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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/17885?offset=700</link>
	<atom:link href="https://bioinformaticsonline.com/related/17885?offset=700" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/4288/new-born-babies-get-ready-to-know-their-whole-genome-soon</guid>
	<pubDate>Thu, 05 Sep 2013 07:24:02 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/4288/new-born-babies-get-ready-to-know-their-whole-genome-soon</link>
	<title><![CDATA[New born babies get ready to know their whole genome soon!!!]]></title>
	<description><![CDATA[<p>USA launch a pilot projects to examine medical information of newborn baby, which are being funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health.</p><p>Awards of $5 million to four grantees have been made in fiscal year 2013 under the Genomic Sequencing and Newborn Screening Disorders research program. The program will be funded at $25 million over five years, as funds are made available.</p><p>"Hundreds of US babies will be pioneers in genomic medicine through a&nbsp;US$25-million programme to sequence their genomes&nbsp;soon after they are born."</p><p><strong>Source</strong>:</p><p><a href="http://blogs.nature.com/news/2013/09/scientists-to-sequence-hundreds-of-newborns-genomes.html">http://blogs.nature.com/news/2013/09/scientists-to-sequence-hundreds-of-newborns-genomes.html</a></p><p><a href="http://www.genome.gov/27554919">http://www.genome.gov/27554919</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/14215/the-8000-years-old-tibetian-gene-mutation</guid>
	<pubDate>Wed, 20 Aug 2014 21:57:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/14215/the-8000-years-old-tibetian-gene-mutation</link>
	<title><![CDATA[The 8000 years old Tibetian gene mutation !!!]]></title>
	<description><![CDATA[<p>A new study has provided insight into how gene mutation around 8,000 years ago helped Tibetans' to survive in the thin air on the Tibetan Plateau, where an average elevation is of 14,800 feet.<br /><br />A study led by University of Utah scientists is the first to find a genetic cause for the adaptation, a single DNA base pair change that dates back 8,000 years and demonstrate how it contributes to the Tibetans' ability to live in low oxygen conditions.</p><p>About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88 percent of Tibetans have the genetic variation, and it was virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.<br /><br />In those without the adaptation, low oxygen caused their blood to become thick with oxygen-carrying red blood cells, an attempt to feed starved tissues, which could cause long-term complications such as heart failure. The researchers found that the newly identified genetic variation protected Tibetans by decreasing the over-response to low oxygen.</p><p>Reference: http://www.nature.com/nature/journal/v512/n7513/abs/nature13408.html</p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/5350/introduction-of-epigenomics</guid>
	<pubDate>Sun, 06 Oct 2013 04:59:30 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/5350/introduction-of-epigenomics</link>
	<title><![CDATA[Introduction of Epigenomics]]></title>
	<description><![CDATA[<ul>
<li><a href="http://www.genome.gov/27532724#al-1">What is the epigenome?</a></li>
<li><a href="http://www.genome.gov/27532724#al-2">What does the epigenome do?</a></li>
<li><a href="http://www.genome.gov/27532724#al-3">What makes up the epigenome?</a></li>
<li><a href="http://www.genome.gov/27532724#al-4">Is the epigenome inherited?</a></li>
<li><a href="http://www.genome.gov/27532724#al-5">What is imprinting?</a></li>
<li><a href="http://www.genome.gov/27532724#al-6">Can the epigenome change?</a></li>
<li><a href="http://www.genome.gov/27532724#al-7">What makes the epigenome change?</a></li>
<li><a href="http://www.genome.gov/27532724#al-8">How do changes in the epigenome contribute to cancer?</a></li>
<li><a href="http://www.genome.gov/27532724#al-9">How are researchers exploring the epigenome?</a></li>
</ul><p>Address of the bookmark: <a href="http://www.genome.gov/27532724" rel="nofollow">http://www.genome.gov/27532724</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12936/assistant-professor-medical-bioinformatics</guid>
  <pubDate>Wed, 23 Jul 2014 05:00:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor - Medical Bioinformatics]]></title>
  <description><![CDATA[
<p>Advt. No : ME-I/A-IV/03/14</p>

<p>No.of Posts:01 (SC)</p>

<p>Pay Scale:</p>

<p>Pay Band of Rs.15600-39100 + Rs.6000/- GP +NPA @ 25% of Basic Pay +Learning Resource Allowance @ Rs.20,000/-P.A.+ Conveyance Allowance @ Rs. 1650/-P.M.+ Academic Allowance @ Rs.2500/- P.M. and other admissible allowances.</p>

