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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32465?offset=190</link>
	<atom:link href="https://bioinformaticsonline.com/related/32465?offset=190" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<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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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42187/scientist-b-at-aiims-new-delhi-delhi</guid>
  <pubDate>Thu, 03 Sep 2020 07:04:11 -0500</pubDate>
  <link></link>
  <title><![CDATA[Scientist B at AIIMS, New Delhi, Delhi]]></title>
  <description><![CDATA[
<p>Scientist B at AIIMS, New Delhi, Delhi</p>

<p>Overview<br />Applications are invited from eligible candidates for the following position under Meity funded research project entitled: Artifical Intelligence in Oncology, Harnsessing big data and advanced computing to provide personalized diganosis and treatment for cancer patients purely on contractual basis</p>

<p>Scientist B</p>

<p>Salary: Rs.80,000/-</p>

<p>Qualification: 1st Class Masters Degree in Bioinformatics/ Computer Science/ Statistics with Ph.D in relevant subject from a recognized University with experience in Machine learning/ AI project plus two years research experience</p>

<p>Age: Upto 40 years</p>

<p>Details<br />Experience:2 Years<br />Location:New Delhi<br />Education:1st Class Masters Degree<br />SALARY: Rs.80,000/-<br />Key Skills: Research Fellowship<br />Desired Profile<br />Two years research experience</p>

<p>Company: AIIMS<br />All India Institute of Medical Sciences, New Delhi is a medical school, hospital and public medical research university</p>

<p>More at https://www.aiims.edu/en/notices/recruitment/aiims-recruitment.html?id=10844<br />PDF https://www.aiims.edu/images/pdf/recruitment/advertisement/Post_BioChem_22_08_20.PDF</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34488/scripts-for-the-analysis-of-hgt-in-genome-sequence-data</guid>
	<pubDate>Wed, 29 Nov 2017 16:44:10 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34488/scripts-for-the-analysis-of-hgt-in-genome-sequence-data</link>
	<title><![CDATA[Scripts for the analysis of HGT in genome sequence data.]]></title>
	<description><![CDATA[<p><span>Scripts for the analysis of HGT in genome sequence data</span></p><p>Address of the bookmark: <a href="https://github.com/reubwn/hgt" rel="nofollow">https://github.com/reubwn/hgt</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42265/doctoral-researcher-phd-in-computational-biology-biostatistics-at-luxembourg-centre-for-systems-biomedicine-lcsb</guid>
  <pubDate>Sun, 25 Oct 2020 22:59:54 -0500</pubDate>
  <link></link>
  <title><![CDATA[Doctoral researcher (PhD) in Computational Biology / Biostatistics at Luxembourg Centre for Systems Biomedicine (LCSB)]]></title>
  <description><![CDATA[
<p>Contract Type: Fixed Term Contract<br />Work Hours: Full Time 40.0 Hours per Week<br />Location: Belval<br />Student and employee status (36 months studies programme, as per university standards) with project funding available for up to 48 months<br />36 months fixed-term contract (renewable depending on thesis progress evaluation)<br />Job Reference: UOL03604<br />Further Information<br />Applications should be submitted online and include:</p>

<p>A detailed Curriculum vitae<br />A motivation letter, including a brief description of past research experience and future interests, as well as the earliest possible starting date<br />Copies of degree certificates and transcripts<br />Name and contact details of at least two referees<br />Early application is highly encouraged, as the applications will be processed upon reception. Please apply ONLINE formally through the HR system. Applications by email will not be considered.</p>

