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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27035?offset=1530</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/28564/dbt-%E2%80%93-bioinformatics-industrial-training-programme-biitp-2016-%E2%80%93-17</guid>
	<pubDate>Wed, 27 Jul 2016 04:09:59 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/28564/dbt-%E2%80%93-bioinformatics-industrial-training-programme-biitp-2016-%E2%80%93-17</link>
	<title><![CDATA[DBT – Bioinformatics Industrial Training Programme (BIITP) 2016 – 17]]></title>
	<description><![CDATA[<p>BIITP is a programme of Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, managed by Biotech Consortium India Limited (BCIL).The objective of BIITP is to provide an opportunity to bioinformatics students to acquire practical skills and experience by working on projects alongside industry experts as well as to provide an opportunity for the industry to identify potential employees.</p><p><strong>DBT Invites online applications from the bioinformatics&nbsp;students and requisitions from biotech/bioinformatics companies.</strong></p><p><strong>Biotech Industry</strong>&nbsp;:</p><p>Biotech/Bioinformatics companies interested to provide hands on industrial training to the students of Bioinformatics under BIITP may apply online. The companies would have no obligation towards any payments to trainees. The companies would be paid bench fee to cover expenses towards training. Trainees would be provided to companies subject to availability.</p><p><strong>Attn: Bioinformatics Students</strong></p><p>Bioinformatics students interested in training in biotech / bioinformatics companies may apply online.&nbsp;<strong>Stipend of Rs. 10,000/- per month</strong>&nbsp;will be paid to candidates placed for training. The candidates will be selected for training through an interview.</p><p><strong>Eligiblity</strong>&nbsp;:</p><p>a) B.E /B.Tech./M.Sc./M.Tech./Advanced Post Graduate Diploma in Bioinformatics from an Indian recognized university with minimum 55% marks or equivalent grade at highest degree/diploma completed in the year 2015 or 2016 are only eligible to apply.</p><p>b) The Advanced Post Graduate diploma should be of at least one year duration after graduation.</p><p>c)&nbsp; Students whose result of last semester/final year is not declared can also apply mentioning their marks upto the semester/year upto which result declared. The final result with original mark sheet(s) of all the semesters/years will have to be produced at the time of interview.</p><p><strong>Application Procedure</strong>&nbsp;:</p><p>The online application form is available below :</p><p><strong><a href="https://www.biotecnika.org/2016/07/dbt-bioinformatics-industrial-training-programme-biitp-2016-17/?xurl=%3A%2F%2Fwww.bcil.nic.in%2Fbiitp2016-17%2Fregistration1.asp" target="_blank">Application Form For Students (New User)</a></strong></p><p><strong><a href="https://www.biotecnika.org/2016/07/dbt-bioinformatics-industrial-training-programme-biitp-2016-17/?xurl=%3A%2F%2Fwww.bcil.nic.in%2Fbiitp2016-17%2Fregistration.asp%3FT1%3DCompany" target="_blank">Requisition form for companies (New User)</a></strong></p><p><strong><a href="https://www.biotecnika.org/2016/07/dbt-bioinformatics-industrial-training-programme-biitp-2016-17/?xurl=%3A%2F%2Fwww.bcil.nic.in%2Fbiitp2016-17%2Findex1.asp" target="_blank">Already registered User Click Here</a></strong></p><p>The following documents are to be sent to Mr. Manoj Gupta, Manager, Biotech Consortium India Limited, 5th floor, Anuvrat Bhawan, 210, Deen Dayal UpadhyayaMarg, New Delhi-110002.</p><p>More at&nbsp;http://www.bcil.nic.in/biitp2016-17/index.asp</p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/28592/bioinformatics-technical-position-at-cdac-pune-india</guid>
  <pubDate>Mon, 01 Aug 2016 03:36:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Technical Position at CDAC Pune - India]]></title>
  <description><![CDATA[
<p>CDAC Pune Recruitment 2016 – Apply Online for Technical Positions: Department of Information Technology under the Ministry of Communications and Information Technology, Government of India, Centre for Development of Advanced Computing (C-DAC), Pune has advertised notification for the recruitment of Technical vacancies for for PwD candidates n direct recruitment basis. Eligible candidates can apply Online from 27-07-2016 at 10.00 AM to 31-08-2016 at 18.00 PM.. Other information like age limit, educational qualification, selection process &amp; how to apply are given below… </p>

