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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/11355?offset=90</link>
	<atom:link href="https://bioinformaticsonline.com/related/11355?offset=90" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/18384/big-genomic-data-on-google-cloud-platform</guid>
	<pubDate>Fri, 17 Oct 2014 02:16:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/18384/big-genomic-data-on-google-cloud-platform</link>
	<title><![CDATA[Big genomic data on Google Cloud Platform]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/ExNxi_X4qug" frameborder="0" allowfullscreen></iframe>As the cost of DNA sequencing has dropped, the volume of data produced has risen into the petabytes. Google is working with the genomics community to define a standard API for working with big genomic data sets in the cloud. Building on Google Cloud Platform, we show how to store, process, explore and share genomic data using technologies like BigQuery, AppEngine MapReduce, R and more.]]></description>
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18579/cluster-innovation-center-university-of-delhi</guid>
  <pubDate>Wed, 22 Oct 2014 10:39:49 -0500</pubDate>
  <link></link>
  <title><![CDATA[CLUSTER INNOVATION CENTER @ UNIVERSITY OF DELHI]]></title>
  <description><![CDATA[
<p>Applications for Pre-selection of  candidates under ‘Institutions Mode’ for DST-ISPIRE Faculty in  Computational Biology/ Systems Biology/ Bioinformatics</p>

<p>Applications are invited for pre-selection  of candidates for Ministry of Science and Technology, Department of Science and Technology INSPIRE Faculty Scheme: a component of “Assured Opportunity for Research Career (AORC)” under INSPIRE in the area of computational Biology/Systems Biology/Bioinformatics.</p>

<p>Candidates having done their B.Tech/B.E.  and or M.Sc./M.Tech in Computer Science or Biotechnology and Ph.D. in Systems/ Computational Biology or Bioinformatics may apply in the following format prescribed by DST to the Director, Cluster Innovation Center, University Stadium, GC Narang Marg, University of Delhi, Delhi -11107. Detials of other qualification, age limits etc., please visit www.inspire-dst.gov.in.</p>

<p>Application on the prescribed format may be submitted by email to director@cic.du.ac.in before October 25, 2014. Selected candidates shall be called for an interview. The date, time and venue of the interview shall be informed by email/telephone. For more information about Cluster Innovation Center, please visit https://ducic.ac.in.</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/19090/deeptools</guid>
	<pubDate>Sat, 08 Nov 2014 15:02:08 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/19090/deeptools</link>
	<title><![CDATA[deepTools]]></title>
	<description><![CDATA[<p>deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.<br /><br />Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full<br /><br />Source Code and Wiki: https://github.com/fidelram/deepTools/wiki<br /><br />Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools<br /><br />and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows</p>]]></description>
	<dc:creator>Martin Jones</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/19631/rosalind-bioinformatics-problems</guid>
	<pubDate>Thu, 18 Dec 2014 10:32:48 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/19631/rosalind-bioinformatics-problems</link>
	<title><![CDATA[Rosalind Bioinformatics problems !!!]]></title>
	<description><![CDATA[<p>Rosalind is a platform for learning bioinformatics and programming through problem solving. <a href="http://rosalind.info/problems/list-view/">Take a tour</a> to get the hang of how Rosalind works.</p>
<p>http://rosalind.info/problems/list-view/</p><p>Address of the bookmark: <a href="http://rosalind.info/problems/list-view/" rel="nofollow">http://rosalind.info/problems/list-view/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26525/ensembl-comparative-genomics-resources</guid>
	<pubDate>Sun, 28 Feb 2016 17:10:20 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26525/ensembl-comparative-genomics-resources</link>
	<title><![CDATA[Ensembl comparative genomics resources]]></title>
	<description><![CDATA[<div>
<p>The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.</p>
<p><strong>Database URL:</strong> <a href="http://www.ensembl.org" target="pmc_ext">http://www.ensembl.org</a>.</p>
</div><p>Address of the bookmark: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/" rel="nofollow">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26306/busco</guid>
	<pubDate>Sun, 07 Feb 2016 16:02:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26306/busco</link>
	<title><![CDATA[BUSCO]]></title>
	<description><![CDATA[<p>Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs</p>
<p>More at http://busco.ezlab.org/</p><p>Address of the bookmark: <a href="http://busco.ezlab.org/" rel="nofollow">http://busco.ezlab.org/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments</guid>
	<pubDate>Fri, 13 May 2016 05:25:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments</link>
	<title><![CDATA[SATSUMA : Highly sensitive whole-genome synteny alignments.]]></title>
	<description><![CDATA[<p>Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.<br> <br> Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs. <br> <br> You can find the manual <a href="http://satsuma.sourceforge.net/manual.html">here</a>.<br> Download the latest source code from <a href="https://sourceforge.net/projects/satsuma/">here.</a><br> Stable versions can also be downloaded from the <a href="https://www.broadinstitute.org/science/programs/genome-biology/spines">Broad Institute's</a> web site.<br> <br> An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is <a href="http://satsuma.sourceforge.net/faq.html">here</a>.<br> <br> If you use Satsuma in your research, please cite:<br> <a href="http://bioinformatics.oxfordjournals.org/content/26/9/1145.long">Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alf&ouml;ldi, J., Di Palma, F., &amp; Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51</a>.</p>
<p><strong>Tutorial at http://evomics.org/learning/genomics/satsuma/</strong></p><p>Address of the bookmark: <a href="http://satsuma.sourceforge.net/" rel="nofollow">http://satsuma.sourceforge.net/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/915/researcher-in-computer-sciencebiology</guid>
  <pubDate>Mon, 15 Jul 2013 18:38:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Researcher in computer science/biology]]></title>
  <description><![CDATA[
<p>Researcher in Computer Science at the Computational Biology Unit - temporary employment</p>