<p>*gn=gender neutral.</p>

<p>More at https://recruitment.uni.lu/en/details.html?id=QMUFK026203F3VBQB7V7VV4S8&amp;nPostingID=54876&amp;nPostingTargetID=74639&amp;mask=karriereseiten&amp;lg=UK</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35131/giggle-a-search-engine-for-large-scale-integrated-genome-analysis</guid>
	<pubDate>Wed, 10 Jan 2018 03:10:45 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35131/giggle-a-search-engine-for-large-scale-integrated-genome-analysis</link>
	<title><![CDATA[GIGGLE: a search engine for large-scale integrated genome analysis]]></title>
	<description><![CDATA[<p><span>GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (</span><a href="https://github.com/ryanlayer/giggle">https://github.com/ryanlayer/giggle</a><span>) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.</span></p>
<p>https://www.nature.com/articles/nmeth.4556</p><p>Address of the bookmark: <a href="https://github.com/ryanlayer/giggle" rel="nofollow">https://github.com/ryanlayer/giggle</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42402/two-postdoc-positions-to-study-multiscale-genome-evolution-and-cephalopod-gene-regulation-university-of-vienna-austria</guid>
  <pubDate>Thu, 17 Dec 2020 11:45:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[Two postdoc positions to study multiscale genome evolution and cephalopod gene regulation (University of Vienna, Austria)]]></title>
  <description><![CDATA[
<p>Vienna Biocenter are seeking two postdoctoral researchers to join our team and work on the ERC funded project "METASCALE: Modes of genome evolution during major metazoan transitions". The task of both positions will be to study co-evolutionary trends within animal genomes and their association with the emergence of new gene regulation. Our group employs methods of comparative and regulatory genomics to study the regulatory impact of transitions in animal genome architecture. More recently, we have identified a major genome reorganization in the "smart" coleoid cephalopod molluscs (squid, octopus, cuttlefish) that, together with other genomic changes, potentially comprises a unique path or mode of genome evolution among animals. We are thus interested in quantifying these modes of genome evolution across all available animal genomes and to test whether their shifts are associated with the emergence of novel regulation (e.g., in cephalopods). One of our main model species is the Hawaiian bobtail squid species Euprymna scolopes.  The tasks of the two candidates will be complimentary and highly collaborative with one position focusing on comparative genomics analyses across all metazoans and the other position on regulatory genomics in the squid. A solid background in in bioinformatics and comparative genomics is highly desired for the first position, whereas the second position will benefit from experience in molecular and regulatory genomics methods such as HiC, ATAC-seq, RNA-seq or single cell transcriptomics.</p>

<p>The postdocs will join an international group and network of researchers at the University of Vienna studying a diverse range of species and questions in molecular evolution, development, morphology and genomics. Our group is also part of the large evolVienna network of more than 50 evolutionary biology labs in Vienna, across several universities and research institutes. Our Faculty will be relocating to a new campus at the Vienna Biocenter in summer 2021 (https://biologiezentrum.univie.ac.at/en/). Vienna is a vibrant historic European capital with a high QOL. Information about postdoctoral salaries in Austria can be found on this webpage: https://www.fwf.ac.at/en/research-funding/personnel-costs/</p>

<p>Earliest start date will be after July 2021. Initial term of employment is for two years with the possibility of extension. Remote working, at least initially, is a possibility.</p>

<p>Requirements:<br />- PhD degree or equivalent by the start date <br />- Publishing record in peer-reviewed journals or evidence thereof <br />- At least 2 letters of support</p>

<p>Applications including a letter of motivation should be submitted via the Job Center to the University of Vienna (https://personalwesen.univie.ac.at/en/jobs-recruiting/job-center/,<br />job reference number 11615).</p>

