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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/11355?offset=60</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/12944/orione-%E2%80%93-a-web-based-framework-for-ngs-analysis-in-microbiology</guid>
	<pubDate>Wed, 23 Jul 2014 06:43:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/12944/orione-%E2%80%93-a-web-based-framework-for-ngs-analysis-in-microbiology</link>
	<title><![CDATA[Orione – a web-based framework for NGS analysis in microbiology]]></title>
	<description><![CDATA[<p>End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult due to a lack of interoperability, reproducibility, and transparency. To overcome these limitations researchers at <a href="http://www.crs4.it/" target="_blank">CRS4</a>, Italy have developed Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for NGS microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.</p>
<p>Reference</p>
<p>Cuccuru G1, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, Fotia G. (2014)<strong> Orione, a web-based framework for NGS analysis in microbiology.</strong> <em>Bioinformatics</em> [Epub ahead of print]. [<a href="http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135.long" target="_blank">article</a>]</p><p>Address of the bookmark: <a href="http://orione.crs4.it/" rel="nofollow">http://orione.crs4.it/</a></p>]]></description>
	<dc:creator>Martin Jones</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/14050/assistant-professor-in-bioinformatics-at-indian-institute-of-technology-delhi</guid>
  <pubDate>Fri, 15 Aug 2014 06:16:06 -0500</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor 	in Bioinformatics at Indian Institute of Technology Delhi]]></title>
  <description><![CDATA[
<p>Indian Institute of Technology Delhi Hauz Khas ,New Delhi – 110016</p>

<p>ROLLING ADVERTISEMENT NO. 01/2014(E-1)<br />ADVERTISEMENT FOR THE POSITIONS OF ASSISTANT PROFESSOR CANDIDATES CAN APPLY ANY TIME DURING THE YEAR.</p>

<p>IIT Delhi invites applications from qualified Indian Nationals, Persons of Indian Origin (PIOs) and Overseas Citizens of India (OCIs) for the following positions in the various Departments/Centres/Schools (in the fields<br />mentioned alongwith them):<br />Post Pay Band Assistant Professor and Assistant Professor (on Contract) Rs.15600-39100 (PB-3) (Minimum pay of Rs.30000/-)+ AGP Rs.8000/-</p>

<p>The following norms will be followed for fixing the basic pay + AGP for Assistant Professors appointed on<br />contract with Ph.D but experience of 3 years or less:-<br />Type Qualification &amp; Experience on the date of joining<br />Assistant Professor (Contract) PB3 (Rs. 15,600-39,100).</p>

<p>MINIMUM QUALIFICATIONS AND EXPERIENCE:<br />Ph.D. with First class at the preceding degree or equivalent in the appropriate branch with very good academic record throughout. A minimum of three years industrial/research/teaching experience, excluding however, the experience gained while Pursuing Ph. D. The candidates should preferably be below<br />35 years of age for male and 38 years for female ( to be relaxed by 5 years in case of persons with physical disability, SC/ST and 3 years in case of OBC-NCL).</p>

<p>Qualified persons include:<br />(a) Indian Nationals,<br />(b) Foreign Nationals who are “Persons of Indian Origin” (PIO) or Overseas<br />Citizens of India (OCI), in whose case, if selected, permission will be sought from Govt. of India<br />before he/she can join IIT Delhi, or<br />(c) Other Foreign Nationals, in whose case, if selected, appointment will be on a contract basis for up to 5 (five) years subject to permission from the Govt. of India before he/she can join IIT Delhi.<br />(d) Institute specifically encourages applicants from SC/ST/OBC category as well as persons<br />with disability to apply for these positions. </p>

<p>AMAR NATH &amp; SHASHI KHOSLA SCHOOL OF INFORMATION TECHNOLOGY:<br />Computational Neuroscience, Medical Applications of Information Technologies, Computational &amp; Systems Biology, Machine to Machine (M2M) Technologies, Embedded Systems &amp; Sensors, Computer Security.<br />KUSUMA SCHOOL OF BIOLOGICAL SCIENCES:<br />In-silico Biology Applications, Systems Biology, Infection Biology, Neurodegeneration. </p>

