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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32485?offset=590</link>
	<atom:link href="https://bioinformaticsonline.com/related/32485?offset=590" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29998/csir-nehru-science-postdoctoral-research-fellowship</guid>
  <pubDate>Tue, 29 Nov 2016 12:34:59 -0600</pubDate>
  <link></link>
  <title><![CDATA[CSIR Nehru Science Postdoctoral Research Fellowship]]></title>
  <description><![CDATA[
<p>CSIR Nehru Science Postdoctoral Research Fellowship</p>

<p>About Fellowship: <br />CSIR Nehru Science Postdoctoral Research Fellowship Scheme is an Research Fellowship awarded/given by HRD Ministry, Govt. of India every year to more than 100 fellows.</p>

<p>It was started to identify promising and young researchers with novel ideas and provide them research opportunities in the areas of basic science, engineering, medicine &amp; agriculture.</p>

<p>The fellowship aims at facilitating their transition from mentored to independent research career.</p>

<p>In addition, check these ICTS Research Fellowships:<br />1.) Max-Planck Partner Group Fellowships 2017-18<br />2.) ICTS-Simons Postdoctoral Fellowships 2017<br />3.) ICTS Post Doctoral Fellowships 2017<br />4.) Airbus Prize Postdoctoral Fellowship 2017-18</p>

<p>Eligibility: To be eligible for this fellowship, you:<br />1.) PhD degree (within 3 years of award of PhD degree), OR<br />2.) Those who have submitted PhD theses.<br />3.) Applicants should have research publications in good impact factor SCI journals.<br />4.) Indian nationals, Persons of Indian Origin (PIO) &amp; Overseas Citizen of India (OCI), a can also apply.<br />5.) Maximum Age Limit: 32 years.</p>

<p>Duration: <br />– 2 Years.<br />– extendable for a maximum of 1 more year based on performance.</p>

<p>Remuneration: <br />– Rs. 50,000/- per month plus House Rent Allowance (HRA)<br />– A contingency grant of Rs. 3.0 lakh per annum.<br />– 25% of the contingency grant can be used for domestic and international travel.</p>

<p>Mode of Selection: You can apply throughout the year, but selection will be made twice a year, in June and December.</p>

<p>How to Apply: <br />– Read the instructions, given at Annexure-I in this PDF file.<br />– And, application form is given as, Annexure-II.<br />– Fill the form &amp; send it to the given address in the PDF file.</p>

<p>Deadline: Rolling Deadline (Applications accepted throughout the year)</p>

<p>Also See: Research Internship/ Fellowship in India:<br />1.) IIT Bombay Research Internship Awards Programme 2016-17<br />2.) IIT Delhi Internship Program 2016-17<br />3.) DAAD WISE – International Internship in Germany<br />4.) Summer Research Fellowship Programme| JNCASR Bangalore<br />5.) Indian Academy of Sciences Summer Internships 2017<br />6.) Winter Internship – IIT Bombay NPDE-TCA<br />7.) Viterbi – India Program 2017 | Research Internship in US<br />8.) Internship – Centre for Stem Cell Research, Vellore</p>

<p>Accommodation &amp; other benefits: <br />– Accommodation may be provided by CSIR, if available.<br />– Medical benefits as per CSIR norms.</p>

<p>For more details: <br />– Check this PDF Notification of Fellowship.<br />– List of CSIR Labs &amp; their work/activities can be seen at www.csir.res.in.</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41602/nucdiff-in-depth-characterization-and-annotation-of-differences-between-two-sets-of-dna-sequences</guid>
	<pubDate>Tue, 05 May 2020 10:35:48 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41602/nucdiff-in-depth-characterization-and-annotation-of-differences-between-two-sets-of-dna-sequences</link>
	<title><![CDATA[NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences]]></title>
	<description><![CDATA[<p>NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly suitable to compare assemblies with each other or with available reference genomes.</p>
<p>NucDiff provides information about the types of differences and their locations. It is possible to upload the results into genome browser for visualization and further inspection. It was written in Python and uses the NUCmer package from MUMmer[1] for sequence comparison.</p>
<p><br><br></p><p>Address of the bookmark: <a href="https://github.com/uio-cels/NucDiff" rel="nofollow">https://github.com/uio-cels/NucDiff</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30027/dbt-india</guid>
	<pubDate>Sun, 04 Dec 2016 22:30:37 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30027/dbt-india</link>
	<title><![CDATA[DBT India]]></title>
	<description><![CDATA[<p>Latest announcement on DBT India.&nbsp;</p>
<p>Calls</p>
<p>Events</p>
<p>Projects</p>
<p>Jobs</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="http://www.dbtindia.nic.in/out-reach/latest-announcements/" rel="nofollow">http://www.dbtindia.nic.in/out-reach/latest-announcements/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43062/jcvi-utility-libraries</guid>
	<pubDate>Sat, 08 May 2021 22:04:02 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43062/jcvi-utility-libraries</link>
	<title><![CDATA[JCVI utility libraries]]></title>
	<description><![CDATA[<p><span>Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.</span></p><p>Address of the bookmark: <a href="https://github.com/tanghaibao/jcvi" rel="nofollow">https://github.com/tanghaibao/jcvi</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30334/postdoc-at-ubritishcolumbia-in-troutgenomics</guid>
  <pubDate>Thu, 22 Dec 2016 08:18:46 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoc at UBritishColumbia in TroutGenomics]]></title>
  <description><![CDATA[
<p>Landscape Genomics Postdoc at UBC A research team at the University of British Columbia’s Department of Zoology and Biodiversity Research Centre is seeking a postdoctoral researcher in landscape genetics of native rainbow trout (Oncorhynchus mykiss). </p>