<p>Qualifications:</p>

<p>Area of Specialization:-</p>

<p>Bioinformatics/Computational/Biology/Genomics/ Proteomics/ Structural Biology</p>

<p>1. Postgraduate qualification, e.g. Master’s Degree in Biotechnology/Bioinformatics/ Biophysics.</p>

<p>2. A Doctorate Degree of recognized University/Institute in a basic or allied Medical Science subject e.g. Medical Biotechnology/Biophysics. Bioinformatics/X-ray Crystallography/</p>

<p>Immunology/Structural Biology etc</p>

<p>Experience:</p>

<p>1.Minimum three years teaching and/or research experience in a recognized medical/research Institution in an allied medical subject after obtaining doctorate degree and preferably in Medical</p>

<p>Molecular Biology/ Biophysics/Structural Biology/Genomics and Clinical Proteomics/Computational Biology.</p>

<p>2. Minimum two publication with atleast one in international journal and atleast one as first author</p>

<p>Desirable:-</p>

<p>Consistently excellent scholastic/academic record, demonstrated ability to write grant proposal/(s) successfully, Post Doctoral training in a frontier area of medical Bioinformatics Research and of direct relevance to clinical diagnosis or patient care (preferably from a recognized top-ranking medical institution abroad)</p>

<p>Send your applications to O/O, Deputy Registrar, Recruitment &amp; Establishment Cell, University of Health Sciences, Rohtak by 08.7.2014</p>

