link @ http://www.scfbio-iitd.res.in/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/32358/list-of-goi-approved-peer-reviewed-bioinformatics-and-computational-biology-journals</guid>
	<pubDate>Tue, 25 Apr 2017 05:03:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/32358/list-of-goi-approved-peer-reviewed-bioinformatics-and-computational-biology-journals</link>
	<title><![CDATA[List of GOI approved peer reviewed bioinformatics and computational biology journals]]></title>
	<description><![CDATA[<p>Unfortunately, we now live in a world where the integrity of peer-reviewed journals is being threatened by the rise of the academic version of fake news &ndash; something many call &ldquo;predatory publishing". &nbsp;Mostly in academic publishing world, "predatory open access publishing" is an exploitative open-access publishing business model that involves charging publication fees to authors without providing the editorial and publishing services associated with legitimate journals (open access or not).</p><p>Nearly 20% of the such journals have a flashy impact factor and quick publication time, which are quick give-aways. Interestingly, under contact address, some journal websites do not even provide any address to contact. All of this has led to the emergence of a new and dark market of deceptive publishers that exploit the concept of open access and provide channels for &ldquo;scientific journal&rdquo; publication with little or no peer review. For a fee, they will publish almost anything &ndash; even if the study was fatally flawed. And these journals provide a forum that can be used as a channel to publish fraudulent &ldquo;advocacy research.&rdquo; You can find list of certain such publishers at "Beall's List" http://beallslist.weebly.com/</p><p>Keeping all these in mind, Government of India (GOI) decided to approved certain bioinformatics and computational biology journals for your research publication.<br /> <br />Following are the list of GOI validated and peer reviewed bioinformatics and computational biology journals:</p><p><strong>NOTE:Each journal details are in following order Tittle\nSource\nSubject. </strong><br /><strong>Point to remember: The list of journals are NOT sorted in any ascending or descending order.</strong></p><p><em>If I missed any other GOI validated bioinformatics journal, then please report me in comment section.</em></p><p><strong>Open Bioinformatics Journal</strong> <br />Scopus <br />Computer Science; Engineering; Medicine</p><p><strong>PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS</strong> <br />WoS <br />BIOLOGY &amp; BIOCHEMISTRY</p><p><strong>Advances and Applications in Bioinformatics and Chemistry</strong><br />Scopus<br />Biochemistry, Genetics and Molecular Biology Chemistry; Computer Science</p><p><strong>Advances in Bioinformatics</strong><br />Scopus<br />Biochemistry, Genetics and Molecular Biology; Computer Science; Engineering</p><p><strong>Applied Bioinformatics</strong><br />Scopus<br />Agricultural and Biological Sciences; Computer Science</p><p><strong>BIOINFORMATICS</strong> <br />WoS &amp; Scopus <br />COMPUTER SCIENCE</p><p><strong>Bioinformatics and Biology Insights</strong> <br />Scopus<br />Biochemistry, Genetics and Molecular Biology; Computer Science; Mathematics</p><p><strong>BMC BIOINFORMATICS</strong> <br />WoS &amp; Scopus <br />COMPUTER SCIENCE</p><p><strong>BRIEFINGS IN BIOINFORMATICS</strong> <br />WoS &amp; Scopus <br />COMPUTER SCIENCE</p><p><strong>Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference</strong> <br />Scopus <br />Medicine</p><p><strong>Current Bioinformatics</strong> <br />WoS &amp; Scopus <br />COMPUTER SCIENCE</p><p><strong>Current Protocols in Bioinformatics</strong> <br />Scopus <br />Biochemistry, Genetics