<p>This project is part of a larger Genome Canada project on genetics and physiology of adaptation to climate change in rainbow trout, and the population genomics component is in the labs of Eric Taylor and Michael Whitlock. The landscape genomics component primarily involves whole genome sequencing approaches to understanding the genomic basis of adaptation to features of habitat, but also to provide insights into phylogeography and the influence of watershed structure on population subdivision in rainbow trout. A PhD in a related field with expertise in basic theory and bioinformatic analysis of population genomics data is required. </p>

<p>The position is available for one year with renewal for up to three additional years. Salary is $55,000 per year plus benefits. To apply, please send a brief cover letter summarizing your qualifications for the position, a CV, and the names, addresses, phone numbers and emails of three references. </p>

<p>Review of applications will begin January 16, 2017. Address application materials to etaylor@zoology.ubc.ca to whom any questions can also be addressed. etaylor@zoology.ubc.ca</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34246/unicycler-hybrid-assembly-pipeline-for-bacterial-genomes</guid>
	<pubDate>Fri, 10 Nov 2017 03:58:27 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34246/unicycler-hybrid-assembly-pipeline-for-bacterial-genomes</link>
	<title><![CDATA[Unicycler: Hybrid assembly pipeline for bacterial genomes]]></title>
	<description><![CDATA[<p><span>Unicycler is an assembly pipeline for bacterial genomes. It can assemble&nbsp;</span><a href="http://www.illumina.com/">Illumina</a><span>-only read sets where it functions as a&nbsp;</span><a href="http://cab.spbu.ru/software/spades/">SPAdes</a><span>-optimiser. It can also assembly long-read-only sets (</span><a href="http://www.pacb.com/">PacBio</a><span>&nbsp;or&nbsp;</span><a href="https://nanoporetech.com/">Nanopore</a><span>) where it runs a&nbsp;</span><a href="https://github.com/lh3/miniasm">miniasm</a><span>+</span><a href="https://github.com/isovic/racon">Racon</a><span>&nbsp;pipeline. For the best possible assemblies, give it both Illumina reads&nbsp;</span><em>and</em><span>&nbsp;long reads, and it will conduct a hybrid assembly.</span></p><p>Address of the bookmark: <a href="https://github.com/rrwick/Unicycler" rel="nofollow">https://github.com/rrwick/Unicycler</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30657/studentship</guid>
  <pubDate>Tue, 24 Jan 2017 04:26:14 -0600</pubDate>
  <link></link>
  <title><![CDATA[Studentship]]></title>
  <description><![CDATA[
<p>Advt. No. ACBR/BTBI/BIF/Manpower/ADV/16-17<br />Research Associate/ Studentship/ Traineeship Jobs opportunity in  University of Delhi - Dr. B.R. Ambedkar Center for Biomedical Research (ACBR) on temporary basis<br />Studentship<br />No. of Post : 01<br />Qualifications : Applicants who are pursuing Post Graduate Degree course/ Diploma in Bioinformatics/ Biomedical Sciences/ Biotechnology/Life Sciences/Chemistry/ Biochemistry with a programme in Bioinformatics to carry out the project.<br />Remuneration : Rs. 8,000/-<br />Traineeship<br />No. of Post : 01<br />Qualifications : Applicants who have completed their Post Graduate degree in Bioinformatics /Biomedical Sciences/Biotechnology/Life Sciences/Chemistry/Biochemistry or any other branch of Life Sciences with knowledge in Bioinformatics<br />Remuneration : Rs. 8,000/-<br />Research Associate<br />No. of Post : 01<br />Qualifications : Ph.D. in Bio-Medical Sciences/Bioinformatics/ Biotechnology/Life Sciences/ Chemistry/ Bio-Chemistry and related areas<br />Remuneration : Rs. 36,000/-</p>