<p>More at http://www.iitd.ac.in/sites/default/files/jobs/faculty/spl-areas-rolling-advt.pdf</p>

<p>http://www.iitd.ac.in/content/faculty-positions</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/17652/arraygen-bioinformatics-genomics-group</guid>
  <pubDate>Sun, 28 Sep 2014 14:09:55 -0500</pubDate>
  <link></link>
  <title><![CDATA[ArrayGen Bioinformatics Genomics Group]]></title>
  <description><![CDATA[
<p>ArrayGen is a global bioinformatics company which is a one stop solution for microarray designing and genomics data analysis. Our novel Array Design Approach Strategy (ADAS) aims to condense the time lag between demands of scientific community and manufacture industry, thereby expediting research processes.</p>

<p>ArrayGen specializes in Genomics data analysis and research, as we believe in the level of precision, predictability, benchmark-ability, and data analysis capability of genomics data over other forms of biological data. ArrayGen constantly strives to develop new solutions, and plug the existing gaps in the technological advancement of the field.</p>

<p>More http://www.arraygen.com/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/18382/google-genomics</guid>
	<pubDate>Fri, 17 Oct 2014 02:14:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/18382/google-genomics</link>
	<title><![CDATA[Google Genomics]]></title>
	<description><![CDATA[<p>Google Genomics provides an API to store, process, explore, and share DNA sequence reads, reference-based alignments, and variant calls, using Google's cloud infrastructure.</p>
<ul>
<li><strong>Store</strong> alignments and variant calls for one genome or a million.</li>
<li><strong>Process</strong> genomic data in batch by running principal component analysis or Hardy-Weinberg equilibrium, in minutes or hours, by using parallel computing frameworks like MapReduce.</li>
<li><strong>Explore</strong> data by slicing alignments and variants by genomic range across one or multiple samples -- for your own algorithms or for visualization; or interactively process entire cohorts to find transition/transversion ratios, allelic frequency, genome-wide association and more using BigQuery.</li>
<li><strong>Share</strong> genomic data with your research group, collaborators, the broader community, or the public. You decide.</li>
</ul>
<p>Google Genomics is implementing the API defined by the <a href="http://genomicsandhealth.org/">Global Alliance for Genomics and Health</a> for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.</p><p>Address of the bookmark: <a href="https://cloud.google.com/genomics/" rel="nofollow">https://cloud.google.com/genomics/</a></p>]]></description>
	<dc:creator>Reshma Khatun</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18578/research-scientist-%E2%80%93-national-institute-of-cholera-and-enteric-diseases</guid>
  <pubDate>Wed, 22 Oct 2014 10:26:46 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Scientist – National Institute of Cholera and Enteric Diseases]]></title>
  <description><![CDATA[
<p>The following post is to be filled up on purely temporary basis under the project entitled "Second phase of Task Force Biomedical Informatics Center of ICMR" under Dr. Santasabuj Das, Scientist 'D' of this Institute:-</p>

<p>01. Scientist II 01<br />Essential: Ph.D. degree in Life Sciences from a recognized university along with a minimum of 2 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.</p>

<p>OR<br />Ph.D. degree in Bioinformatics from a recognized university.</p>

<p>OR<br />M.Sc. in Bioinformatics from a recognized university along with a minimum of 3 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.</p>

<p>Desirable:<br />Thorough Knowledge about In silico genome analysis and comparative genomics.<br />Experience with in silico identification of novel virulence factors of pathogens, host-pathogen interactions and Systems Biology.<br />Additional Postdoctoral research experience in relevant subjects from a recognized institutions.</p>

<p>Rs. 44,000/- p.m. (consolidated) plus 30% HRA</p>

<p>Below 40 years</p>

<p>Applications along with Bio-Data containing detail work experience and full list of publications may be sent via email tosantasabujdas@yahoo.com latest by October 27, 2014.</p>

<p>Short-listed candidates will be called via email for an interview to be held at the institute in the second week of November, 2014.</p>