<p>Application deadline: January 15th 2021.<br />Application link: https://univis.univie.ac.at/ebewerbung</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35920/mesquite-a-modular-system-for-evolutionary-analysis</guid>
	<pubDate>Tue, 13 Mar 2018 06:54:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35920/mesquite-a-modular-system-for-evolutionary-analysis</link>
	<title><![CDATA[Mesquite: A modular system for evolutionary analysis]]></title>
	<description><![CDATA[<p><span>Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.</span></p>
<p><span>https://github.com/MesquiteProject/MesquiteCore</span></p><p>Address of the bookmark: <a href="http://mesquiteproject.org/" rel="nofollow">http://mesquiteproject.org/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42707/bioinformatics-in-africa-part-1</guid>
	<pubDate>Sun, 31 Jan 2021 09:04:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42707/bioinformatics-in-africa-part-1</link>
	<title><![CDATA[Bioinformatics in Africa:- Part 1]]></title>
	<description><![CDATA[<p>The Institut Pasteur de C&ocirc;te d&rsquo;Ivoire was created by the N&deg;72&shy;511 law of July 27th, 1972 under the Presidency of his Excellency Felix Houphou&euml;t Boigny and Professor Jacques Monod, then Leading of&nbsp;the&nbsp;Pasteur&nbsp;institute&nbsp;of&nbsp;Paris.</p><p>The&nbsp;objectives&nbsp;of&nbsp;the&nbsp;Bioinformatics&nbsp;pole&nbsp;are:</p><p>&bull; Encourage the access to innovations in research and the best exploitation of research data management.</p><p>&bull; Develop&nbsp;the&nbsp;critical&nbsp;spirit&nbsp;of&nbsp;the&nbsp;researchers&nbsp;around&nbsp;their&nbsp;axis&nbsp;of&nbsp;research.</p><p>&bull; Bring an active help to the improvement of the public health while having for constant worries&nbsp;to&nbsp;feed&nbsp;it&nbsp;by&nbsp;research&nbsp;and&nbsp;the&nbsp;innovation.&nbsp;</p><p>&bull; Start&nbsp;training&nbsp;researchers&nbsp;to&nbsp;use&nbsp;bioinformatics&nbsp;as&nbsp;an&nbsp;indispensable&nbsp;tool&nbsp;to&nbsp;research.</p><p>&bull; Encourage interdisciplinary creating a network of scientific information available to the researchers&nbsp;of&nbsp;the&nbsp;institute&nbsp;and&nbsp;partners</p><p>Long&shy;term&nbsp;training&nbsp;activities:</p><p>&bull; To&nbsp;integrate&nbsp;the&nbsp;bioinformatics&nbsp;in&nbsp;the&nbsp;training&nbsp;programs&nbsp;of&nbsp;academic&nbsp;scientists.</p><p>&bull; Development&nbsp;of&nbsp;West&nbsp;Africa&nbsp;Centre&nbsp;training&nbsp;in&nbsp;bioinformatics&nbsp;and&nbsp;genome&nbsp;data&nbsp;analysis.</p><p>Short&shy;term&nbsp;training&nbsp;activities:</p><p>The IPCI will organize in the month of May 2007 a yearly regional course of initiation and using genome data analysis with the participation of the Centre Biotechnologique de Sfax, Tunisia (Pr Ahmed&nbsp;Reba&iuml;,&nbsp;Department&nbsp;of&nbsp;bioinformatics).</p><p>More at&nbsp;https://www.pasteur.ci/</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39441/snakepipes-a-toolkit-based-on-snakemake-and-python-for-analysis-of-ngs-data</guid>
	<pubDate>Thu, 30 May 2019 04:06:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39441/snakepipes-a-toolkit-based-on-snakemake-and-python-for-analysis-of-ngs-data</link>
	<title><![CDATA[snakepipes: A toolkit based on snakemake and python for analysis of NGS data]]></title>
	<description><![CDATA[<p><span><span>snakePipes are flexible and powerful workflows built using&nbsp;</span><a href="https://github.com/maxplanck-ie/snakepipes/blob/master/snakemake.readthedocs.io">snakemake</a><span>&nbsp;that simplify the analysis of NGS data.</span></span></p>