<p>Applicant are required to bring applications on plain paper, stating the name, address, date of birth. educational qualifications and experiences and Institute, along with attested photocopies of mark sheets and certificates etc. at the time of Interview. Applications should also be sent by Entail to Dr. Madhu Chopra, Coordinator, BIF Facility. Email: acbrdu.blisnet@nic.in;  mchopradu@gmail.com.<br />Interview Date : 13.02.2017<br />Time : 10:00 am-12:00 noon<br />Venue : ACBR</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34914/ra-assembler-a-de-novo-dna-assembler-for-third-generation-sequencing-data</guid>
	<pubDate>Wed, 27 Dec 2017 20:36:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34914/ra-assembler-a-de-novo-dna-assembler-for-third-generation-sequencing-data</link>
	<title><![CDATA[Ra assembler - a de novo DNA assembler for third generation sequencing data]]></title>
	<description><![CDATA[<p>Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).</p>
<p>Ra is in development since 2014 in the form of several separate components that used to be run individually.<br>This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.</p>
<p>Unlike other state-of-the-art assemblers,&nbsp;<span>Ra does not have an error correction step.</span>&nbsp;Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler",&nbsp;<a href="https://github.com/isovic/graphmap">https://github.com/isovic/graphmap</a>) and constructing and reducing an overlap graph (Ra layout,&nbsp;<a href="https://github.com/mariokostelac/ra">https://github.com/mariokostelac/ra</a>).</p><p>Address of the bookmark: <a href="https://github.com/mariokostelac/ra-integrate/" rel="nofollow">https://github.com/mariokostelac/ra-integrate/</a></p>]]></description>
	<dc:creator>biogeek</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30696/many-core-engine-mce-for-perl-example</guid>
	<pubDate>Tue, 31 Jan 2017 05:37:50 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30696/many-core-engine-mce-for-perl-example</link>
	<title><![CDATA[Many-Core Engine (MCE) for Perl example]]></title>
	<description><![CDATA[<p><span>MCE spawns a pool of workers and therefore does not fork a new process per each element of data. Instead, MCE follows a bank queuing model. Imagine the line being the data and bank-tellers the parallel workers. MCE enhances that model by adding the ability to chunk the next n elements from the input stream to the next available worker.</span></p>
<p>CORE MODULES</p>
<p>Three modules make up the core engine for MCE.</p>
<dl><dt id="MCE::Core"><a href="https://metacpan.org/pod/MCE#MCE::Core"><span></span></a><a></a><a href="https://metacpan.org/pod/distribution/MCE/lib/MCE/Core.pod">MCE::Core</a></dt><dd>
<p>Provides the Core API for Many-Core Engine. The various MCE options are described here.</p>
</dd><dt id="MCE::Signal"><a href="https://metacpan.org/pod/MCE#MCE::Signal"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Signal">MCE::Signal</a></dt><dd>
<p>Temporary directory creation, cleanup, and signal handling.</p>
</dd><dt id="MCE::Util"><a href="https://metacpan.org/pod/MCE#MCE::Util"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Util">MCE::Util</a></dt><dd>
<p>Utility functions for Many-Core Engine.</p>
</dd></dl>
<p><a href="https://metacpan.org/pod/MCE#MCE-EXTRAS"><span></span></a><a></a>MCE EXTRAS</p>
<p>There are 4 add-on modules for use with MCE.</p>
<dl><dt id="MCE::Candy"><a href="https://metacpan.org/pod/MCE#MCE::Candy"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Candy">MCE::Candy</a></dt><dd>
<p>Provides a collection of sugar methods and output iterators for preserving output order.</p>
</dd><dt id="MCE::Mutex"><a href="https://metacpan.org/pod/MCE#MCE::Mutex"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Mutex">MCE::Mutex</a></dt><dd>
<p>Provides a simple semaphore implementation supporting threads and processes.</p>
</dd><dt id="MCE::Queue"><a href="https://metacpan.org/pod/MCE#MCE::Queue"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Queue">MCE::Queue</a></dt><dd>
<p>Provides a hybrid queuing implementation for MCE supporting normal queues and priority queues from a single module. MCE::Queue exchanges data via the core engine to enable queuing to work for both children (spawned from fork) and threads.</p>