<p>Advertisement: www.niced.org.in/placements.htm</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics</guid>
	<pubDate>Thu, 18 Dec 2014 11:05:42 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics</link>
	<title><![CDATA[Google Genomics]]></title>
	<description><![CDATA[<ul>
<li>
<p><strong>Explore genetic variation interactively.</strong> Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.</p>
</li>
<li>
<p><strong>Process big genomic data easily.</strong> Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.</p>
</li>
<li>
<p><strong>Use Google's infrastructure and big data expertise.</strong> Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.</p>
</li>
<li>
<p><strong>Support emerging global standards.</strong> Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.</p>
</li>
</ul><p>Address of the bookmark: <a href="https://cloud.google.com/genomics/" rel="nofollow">https://cloud.google.com/genomics/</a></p>]]></description>
	<dc:creator>Tenzin Paul</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl</guid>
	<pubDate>Wed, 21 Jan 2015 08:31:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl</link>
	<title><![CDATA[Comparative Genomics in Ensembl]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/dDRdCnZOMCM" frameborder="0" allowfullscreen></iframe>The Ensembl browser provides viewable whole-genome alignments, homologues and phylogenetic gene trees, protein families, and ancestral sequences.  Learn how to view and export these data in this video.]]></description>
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25284/rajiv-gandhi-centre-for-biotechnology-rgcb-invites-applications-for-the-following-three-faculty-scientist</guid>
  <pubDate>Tue, 24 Nov 2015 22:13:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following three faculty scientist]]></title>
  <description><![CDATA[
<p>Scientist Positions<br />Advt. No.RGCB Advt./SCI 2015/1<br /> <br />November 11, 2015</p>

<p>Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following three faculty scientist positions:</p>

<p>Scientist E-II or F in Bioinformatics &amp; Computational Biology</p>

<p>SCIENTIST E-II OR F IN COMPUTATIONAL BIOLOGY &amp; BIOINFORMATICS</p>

<p>Highly motivated and innovative individual who will pursue basic research, solve biological problems with emphasis on computational and quantitative experimental methods and build active bridges to translational research. The scientist will also provide computational biology support to ongoing research programs in disease biology, provide assistance to analyze complex data sets generated by RGCB scientists and collaborators inclusive of including high dimensional “omics” data and next generation sequencing data, such as whole genome, exome, RNA-seq and ChIP-seq as well as provide leadership for high quality training for junior scientists and regular teaching programs of the institute. Areas of research of interest to RGCB include but are not limited to computational, systems, or quantitative biology with applications to cell biology, developmental biology, metabolism, genomics, proteomics, biophysics, biological information systems, network pharmacology, drug design and cancer research. The scientist’s responsibilities include efforts for the integration of DNA variant annotation with statistical genetic analysis methods including linkage, imputation and association methods, adopting novel and innovative methodologies to analyze, integrate and interpret high dimensional data sets, provision of annotation to robust genetics and genomics findings using several data sources and methods, data management of exploratory clinical and R&amp;D studies in partnership with other lines of genetic data generated from internal and external studies, delivery and documentation of genomic information to support genetic studies, ensuring high-quality genetic and genomic data is incorporated into exploratory- clinical research programs, developing tools that make maximum use of multiple data sources to support annotation of DNA variation and contributes to systems biology initiatives within RGCB </p>

<p>More at http://rgcb.res.in/scientist-positions/</p>

<p>Application Form http://rgcb.res.in/wp-content/uploads/2015/11/APPLICATION-FORMAT-FOR-SCIENTISTS.docx</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26303/maker</guid>
	<pubDate>Sun, 07 Feb 2016 15:59:24 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26303/maker</link>
	<title><![CDATA[MAKER]]></title>
	<description><![CDATA[<p>MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.</p>
<p>More at http://www.yandell-lab.org/software/maker.html</p><p>Address of the bookmark: <a href="http://www.yandell-lab.org/software/maker.html" rel="nofollow">http://www.yandell-lab.org/software/maker.html</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26453/stacks</guid>
	<pubDate>Wed, 24 Feb 2016 15:52:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26453/stacks</link>
	<title><![CDATA[Stacks]]></title>
	<description><![CDATA[<p>Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.</p>
<p>More at http://catchenlab.life.illinois.edu/stacks/</p><p>Address of the bookmark: <a href="http://catchenlab.life.illinois.edu/stacks/" rel="nofollow">http://catchenlab.life.illinois.edu/stacks/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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