<p>CDAC Pune Vacancy Details:<br />Total No. of Posts: 23 </p>

<p>Name of the Post: Technical </p>

<p>Name of the Discipline:<br />A. Computer Science/ Information Technology and Allied disciplines. </p>

<p>B.Electronics Communications/ Electrical/ Telecommunication/Instrumentation &amp; Control/ Medical Electronics/ Power Electronics/ VLSI &amp; Embedded System and Allied disciplines. </p>

<p>C.Biotechnology/ Bioinformatics/ Health informatics/ Geoinformatics/ Meteorology/ Environmental Science/ Ocean Sciences/Oceanography/Environmental Engineering </p>

<p>1. Visually Impaired: 09 Posts </p>

<p>2. Hearing Impaired: 08 Posts </p>

<p>3. Orthopedically Impaired: 06 Posts </p>

<p>Educational Qualification : Candidates should possess Graduation in relvany discpline with relevant experience. </p>

<p>Selection Process: Candidates will be selected based on applicants performance in interview. </p>

<p>How to Apply: Eligible candidates can apply online through the website www.cdac.in from 27-07-2016 at 10.00 AM to 31-08-2016 at 18.00 PM. </p>

<p>More at http://www.cdac.in/index.aspx?id=current_jobs</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36890/price-paired-read-iterative-contig-extension-a-de-novo-genome-assembler-implemented-in-c</guid>
	<pubDate>Mon, 11 Jun 2018 03:08:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36890/price-paired-read-iterative-contig-extension-a-de-novo-genome-assembler-implemented-in-c</link>
	<title><![CDATA[PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.]]></title>
	<description><![CDATA[We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler.

http://derisilab.ucsf.edu/software/price/<p>Address of the bookmark: <a href="http://derisilab.ucsf.edu/software/price/" rel="nofollow">http://derisilab.ucsf.edu/software/price/</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/28819/research-project-at-iit-madras</guid>
  <pubDate>Wed, 17 Aug 2016 03:26:06 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Project at IIT, Madras]]></title>
  <description><![CDATA[
<p>Two project positions are available to work on (i) molecular modeling and molecular dynamics simulations and (ii) development of bioinformatics databases and tools at Protein Bioinformatics Lab, Department of Biotechnology, IIT Madras.</p>

<p>Duration : Initially for a period of one year. Extendable based on the performance.</p>

<p>Qualification: (i) MSc in Bioinformatics, Biotechnology, Physics, Biophysics, Biochemistry,Computer Science with NET (UGC/CSIR/GATE/BINC/INSPIRE etc) qualification. (OR) (ii) M. Tech in Bioinformatics, Biotechnology</p>

<p>Additional qualification: Programming skills</p>

<p>Candidates who fulfill the requirements of IIT have the possibility to register for PhD.</p>

<p>Fellowship: Rs.25,000 and HRA.</p>

<p>Applicants are encouraged to send the CV to the coordinator by postal mail and e-mail. The deadline to receive the applications is 31st August 2016. The project coordinator has the discretion to restrict the number of candidates to be called for interview to a reasonable limit on the basis of qualifications and experience higher than the minimum prescribed in the announcement.</p>

<p>Project Co-ordinator:</p>

<p>Dr. M. Michael Gromiha <br />Department of Biotechnology <br />Indian Institute of Technology Madras <br />Chennai 600036 <br />Email: gromiha@iitm.ac.in</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29208/srf-bioinformatics-job-position-in-national-institute-of-plant-genome-research-nipgr</guid>
  <pubDate>Mon, 19 Sep 2016 05:43:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[SRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR)]]></title>
  <description><![CDATA[
<p>SRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR)<br />Title : “Transcriptome and small RNA diversity analysis of developing seed contrasting rice varieties” <br />Qualification : Candidates having M.Sc./M.Tech. degree or equivalent (with minimum 60% marks) in Bioinformatics with a minimum of two years of post M.Sc./M.Tech research experience are eligible to apply.<br />No. of Post : 01<br />How to apply<br />Application should reach to Dr. Pinky Agarwal, Staff Scientist, National Institute of Plant Genome Research (NIPGR) Aruna Asaf Ali Marg, P.O. Box NO. 10531, New Delhi - 110067 on or before 30/09/2016</p>