<p>For more details,please visit website:http://pgimsrohtak.nic.in/2014%20AP%20Advt.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/10379/your-stressdepression-came-from-ancestor</guid>
	<pubDate>Sun, 04 May 2014 18:46:20 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/10379/your-stressdepression-came-from-ancestor</link>
	<title><![CDATA[Your stress/depression came from ancestor]]></title>
	<description><![CDATA[<p>"A study published in&nbsp;<em>Nature Neuroscience</em>&nbsp;finds that stress in early life alters the production of small RNAs, called microRNAs, in the sperm of mice. The mice show depressive behaviours that persist in their progeny."</p><p>Source:</p><p>http://www.nature.com/news/sperm-rna-carries-marks-of-trauma-1.15049</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/13025/the-5-reasons-to-mistakes-at-bioinformatics-work</guid>
	<pubDate>Thu, 24 Jul 2014 02:51:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/13025/the-5-reasons-to-mistakes-at-bioinformatics-work</link>
	<title><![CDATA[The 5 reasons to mistakes at bioinformatics work !!!]]></title>
	<description><![CDATA[<p>When you're just starting out with biological programming, it's easy to run into complex problems that make you wonder how anyone has ever managed to write a program. There are some problems that trip up nearly every bioinformatician--everything from getting started understanding the biological problems to dealing with program design. Some random mistakes are so prominent that even experienced biological programmers do it. The 8 years in bioinformatics and my few random observations, most of them are snarky. These reasons will always take longer than expected and compel you to postpone your project deadline.</p><p><strong>1.Stupid for biologist:</strong> Biology is so complex that it will make bioinformatician feel stupid. There are no any universal fixed rules; it can surprise you any time. So be nice to biologists who ask questions and resolve your biological puzzles. Sometime you will have no idea what the hell you were doing either.<br /><br /><strong>2.Puzzling why:</strong> Do not hesitate to ask question. Especially. at the beginning of project you will have to ask a lot of questions. Instead of puzzling it out at end check out and clear your doubt even for a single error. It may can leads to wrong conclusion.<br /><br /><strong>3.Running marathon:</strong> The most of the biological software&rsquo;s documentation is always incomplete. In other word they are no more than 95 percent complete. Sometime a single problem can halt your entire project for months. Compilation and running the pipelines in tedious because almost all are interdependent and need proper configuration. I face the same kind of problem with Evolver :( &hellip; <br /><br /><strong>4.Folders missing:</strong> The pipelines generate lots of data, and we keep them in several folders for future use. But sometime we delete them by mistake and move to recovery&hellip;<br /><br /><strong>5.Digging deeper:</strong> Digging deeper is fruitful, but some time it can be catastrophic. You may get frustrated or direction less. So keep a biologist with you for rescue &hellip;. Sometime an expert computer programmer to handle your server. Remember, the server will always go down when you need it the most.<br /><br />The most common frustrating&nbsp; common line: Why do we do this again?</p>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/34221/alignment-free-sequence-comparison-tools-available-for-next-generation-sequencing-data-analysis</guid>
	<pubDate>Tue, 07 Nov 2017 05:33:33 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/34221/alignment-free-sequence-comparison-tools-available-for-next-generation-sequencing-data-analysis</link>
	<title><![CDATA[Alignment-free sequence comparison tools available for next-generation sequencing data analysis]]></title>
	<description><![CDATA[<div><p><span>kallisto</span></p></div><div><p>Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)</p><p>Software (C++)</p><p><a href="https://pachterlab.github.io/kallisto/">https://pachterlab.github.io/kallisto/</a></p><p>Sailfish</p><p>Estimation of isoform abundances from reference sequences and RNA-seq data (<em>k</em>-mer based)</p><p>Software (C++)</p><p><a href="http://www.cs.cmu.edu/~ckingsf/software/sailfish/">http://www.cs.cmu.edu/~ckingsf/software/sailfish/</a></p><p>Salmon</p><p>Quantification of the expression of transcripts using RNA-seq data (uses&nbsp;<em>k</em>-mers)</p><p><a href="https://combine-lab.github.io/salmon/">https://combine-lab.github.io/salmon/</a></p><p>RNA-Skim</p><p>RNA-seq quantification at transcript-level (partitions the transcriptome into disjoint transcript clusters; uses&nbsp;<em>sig</em>-mers, a special type of&nbsp;<em>k</em>-mers)</p><p>Software (C++)</p><p><a href="http://www.csbio.unc.edu/rs/">http://www.csbio.unc.edu/rs/</a></p><p>Variant calling</p><p>ChimeRScope</p><p>Fusion transcript prediction using gene&nbsp;<em>k</em>-mers profiles of the RNA-seq paired-end reads</p><p>Software (Java)</p><p><a href="https://github.com/ChimeRScope/ChimeRScope/wiki">https://github.com/ChimeRScope/ChimeRScope/wiki</a></p><p>FastGT</p><p>Genotyping of known SNV/SNP variants directly from raw NGS sequence reads by counting unique&nbsp;<em>k</em>-mers</p><p>Software (C)</p><p><a href="https://github.com/bioinfo-ut/GenomeTester4/">https://github.com/bioinfo-ut/GenomeTester4/</a></p><p>Phy-Mer</p><p>Reference-independent mitochondrial haplogroup classifier from NGS data (<em>k</em>-mer based)</p><p>Software (Python)</p><p><a href="https://github.com/danielnavarrogomez/phy-mer">https://github.com/danielnavarrogomez/phy-mer</a></p><p>LAVA</p><p>Genotyping of known SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from raw NGS reads (<em>k</em>-mer based)</p><p>Software (C)</p><p><a href="http://lava.csail.mit.edu/">http://lava.csail.mit.edu/</a></p><p>MICADo</p><p>Detection of mutations in targeted third-generation NGS data (can distinguish patients&rsquo; specific mutations; algorithm uses&nbsp;<em>k</em>-mers and is based on colored de Bruijn graphs)</p><p>Software (Python)</p><p><a href="http://github.com/cbib/MICADo">http://github.com/cbib/MICADo</a></p><p>General mapper</p><p>Minimap</p><p>Lightweight and fast read mapper and read overlap detector (uses the concept of &ldquo;minimazers&rdquo;, a special type of&nbsp;<em>k</em>-mers)</p><p>Software (C)</p><p><a href="https://github.com/lh3/minimap">https://github.com/lh3/minimap</a></p><p>Assembly</p><p>De novo genome assembly</p><p>MHAP</p><p>Produces highly continuous assembly (fully resolved chromosome arms) from third-generation long and noisy reads (10 kbp) using a dimensionality reduction technique MinHash</p><p>Software (Java)</p><p><a href="https://github.com/marbl/MHAP">https://github.com/marbl/MHAP</a></p><p>Miniasm</p><p>Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout Consensus (OLC) approach without the necessity of an error correction stage (uses minimap)</p><p>Software (C)</p><p><a href="https://github.com/lh3/miniasm">https://github.com/lh3/miniasm</a></p><p>LINKS</p><p>Scaffolding genome assembly with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes)</p><p>Software (Perl)</p><p><a href="https://github.com/warrenlr/LINKS/">https://github.com/warrenlr/LINKS/</a></p><p>Read clustering</p><p>afcluster</p><p>Clustering of reads from different genes and different species based on&nbsp;<em>k</em>-mer counts</p><p>Software (C++)</p><p><a href="https://github.com/luscinius/afcluster">https://github.com/luscinius/afcluster</a></p><p>QCluster</p><p>Clustering of reads with alignment-free measures (<em>k</em>-mer based) and quality values</p><p>Software (C++)</p><p><a href="http://www.dei.unipd.it/~ciompin/main/qcluster.html">http://www.dei.unipd.it/~ciompin/main/qcluster.html</a></p><p>Reads error correction</p><p>Lighter</p><p>Correction of sequencing errors in raw, whole genome sequencing reads (<em>k</em>-mer based)</p><p>Software (C++)</p><p><a href="https://github.com/mourisl/Lighter">https://github.com/mourisl/Lighter</a></p><p>QuorUM</p><p>Error corrector for Illumina reads using k-mers</p><p>Software (C++)</p><p><a href="https://github.com/gmarcais/Quorum">https://github.com/gmarcais/Quorum</a></p><p>Trowel</p><p>Software (C++)</p><p><a href="https://sourceforge.net/projects/trowel-ec/">https://sourceforge.net/projects/trowel-ec/</a></p><p>Metagenomics</p><p>Assembly-free phylogenomics</p><p>AAF</p><p>Phylogeny reconstruction directly from unassembled raw sequence data from whole genome sequencing projects; provides bootstrap support to assess uncertainty in the tree topology (<em>k</em>-mer based)</p><p>Software (Python)</p><p><a href="https://github.com/fanhuan/AAF">https://github.com/fanhuan/AAF</a></p><p>kSNP v3</p><p>Reference-free SNP identification and estimation of phylogenetic trees using SNPs (based on&nbsp;<em>k</em>-mer analysis)</p><p>Software (C)</p><p><a href="https://sourceforge.net/projects/ksnp/files/">https://sourceforge.net/projects/ksnp/files/</a></p><p>NGS-MC</p><p>Phylogeny of species based on NGS reads using alignment-free sequence dissimilarity measures d2* and d2&nbsp;S&nbsp;under different Markov chain models (using&nbsp;<em>k</em>-words)</p><p>R package</p><p><a href="http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html">http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html</a></p><p>Species identification/taxonomic profiling</p><p>CLARK</p><p>Taxonomic classification of metagenomic reads to known bacterial genomes using&nbsp;<em>k</em>-mer search and LCA assignment</p><p>Software (C++)</p><p><a href="http://clark.cs.ucr.edu/">http://clark.cs.ucr.edu/</a></p><p>FOCUS</p><p>Reports organisms present in metagenomic samples and profiles their abundances (uses composition-based approach and non-negative least squares for prediction)</p><p>Web service Software (Python)</p><p><a href="http://edwards.sdsu.edu/FOCUS/">http://edwards.sdsu.edu/FOCUS/</a></p><p>GSM</p><p>Estimation of abundances of microbial genomes in metagenomic samples (<em>k</em>-mer based)</p><p>Software (Go)</p><p><a href="https://github.com/pdtrang/GSM">https://github.com/pdtrang/GSM</a></p><p>Mash</p><p>Species identification using assembled or unassembled Illumina, PacBio, and ONT data (based on MinHash dimensionality-reduction technique)</p><p>Software (C++)</p><p><a href="https://github.com/marbl/mash">https://github.com/marbl/mash</a></p><p>Kraken</p><p>Taxonomic assignment in metagenome analysis by exact&nbsp;<em>k</em>-mer search; LCA assignment of short reads based on a comprehensive sequence database</p><p>Software (C++)</p><p><a href="https://ccb.jhu.edu/software/kraken/">https://ccb.jhu.edu/software/kraken/</a></p><p>LMAT</p><p>Assignment of taxonomic labels to reads by&nbsp;<em>k</em>-mers searches in precomputed database</p><p>Software (C++/Python)</p><p><a href="https://sourceforge.net/projects/lmat/">https://sourceforge.net/projects/lmat/</a></p><p>stringMLST</p><p><em>k</em>-mer-based tool for MLST directly from the genome sequencing reads</p><p>Software (Python)</p><p><a href="http://jordan.biology.gatech.edu/page/software/stringMLST">http://jordan.biology.gatech.edu/page/software/stringMLST</a></p><p>Taxonomer</p><p><em>k</em>-mer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from clinical and environmental samples</p><p>Web service</p><p><a href="http://taxonomer.iobio.io/">http://taxonomer.iobio.io/</a></p><p>Other</p><p>d2-tools</p><p>Word-based (<em>k</em>-tuple) comparison (pairwise dissimilarity matrix using d2S measure) of metatranscriptomic samples from NGS reads</p><p>Software (Python/R)</p><p><a href="https://code.google.com/p/d2-tools/">https://code.google.com/p/d2-tools/</a></p><p>VirHostMatcher</p><p>Prediction of hosts from metagenomic viral sequences based on ONF using various distance measures (e.g., d2)</p><p>Software (C++)</p><p><a href="https://github.com/jessieren/VirHostMatcher">https://github.com/jessieren/VirHostMatcher</a></p><p>MetaFast</p><p>Statistics calculation of metagenome sequences and the distances between them based on assembly using de Bruijn graphs and Bray&ndash;Curtis dissimilarity measure</p><p>Software (Java)</p><p><a href="https://github.com/ctlab/metafast">https://github.com/ctlab/metafast</a></p></div>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/13337/phd-opportunity-at-universite-de-liege-belgium</guid>
  <pubDate>Sat, 02 Aug 2014 01:12:43 -0500</pubDate>
  <link></link>
  <title><![CDATA[PhD opportunity at Université de Liège - Belgium]]></title>
  <description><![CDATA[
<p>PhD opportunity at Université de Liège - Belgium</p>