<p>The Department of Informatics is a vacant position as a researcher in computer science, related to Computational Biology Unit (CBU), for 3 years.<br /> <br />The position is part of CBU Service Group and will focus on bioinformatic analysis project and especially the analysis of high-throughput data, including NGS (sequencing), and proteomics data.<br /> <br />The successful candidate will be part of the Norwegian bioinformatics platform's national helpdesk within the project ELIXIR.NO<br /> <br />Applicants must hold a PhD in a relevant subject such as computer science, mathematics, molecular biology and also possess expertise and experience in bioinformatics statistics and analysis of data from high-throughput molecular experiment.<br /> <br />Basic programming or scripting skills are required. Experience in Python, R, Perl, Linux-based operating systems and moreover knowledge of databases and web programming will be a strength for applicants.<br /> <br />We expect enthusiasm and independence and moreover the ability to work in an interdisciplinary team environment.<br /> <br />Good knowledge of English is required.<br /> <br />Salaries start at level 57 (code 1109/LR 24.1) by appointment. Further promotion occurs after<br />service seniority in the position (at grade 57-65). Of particularly highly qualified applicants may be considered a higher salary.<br /> <br />Further information about the position is available from the chair of the CBU, <br />Professor Inge Jonassen, e-mail: Inge.Jonassen @ ii.uib.no<br /> <br />The successful applicant must comply with the guidelines that apply at any given time the position.<br /> <br />State employment shall as far as possible reflect the diversity of the population. It is therefore an objective to achieve a balanced age and sex composition and the recruitment of persons with immigrant backgrounds. Persons with immigrant background are requested to apply for the position.<br /> <br />Women are particularly encouraged to apply. If the experts find that several applicants have approximately equivalent qualifications, the rules on equal in the Personnel Regulations for Academic Positions will be applied.<br /> <br />University of Bergen applies the principles of public openness when recruiting staff to scientific positions.<br /> <br />Information about the applicant may be made public even though the applicant has requested not to be named in the list of applicants. If the request does not host admitted to the result, the applicant shall be notified of this.<br /> <br />Send application, CV, certificates, diplomas, undergraduate work and a list of publications (list of publications) online by clicking on https://www.jobbnorge.no/jobbsoknet/login.aspx?returnurl=/jobbsoknet/jobapplication.aspx?jobid=95196<br /> <br />You need to upload certified translations into English or a Scandinavian language of appendices, such as diplomas and transcripts.<br /> <br />Applications sent by email to individuals at the institute will not be considered.<br /> <br />Deadline: 9 August 2013</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/1514/list-of-pharmacogenomics-companies-worldwide</guid>
	<pubDate>Fri, 09 Aug 2013 13:24:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/1514/list-of-pharmacogenomics-companies-worldwide</link>
	<title><![CDATA[List of pharmacogenomics companies worldwide]]></title>