<ul>
<li>DNA-mapping*</li>
<li>ChIP-seq*</li>
<li>RNA-seq*</li>
<li>ATAC-seq*</li>
<li>scRNA-seq</li>
<li>Hi-C</li>
<li>Whole Genome Bisulfite Seq/WGBS</li>
</ul>
<p><span>(*Also available in "allele-specific" mode)</span></p>
<p><span>snakePipes can be installed via conda : </span></p>
<p><span>'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'. </span></p>
<p><span>Source code (</span><a href="https://github.com/maxplanck-ie/snakepipes" target="">https://github.com/maxplanck-ie/snakepipes</a><span>) and documentation (</span><a href="https://snakepipes.readthedocs.io/en/latest/" target="">https://snakepipes.readthedocs.io/en/latest/</a><span>) are available online.</span></p><p>Address of the bookmark: <a href="https://github.com/maxplanck-ie/snakepipes" rel="nofollow">https://github.com/maxplanck-ie/snakepipes</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42813/bioinformatics-in-africa-part5-nigeria</guid>
	<pubDate>Sat, 06 Feb 2021 21:13:47 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42813/bioinformatics-in-africa-part5-nigeria</link>
	<title><![CDATA[Bioinformatics in Africa: Part5 - Nigeria]]></title>
	<description><![CDATA[<p>Covenant University (CU)&shy;Ota:<br />Covenant University (with her enriching and growing state&shy;of&shy;the&shy;art laboratories in the area of &nbsp;science and technology, arts, business and social sciences) is presently the Best University in &nbsp;Nigeria (Private University category), based on the recent over&shy;all rating just concluded by the &nbsp;Nigeria &nbsp; University &nbsp; Commission &nbsp; (NUC). &nbsp; Recently, &nbsp; Covenant &nbsp; University &nbsp; has &nbsp; initiated &nbsp; the &nbsp;establishment of a Centre for Applied Biotech, Bio&shy;Informatics and Microbiology (CBBM) to be &nbsp;situated at the University. The institute has been designed to be a Public&shy;Private Partnership for a productive synergy b/w Academia, Industry and Government. The whole concept is still evolving &nbsp;and more details will be release soon. As regards CBBM, a dedicated computing lab is in plan, but even our computing capacity is &nbsp;presently enormous. In the department of Computer and Information Sciences, we have more than &nbsp;250 Pentium 4 PCs set aside for teaching and research purposes. Furthermore, we have several &nbsp;moderate speed PCs at the Postgraduate research lab and our engineering departments and units. &nbsp;Our wet lab facilities is presently minimal (basic for teaching), the Centre requirement as it touches &nbsp;the wet&shy;laboratories is also set to upgrade this to basic tools expected at an international centre of learning.</p><p>University&nbsp;of&nbsp;Ibadan&nbsp;(UIB)&shy;Ibadan:<br />There&nbsp;has&nbsp;been&nbsp;significant&nbsp;increase&nbsp;in&nbsp;the&nbsp;number&nbsp;of&nbsp;bioinformatics&nbsp;activities&nbsp;in&nbsp;Nigeria&nbsp;(and&nbsp;West Africa)&nbsp;since&nbsp;2003&nbsp;when&nbsp;the&nbsp;program&nbsp;was&nbsp;initiated&nbsp;by&nbsp;the&nbsp;West&nbsp;African&nbsp;Biotechnology&nbsp;Workshops Series&nbsp;(WABWS,&nbsp;http://www.wabw.org)&nbsp;at&nbsp;the&nbsp;University&nbsp;of&nbsp;Ibadan,&nbsp;Nigeria&nbsp;(in&nbsp;collaboration&nbsp;with&nbsp; the&nbsp;South&nbsp;African&nbsp;National&nbsp;Bioinformatics&nbsp;Institute&nbsp;(SANBI,&nbsp;http:/www.sanbi.ac.za).&nbsp;Workshops&nbsp; that&nbsp;were&nbsp;open&nbsp;to&nbsp;scientists&nbsp;from&nbsp;all&nbsp;African&nbsp;countries&nbsp;have&nbsp;seen&nbsp;a&nbsp;very&nbsp;high&nbsp;number&nbsp;of&nbsp;applications&nbsp; from&nbsp;scientists&nbsp;based&nbsp;in&nbsp;West&nbsp;Africa.