<p>The Bioinformatics and Systems Biology Unit of Université de Liège (Belgium) is looking for a highly motivated master student with programming skills for a PhD thesis project (4 years, fully funded) with the goal of designing computational tools that use literature, genomic and structural data in order to infer regulatory and metabolic networks.  </p>

<p>Applicants are invited to send their resume and a recommendation letter to Prof. Patrick Meyer (more details at   www.biosys.ulg.ac.be )</p>

<p>For more information : www.biosys.ulg.ac.be</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34748/airvf-a-filtering-toolbox-for-precise-variant-calling-in-ion-torrent-sequencing</guid>
	<pubDate>Fri, 22 Dec 2017 00:31:06 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34748/airvf-a-filtering-toolbox-for-precise-variant-calling-in-ion-torrent-sequencing</link>
	<title><![CDATA[AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing]]></title>
	<description><![CDATA[<p><span>AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to &sim;98% reduction of false variants when combined to conventional public pipelines and &sim;48% to the in-house commercial solution, with a minimal loss of sensitivity</span></p>
<p><span><span>The program with a detailed manual is available at&nbsp;</span><a href="https://sourceforge.net/projects/airvf/" target="">https://sourceforge.net/projects/airvf/</a></span></p><p>Address of the bookmark: <a href="https://sourceforge.net/projects/airvf/" rel="nofollow">https://sourceforge.net/projects/airvf/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/13523/megadock-40</guid>
	<pubDate>Thu, 07 Aug 2014 18:08:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/13523/megadock-40</link>
	<title><![CDATA[MEGADOCK 4.0]]></title>
	<description><![CDATA[<p>An ultra&ndash;high-performance protein&ndash;protein docking software for heterogeneous supercomputers</p>
<p id="p-4"><strong>Summary:</strong> The application of protein&ndash;protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of over 97% strong scaling.</p>
<p id="p-5"><strong>Availability and Implementation:</strong> MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: <a href="http://www.bi.cs.titech.ac.jp/megadock">http://www.bi.cs.titech.ac.jp/megadock</a>.</p>
<p id="p-6"><strong>Contact:</strong> <a href="mailto:akiyama@cs.titech.ac.jp">akiyama@cs.titech.ac.jp</a></p><p>Address of the bookmark: <a href="http://bioinformatics.oxfordjournals.org/content/early/2014/08/06/bioinformatics.btu532.short" rel="nofollow">http://bioinformatics.oxfordjournals.org/content/early/2014/08/06/bioinformatics.btu532.short</a></p>]]></description>
	<dc:creator>Suleman Khan</dc:creator>
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