	<description><![CDATA[<div><div><p>Pharmacogenomics are the most promising area of research. Here is the list of some Pharmacogenomics companies worldwide. Feel free to add more pharmacogenomics companies if not mentioned in here.</p><p>Great Pharmacogenomics companies <br /><a href="http://www.aruplab.com/">www.aruplab.com</a> <br /><a href="http://www.clarientinc.com/">www.clarientinc.com</a> <br /><a href="http://www.cns-hts.com/">www.cns-hts.com</a> <br /><a href="http://www.dnanow.com/">www.dnanow.com</a> <br /><a href="http://www.dnavision.be/">www.dnavision.be</a> <br /><a href="http://www.dnavision.com/">www.dnavision.com</a> <br /><a href="http://www.dxsdiagnostics.com/">www.dxsdiagnostics.com</a> <br /><a href="http://www.entrogen.com/">www.entrogen.com</a> <br /><a href="http://www.exiqon.com/">www.exiqon.com</a> <br /><a href="http://www.gene.com/">www.gene.com</a> <br /><a href="http://www.genomichealth.com/">www.genomichealth.com</a> <br /><a href="http://www.genoptix.com/">www.genoptix.com</a> <br /><a href="http://www.genpathdiagnostics.com/">www.genpathdiagnostics.com</a> <br /><a href="http://www.gentris.com/">www.gentris.com</a> <br /><a href="http://www.immunicon.com/">www.immunicon.com</a> <br /><a href="http://www.ingenuity.com/">www.ingenuity.com</a> <br /><a href="http://www.lab21.com/">www.lab21.com</a> <br /><a href="http://www.labcorp.com/">www.labcorp.com</a> <br /><a href="http://www.lion-ag.de/">www.lion-ag.de</a> <br /><a href="http://www.lynxgen.com/">www.lynxgen.com</a> <br /><a href="http://www.mayoclinic.com/">www.mayoclinic.com</a> <br /><a href="http://www.mesoscale.com/">www.mesoscale.com</a> <br /><a href="http://www.microcide.com/">www.microcide.com</a> <br /><a href="http://www.mitokor.com/">www.mitokor.com </a> <br /><a href="http://www.monarchlifesciences.com/">www.monarchlifesciences.com</a> <br /><a href="http://www.mplnet.com/">www.mplnet.com</a> <br /><a href="http://www.orchidbio.com/">www.orchidbio.com</a> <br /><a href="http://www.pebio.com/">www.pebio.com</a> <br /><a href="http://www.phenomenome.com/">www.phenomenome.com</a> <br /><a href="http://www.phenopath.com/">www.phenopath.com</a> <br /><a href="http://www.ppgx.com/">www.ppgx.com</a> <br /><a href="http://www.prometheuslabs.com/">www.prometheuslabs.com</a> <br /><a href="http://www.protogene.com/">www.protogene.com</a> <br /><a href="http://www.questdiagnostics.com/">www.questdiagnostics.com</a> <br /><a href="http://www.rigelinc.com/">www.rigelinc.com</a> <br /><a href="http://www.rii.com/">www.rii.com</a> <br /><a href="http://www.saladax.com/">www.saladax.com</a> <br /><a href="http://www.tmdlab.com/">www.tmdlab.com</a> <br /><a href="http://www.transgenomic.com/">www.transgenomic.com</a> <br /><a href="http://www.twt.com/">www.twt.com</a> <br /><a href="http://www.uslabs.net/">www.uslabs.net</a> <br /><a href="http://www.variagenics.com/">www.variagenics.com</a> <br /><br />Great Equipment Companies for Genomics <br /><a href="http://www.affymetrix.com/">www.affymetrix.com</a> <br /><a href="http://www.illumina.com/">www.illumina.com</a> <br /><a href="http://www.iontorrent.com/">www.iontorrent.com</a> <br /><a href="http://www.sequenom.com/">www.sequenom.com</a> <br /><a href="http://www.appliedbiosystems.com/">www.appliedbiosystems.com</a> <br /><a href="http://www.454.com/">www.454.com</a> <br /><a href="http://www.appliedbiosystems.com/">www.appliedbiosystems.com</a><br /><br />Genomics in India <br /><a href="http://www.ganitlabs.in/">www.ganitlabs.in</a> <br /><a href="http://www.sandor.co.in/">www.sandor.co.in</a> <br /><a href="http://www.igib.res.in/">www.igib.res.in</a> <br /><a href="http://www.genotypic.co.in/">www.genotypic.co.in</a> <br /><a href="http://www.ocimumbio.com/">www.ocimumbio.com</a> <br /><a href="http://www.abcgenomics.com/">www.abcgenomics.com</a> <br /><a href="http://www.xcelrisgenomics.com/">www.xcelrisgenomics.com</a> <br /><a href="http://www.ayugen.com/">www.ayugen.com</a> <br /><a href="http://www.geneombiotech.com/">www.geneombiotech.com</a> <br /><br /> Large Global Whole Genome Companies <br /><a href="http://www.decode.com/">www.decode.com</a> <br /><a href="http://www.23andme.com/">www.23andme.com</a> <br /><a href="http://www.navigenics.com/">www.navigenics.com</a><br />www.pathway.com<br /><br /> Global companies offering genomics services <br /><a href="http://www.asuragen.com/">www.asuragen.com</a> <br /><a href="http://www.baseclear.com/">www.baseclear.com</a> <br /><a href="http://www.agtcenter.com/">www.agtcenter.com</a> <br /><a href="http://www.ambrygen.com/">www.ambrygen.com</a> <br /><a href="http://www.arosab.com/">www.arosab.com</a> <br /><a href="http://www.agrf.org.au/">www.agrf.org.au</a> <br /><a href="http://www.beckmangenomics.com/">www.beckmangenomics.com</a> <br /><a href="http://www.genomics.cn/">www.genomics.cn</a> <br /><a href="http://www.bsf.a-star.edu.sg/">www.bsf.a-star.edu.sg</a> <br /><a href="http://www.cbm.fvg.it/">www.cbm.fvg.it</a> <br /><a href="http://www.cincinnatichildrens.org/">www.cincinnatichildrens.org</a> <br /><a href="http://www.cofactorgenomics.com/">www.cofactorgenomics.com</a> <br /><a href="http://www.covance.com/">www.covance.com</a> <br /><a href="http://www.dnalandmarks.ca/">www.dnalandmarks.ca</a> <br /><a href="http://www.dnavision.com/">www.dnavision.com</a> <br /><a href="http://www.expressionanalysis.com/">www.expressionanalysis.com</a> <br /><a href="http://www.fasteris.com/">www.fasteris.com</a> <br /><a href="http://www.gatc-biotech.com/">www.gatc-biotech.com</a> <br /><a href="http://www.genesdiffusion.com/">www.genesdiffusion.com</a> <br /><a href="http://www.geneseek.com/">www.geneseek.com</a> <br /><a href="http://www.geneticvisions.com/">www.geneticvisions.com</a> <br /><a href="http://www.geneworks.com.au/">www.geneworks.com.au</a> <br /><a href="http://www.genizon.com/">www.genizon.com</a> <br /><a href="http://www.genoskan.dk/uk">www.genoskan.dk/uk</a> <br /><a href="http://www.gpbio.jp/">www.gpbio.jp</a> <br /><a href="http://www.igatechnology.com/">www.igatechnology.com</a> <br /><a href="http://www.igenixinc.com/">www.igenixinc.com</a> <br /><a href="http://www.auxologico.it/">www.auxologico.it</a> <br /><a href="http://www.lifeandbrain.com/">www.lifeandbrain.com</a> <br /><a href="http://www.macrogen.co.kr/eng">www.macrogen.co.kr/eng</a> <br /><a href="http://www.gqinnovationcenter.com/">www.gqinnovationcenter.com</a> <br /><a href="http://www.mftservices.de/">www.mftservices.de</a> <br /><a href="http://www.ncgr.org/">www.ncgr.org</a> <br /><a href="http://www.ramaciotti.unsw.edu.au/">www.ramaciotti.unsw.edu.au</a> <br /><a href="http://www.rikengenesis.jp/">www.rikengenesis.jp</a> <br /><a href="http://www.sabiosciences.com/">www.SABiosciences.com</a> <br /><a href="http://www.sequensysbio.com/">www.sequensysbio.com</a> <br /><a href="http://www.servicexs.com/">www.servicexs.com</a> <br /><a href="http://www.snp-genetics.com/">www.snp-genetics.com</a> <br /><a href="http://www.takara-bio.com/">www.takara-bio.com</a> <br /><a href="http://www.gen-probe.com/">www.gen-probe.com</a> <br /><a href="http://www.traitgenetics.com/">www.traitgenetics.com</a></p></div></div>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/2054/postdoc-positions-mammalian-transcriptome-evolution-at-sib</guid>
  <pubDate>Mon, 12 Aug 2013 19:58:33 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoc Positions - Mammalian Transcriptome Evolution at SIB]]></title>
  <description><![CDATA[
<p>BIOINFORMATICS POSTDOC IN FUNCTIONAL EVOLUTIONARY GENOMICS</p>