&nbsp;The&nbsp;encouraging&nbsp;desire&nbsp;to&nbsp;acquire&nbsp;cutting&shy;edge&nbsp;skills&nbsp;to&nbsp; computational&nbsp;process&nbsp;data&nbsp;and&nbsp;extract&nbsp;useful&nbsp;knowledge&nbsp;from&nbsp;genome&nbsp;projects&nbsp;led&nbsp;to&nbsp;the&nbsp;interest&nbsp;of&nbsp; the&nbsp;West&nbsp;African&nbsp;Biotechnology&nbsp;Workshops&nbsp;(WABW)&nbsp;to&nbsp;develop&nbsp;an&nbsp;agenda&nbsp;to&nbsp;address&nbsp;the&nbsp; bioinformatics&nbsp;skills&nbsp;gap&nbsp;among&nbsp;scientists&nbsp;in&nbsp;West&nbsp;Africa.&nbsp;An&nbsp;increased&nbsp;commitment&nbsp;from&nbsp;agencies&nbsp; like&nbsp;NEPAD&nbsp;would&nbsp;be&nbsp;required&nbsp;in&nbsp;the&nbsp;provision&nbsp;of&nbsp;infrastructure&nbsp;to&nbsp;establish&nbsp;and&nbsp;sustain&nbsp;regional&nbsp; and&nbsp;national&nbsp;networks.</p><p>University&nbsp;of&nbsp;Ilorin&nbsp;(UIL)&shy;Ilorin:<br />The&nbsp;University&nbsp;of&nbsp;Ilorin&nbsp;was&nbsp;established&nbsp;in&nbsp;1976&nbsp;by&nbsp;the&nbsp;Federal&nbsp;Government&nbsp;of&nbsp;Nigeria.&nbsp; Bioinformatics&nbsp;activities&nbsp;started&nbsp;at&nbsp;the&nbsp;University&nbsp;in&nbsp;February&nbsp;2003&nbsp;with&nbsp;the&nbsp;establishment&nbsp;of&nbsp;the&nbsp; West&nbsp;African&nbsp;Bioinformatics&nbsp;Research&nbsp;Initiative&nbsp;(WABRI).&nbsp;However,&nbsp;progress&nbsp;has&nbsp;been&nbsp;rather&nbsp;slow&nbsp; due&nbsp;to&nbsp;inadequate&nbsp;funding.&nbsp;We&nbsp;are&nbsp;mainly&nbsp;engaged&nbsp;in&nbsp;Bioinformatics&nbsp;training&nbsp;at&nbsp;the&nbsp;introductory&nbsp; level&nbsp;and&nbsp;proteomics&nbsp;studies&nbsp;on&nbsp;various&nbsp;species&nbsp;of&nbsp;malaria&nbsp;parasites.&nbsp;Recently,&nbsp;we&nbsp;became&nbsp;interested&nbsp; in&nbsp;comparative&nbsp;genome&nbsp;analysis&nbsp;of&nbsp;various&nbsp;species&nbsp;of &nbsp;Plasmodium&nbsp; and&nbsp;the&nbsp;comparison&nbsp;of&nbsp; chloroquine&nbsp;sensitive&nbsp;and&nbsp;chloroquine&nbsp;resistant&nbsp;strains&nbsp;of&nbsp;Plasmodium&nbsp;falciparum.&nbsp;Other&nbsp;activities&nbsp; and&nbsp;areas&nbsp;of&nbsp;interest&nbsp;can&nbsp;be&nbsp;seen&nbsp;on&nbsp;our&nbsp;website,&nbsp;http://www.wabri.org,&nbsp;although&nbsp;not&nbsp;all&nbsp;our&nbsp; proposed&nbsp;interests&nbsp;have&nbsp;been&nbsp;fully&nbsp;implemented&nbsp;due&nbsp;to&nbsp;our&nbsp;level&nbsp;of&nbsp;funding.</p><p>Training:<br />The&nbsp;University&nbsp;of&nbsp;Ilorin&nbsp;has&nbsp;introduced&nbsp;M.Sc.&nbsp;and&nbsp;Ph.D.&nbsp;programmes&nbsp;in&nbsp;Computer&nbsp;Science&nbsp;(with&nbsp; options&nbsp;in&nbsp;Bioinformatics).&nbsp;The&nbsp;programme&nbsp;is&nbsp;based&nbsp;in&nbsp;the&nbsp;Department&nbsp;of&nbsp;Computer&nbsp;Science&nbsp;and&nbsp; emphasis&nbsp;is&nbsp;on&nbsp;the&nbsp;development&nbsp;of&nbsp;algorithms&nbsp;to&nbsp;solve&nbsp;problems&nbsp;in&nbsp;bioinformatics. The&nbsp;Covenant&nbsp;University&nbsp;offers&nbsp;M.Sc.&nbsp;and&nbsp;Ph.D&nbsp;in&nbsp;Computer&nbsp;Science&nbsp;with&nbsp;option&nbsp;in&nbsp;Bioinformatics&nbsp; (Computational&nbsp;Biology).&nbsp;Furthermore,&nbsp;through&nbsp;affiliated&nbsp;departments,&nbsp;the&nbsp;CBBM&nbsp;is&nbsp;been&nbsp;design&nbsp;to&nbsp;award&nbsp;Diploma&nbsp;and&nbsp;Degree&nbsp;certificates&nbsp;in&nbsp;Biotechnology.</p><p>Web&nbsp;sites&nbsp;and&nbsp;links: http://www.covenantuniversity.com http://www.run.edu.ng http://www.uniben.edu http://www.wabri.org http://www.wabw.org http://www.unilorin.edu.ng http://www.wabri.org http://www.asopah.org</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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