<p>More at http://www.nipgr.res.in/careers/vacancies_latest.php#</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34501/dnapipete-de-novo-assembly-annotation-pipeline-for-transposable-elements</guid>
	<pubDate>Sat, 02 Dec 2017 18:25:44 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34501/dnapipete-de-novo-assembly-annotation-pipeline-for-transposable-elements</link>
	<title><![CDATA[dnaPipeTE: de-novo assembly &amp; annotation Pipeline for Transposable Elements]]></title>
	<description><![CDATA[<p>dnaPipeTE (for de-novo assembly &amp; annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (&lt; 1X).</p>
<ul>
<li>
<p>dnaPipeTE is developped by Cl&eacute;ment Goubert, Laurent Modolo and the TREEP team of the LBBE:&nbsp;<a href="http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en">http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en</a></p>
</li>
<li>
<p>You can find the original publication in GBE here:&nbsp;<a href="https://academic.oup.com/gbe/article/7/4/1192/533768">https://academic.oup.com/gbe/article/7/4/1192/533768</a></p>
</li>
</ul>
<p><a href="https://github.com/clemgoub/dnaPipeTE/blob/dev/dnaPipefront.png" target="_blank"><img src="https://github.com/clemgoub/dnaPipeTE/raw/dev/dnaPipefront.png" alt="Front" style="border: 0px;"></a><em>output examples of quantification and TE landscape (relative age) produced by dnaPipeTE</em></p>
<p><em>&nbsp;</em></p><p>Address of the bookmark: <a href="https://github.com/clemgoub/dnaPipeTE" rel="nofollow">https://github.com/clemgoub/dnaPipeTE</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34931/3d-dna-3d-de-novo-assembly-3d-dna-pipeline</guid>
	<pubDate>Thu, 28 Dec 2017 10:09:37 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34931/3d-dna-3d-de-novo-assembly-3d-dna-pipeline</link>
	<title><![CDATA[3d-dna: 3D de novo assembly (3D DNA) pipeline]]></title>
	<description><![CDATA[<p>This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in:&nbsp;<a href="http://science.sciencemag.org/content/early/2017/03/22/science.aal3327.full">Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017.</a></p>
<p>Unless otherwise noted, all terminology below is consistent with this paper, and all references to figures and tables in this readme refer to this paper. Specifically, some of the terminology used below is outlined in&nbsp;<code>Figure S2</code>. The assembly procedure is described in detail in the&nbsp;<a href="http://science.sciencemag.org/content/suppl/2017/03/22/science.aal3327.DC1?_ga=1.9816115.760837492.1490574064">Supporting Online Materials</a>, specifically in the section labelled &ldquo;Pipeline description&rdquo;.</p>
<p>In addition, the pipeline uses tools and methods from&nbsp;<a href="http://www.cell.com/cell-systems/abstract/S2405-4712(16)30219-8">Juicer (Durand &amp; Shamim et al., Cell Systems, 2016)</a>&nbsp;and&nbsp;<a href="http://www.cell.com/cell-systems/abstract/S2405-4712(15)00054-X">Juicebox (Durand &amp; Robinson et al., Cell Systems, 2016)</a>, as well as additional dependencies noted below.</p>
<p>Feel free to post your questions and comments at:&nbsp;<a href="http://www.aidenlab.org/forum.html">http://www.aidenlab.org/forum.html</a></p>
<p>http://aidenlab.org/documentation.html</p><p>Address of the bookmark: <a href="https://github.com/theaidenlab/3d-dna" rel="nofollow">https://github.com/theaidenlab/3d-dna</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29217/bioinformatics-openings-at-sri-venkateswara-college-university-of-delhi</guid>
  <pubDate>Tue, 20 Sep 2016 05:43:24 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics openings at Sri Venkateswara College, University of Delhi]]></title>
  <description><![CDATA[
<p>Bioinformatics center</p>

<p>Sri Venkateswara College (University of Delhi)</p>

<p>New Delhi- 110021</p>

<p>1. Junior Research Fellow (1 Post)</p>

<p>Applications are invited for the post of Junior Research Fellow (JRF) under DST funded project which is purely temporary and is strictly for project duration only.</p>

<p>Title of project</p>

<p>No. of post</p>

<p>Remuneration (Rs.)</p>

<p>“Computational assisted Design and Synthesis of Novel Antimalarial Agents Embodying Structural Diversity Suitable for Protease Inhibitors”</p>