and Molecular Biology</p><p><strong>JOURNAL OF COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS</strong> <br />ICI <br />BIOLOGICAL SCIENCE</p><p><strong>Journal of integrative bioinformatics</strong> <br />Scopus <br />Medicine</p><p><strong>Journal of Proteomics and Bioinformatics</strong> <br />Scopus<br />Biochemistry, Genetics and Molecular Biology; Computer Science</p><p><strong>Mathematical Biology and Bioinformatics</strong> <br />Scopus <br />Engineering; Mathematics</p><p><strong>Trends in Bioinfprmatics</strong><br />Scopus <br />Computer Science</p><p><strong>Eurasip Journal on Bioinformatics and Systems Biology</strong> <br />Scopus<br />General; Computer Science; Mathematics; Medicine</p><p><strong>Evolutionary Bioinformatics</strong> <br />WoS &amp; Scopus <br />COMPUTER SCIENCE</p><p><strong>Genomics, Proteomics and Bioinformatics</strong> <br />Scopus<br />Biochemistry, Genetics and Molecular Biology;Mathematics</p><p><strong>IEEE/ACM Transactions on Computational Biology and Bioinformatics</strong> <br />Scopus<br />Biochemistry, Genetics and Molecular Biology;Mathematics</p><p><strong>IEEE-ACM Transactions on Computational Biology and Bioinformatics</strong> <br />WoS <br />COMPUTER SCIENCE</p><p><strong>International Journal of Bioinformatics Research and Application</strong><br />Scopus<br />Biochemistry, Genetics and Molecular Biology; Medicine, Health</p><p><strong>International Journal o f Data M ining and Bioinformatics</strong> <br />WoS &amp; Scopus <br />COMPUTER SCIENCE</p><p><strong>IPSJ Transactions on Bioinformatics</strong> <br />Scopus <br />Biochemistry, Genetics and Molecular Biology;Computer Science</p><p><strong>Journal of Bioinformatics and Computational Biology</strong> <br />WoS &amp; Scopus<br />COMPUTER SCIENCE</p><p><strong>Journal of Clinical Bioinformatics</strong> <br />Scopus <br />Medicine</p><p><strong>PLoS Computational Biology</strong> <br />WoS &amp; Scopus <br />BIOLOGY &amp; BIOCHEMISTRY</p><p><strong>Reviews in Computational Chemistry</strong> <br />WoS &amp; Scopus <br />CHEMISTRY</p><p><strong>RSC Theoretical and Computational Chemistry Series</strong><br />Scopus <br />Chemistry; Computer Science</p><p><strong>Annual Reports in Computational Chemistry</strong> <br />Scopus <br />Chemistry; Mathematics</p><p><strong>Computational and Structural Biotechnology Journal</strong> <br />Scopus<br />Biochemistry, Genetics and Molecular Biology; Computer Science</p><p><strong>Computational and Theoretical Chemistry</strong> <br />WoS &amp; Scopus <br />CHEMISTRY</p><p><strong>COMPUTATIONAL BIOLOGY AND CHEMISTRY</strong> <br />WoS &amp; Scopus<br />COMPUTER SCIENCE</p><p><strong>COMPUTATIONAL CHEMISTRY</strong> <br />WoS <br />CHEMISTRY</p><p><strong>Journal of Theoretical and Computational Chemistry</strong> <br />Scopus<br />Chemistry; Computer Science</p><p><strong>Theoretical and Computational Chemistry</strong> <br />Scopus <br />Chemistry</p><p><strong>Wiley Interdisciplinary Reviews: Computational Molecular Science</strong> <br />Scopus<br />Biochemistry, Genetics and Molecular Biology;Chemistry; Computer Science; Materials Science; Mathematics</p><p><strong>Wiley Interdisciplinary Reviews- Computational Molecular Science</strong> <br />WoS <br />CHEMISTRY</p><p><strong>Interdisciplinary sciences, computational life sciences</strong><br />Scopus<br />Medicine</p><p><strong>Interdisciplinary Sciences-Computational Life Science</strong><br />WoS<br />Biology and Biochemistry</p><p><strong>International Journal of Computational Biology and Drug Design</strong><br />Scopus<br />Computer Science; Pharmacology, Toxicology and Pharmaceutics</p>]]></description>
	<dc:creator>Jit</dc:creator>
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