<p>Center for Integrative Genomics, University of Lausanne, Switzerland</p>

<p>Two postdoctoral positions (2 years with possible extensions up to 5 years) are available immediately in the evolutionary genomics group of Henrik Kaessmann.</p>

<p>We are seeking highly qualified and enthusiastic applicants with strong skills in computational biology/bioinformatics, preferably also with experience in data mining and comparative or evolutionary genome analysis.</p>

<p>We have been interested in a range of topics related to the functional evolution of genomes from primates (e.g., the emergence of new genes and their functions) and other mammals (e.g., the origin and evolution of mammalian sex chromosomes). In the framework of a recently launched series of projects, a large amount of transcriptome and genome (e.g., epigenome) data are being produced by the wet lab unit of the group using next generation sequencing technologies for a unique collection of tissues from representative mammals and outgroup species (e.g., birds). Topics of current projects based on these data include the origins and/or evolution of protein-coding genes, alternative splicing, microRNAs, long noncoding RNAs, and dosage compensation.</p>

<p>The postdoctoral fellow will perform integrated evolutionary/bioinformatics analyses based on data produced in the lab and available genomic data. The specific project will be developed together with the candidate.</p>

<p>The language of the institute is English, and its members form an international group that is rapidly expanding. The institute is located in Lausanne, a beautiful city at Lake Geneva.</p>

<p>For more information on the group and our institute more generally, please refer to our website: http://www.unil.ch/cig/page7858_en.html</p>

<p>Please submit a CV, statement of research interest, and names of three references to: Henrik Kaessmann (Henrik.Kaessmann@unil.ch).</p>

<p>Webpage : http://www.unil.ch/cig/page7858.html</p>
]]></description>
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