<p>(One)</p>

<p>Fellowship and HRA as per DST guidelines</p>

<p>Qualification</p>

<p>Post Graduate Degree in Basic Science (M.Sc./M.Tech in Bioinformatics/Biophysics) from a recognized University in India or abroad with at least 55% marks with NET qualification or Graduate Degree in Professional Course with NET Qualification or Post Graduate Degree in Professional Course.</p>

<p>Desirable</p>

<p>Fair knowledge of Computer Aided Drug Designing (CADD), Protein Structure modeling, molecular docking, and simulations are preferable.</p>

<p>2. Traineeship (1 Post)</p>

<p>Applications are invited for the position of traineeship in DBT-BTISnet funded Bioinformatics Infrastructure Facility (BIF) to carry out project work in the area of Bioinformatics.</p>

<p>Qualification</p>

<p>Applicant should be possess PG degree/PG diploma in Bioinformatics for traineeship. The traineeship is awarded for a period of six months from the date of joining and is not extendable. The selected candidates are entitled to receive a stipend of Rs. 8000/- per month (consolidate) for a period of 6 months.</p>

<p>=====================================================================</p>

<p>3. Studentship (1 Post)</p>

<p>Applications are invited for the position of Studentship in DBT-BTISnet funded Bioinformatics Infrastructure Facility (BIF) to carry out project work in the area of Bioinformatics.</p>

<p>Qualification</p>

<p>Candidates pursuing the Final Year of Post Graduate Degree in Basic Science (M.Sc.) or Post Graduate/ Graduate Degree in Professional Course (M.Tech/B.Tech) in Bioinformatics from a recognized University in India or abroad. The selected candidates are entitled to receive a stipend of Rs. 8000/- per month (consolidate) for a period of 6 months.</p>

<p>How to Apply?</p>

<p>Applicants are required to send applications on plain paper, stating the name, address, date of birth, educational qualification, experience and Institute, along with attested photocopies of mark sheets and certificates etc. by September 20, 2016 to:</p>

<p>The Coordinator</p>

<p>Bioinformatics Center, Sri Venkateswara College</p>

<p>Benito Juarez Road, Dhaula Kuan, New Delhi- 110021</p>

<p>Applications may also be sent by email to contact@bic-svc.ac.in. Strictly mention "Application for JRF, Traineeship or Studentship" in the subject line as the case may be.</p>

<p>Short listed candidates will be called for an interview. Canvassing in any form will be a disqualification. No TA/DA will be paid either for attending the interview or joining the post.</p>

<p>For more details visit our lab webpage: http://www.bic-svc.ac.in</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37223/chopstitch-exon-annotation-and-splice-graph-construction-using-transcriptome-assembly-and-whole-genome-sequencing-data</guid>
	<pubDate>Tue, 03 Jul 2018 04:14:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37223/chopstitch-exon-annotation-and-splice-graph-construction-using-transcriptome-assembly-and-whole-genome-sequencing-data</link>
	<title><![CDATA[ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data]]></title>
	<description><![CDATA[ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a Bloom filter that represents the k-mer spectrum of WGSS reads. The algorithm also detects base substitutions in transcript sequences corresponding to sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon-exon boundaries to detect transcript isoforms, which are reported as splice graphs in dot output format.<p>Address of the bookmark: <a href="https://github.com/bcgsc/ChopStitch" rel="nofollow">https://github.com/bcgsc/ChopStitch</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29272/decipher</guid>
	<pubDate>Fri, 30 Sep 2016 09:33:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29272/decipher</link>
	<title><![CDATA[DECIPHER]]></title>
	<description><![CDATA[<p>DECIPHER is a software toolset that can be used to maintain, analyze, and decipher large amounts of DNA sequence data. To install DECIPHER, see the <a href="http://DECIPHER.cee.wisc.edu/Download.html">Downloads</a> page.<br><br> To begin using DECIPHER read the "Getting Started DECIPHERing" tutorial. Refer to the PDF documents below for instructions on how to use DECIPHER for various tasks.</p><p>Address of the bookmark: <a href="http://decipher.cee.wisc.edu/Documentation.html" rel="nofollow">http://decipher.cee.wisc.edu/Documentation.html</a></p>]]></description>
	<dc:creator>Anjana</dc:creator>
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