</dd><dt id="MCE::Relay"><a href="https://metacpan.org/pod/MCE#MCE::Relay"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Relay">MCE::Relay</a></dt><dd>
<p>Enables workers to receive and pass on information orderly with zero involvement by the manager process while running.</p>
</dd></dl>
<p><a href="https://metacpan.org/pod/MCE#MCE-MODELS"><span></span></a><a></a>MCE MODELS</p>
<p>The models take Many-Core Engine to a new level for ease of use. Two options (chunk_size and max_workers) are configured automatically as well as spawning and shutdown.</p>
<dl><dt id="MCE::Loop"><a href="https://metacpan.org/pod/MCE#MCE::Loop"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Loop">MCE::Loop</a></dt><dd>
<p>Provides a parallel loop utilizing MCE for building creative loops.</p>
</dd><dt id="MCE::Flow"><a href="https://metacpan.org/pod/MCE#MCE::Flow"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Flow">MCE::Flow</a></dt><dd>
<p>A parallel flow model for building creative applications. This makes use of user_tasks in MCE. The author has full control when utilizing this model. MCE::Flow is similar to MCE::Loop, but allows for multiple code blocks to run in parallel with a slight change to syntax.</p>
</dd><dt id="MCE::Grep"><a href="https://metacpan.org/pod/MCE#MCE::Grep"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Grep">MCE::Grep</a></dt><dd>
<p>Provides a parallel grep implementation similar to the native grep function.</p>
</dd><dt id="MCE::Map"><a href="https://metacpan.org/pod/MCE#MCE::Map"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Map">MCE::Map</a></dt><dd>
<p>Provides a parallel map model similar to the native map function.</p>
</dd><dt id="MCE::Step"><a href="https://metacpan.org/pod/MCE#MCE::Step"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Step">MCE::Step</a></dt><dd>
<p>Provides a parallel step implementation utilizing MCE::Queue between user tasks. MCE::Step is a spin off from MCE::Flow with a touch of MCE::Stream. This model, introduced in 1.506, allows one to pass data from one sub-task into the next transparently.</p>
</dd><dt id="MCE::Stream"><a href="https://metacpan.org/pod/MCE#MCE::Stream"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Stream">MCE::Stream</a></dt><dd>
<p>Provides an efficient parallel implementation for chaining multiple maps and greps together through user_tasks and MCE::Queue. Like with MCE::Flow, MCE::Stream can run multiple code blocks in parallel with a slight change to syntax from MCE::Map and MCE::Grep.</p>
</dd></dl>
<p><a href="https://metacpan.org/pod/MCE#MISCELLANEOUS"><span></span></a>MISCELLANEOUS</p>
<p>Miscellaneous additions included with the distribution.</p>
<dl><dt id="MCE::Examples"><a href="https://metacpan.org/pod/MCE#MCE::Examples"><span></span></a><a></a><a href="https://metacpan.org/pod/distribution/MCE/lib/MCE/Examples.pod">MCE::Examples</a></dt><dd>
<p>Describes various demonstrations for MCE including a Monte Carlo simulation.</p>
</dd><dt id="MCE::Subs"><a href="https://metacpan.org/pod/MCE#MCE::Subs"><span></span></a><a></a><a href="https://metacpan.org/pod/MCE::Subs">MCE::Subs</a></dt><dd>
<p>Exports functions mapped directly to MCE methods; e.g. mce_wid. The module allows 3 options; :manager, :worker, and :getter.</p>
</dd></dl>
<p><a href="https://metacpan.org/pod/MCE#REQUIREMENTS"><span></span></a>REQUIREMENTS</p>
<p>Perl 5.8.0 or later. PDL::IO::Storable is required in scripts running PDL.</p>
<p><a href="https://metacpan.org/pod/MCE#SOURCE-AND-FURTHER-READING"><span></span></a><a></a>SOURCE AND FURTHER READING</p>
<p>The source, cookbook, and examples are hosted at GitHub.</p>
<ul>
<li>
<p><a href="https://github.com/marioroy/mce-perl">https://github.com/marioroy/mce-perl</a></p>
</li>
<li>
<p><a href="https://github.com/marioroy/mce-cookbook">https://github.com/marioroy/mce-cookbook</a></p>
</li>
<li>
<p><a href="https://github.com/marioroy/mce-examples">https://github.com/marioroy/mce-examples</a></p>
</li>
</ul>
<p><a href="https://metacpan.org/pod/MCE#SEE-ALSO"><span></span></a><a></a>SEE ALSO</p>
<p><code>MCE::Shared</code>&nbsp;provides data sharing capabilities for&nbsp;<code>MCE</code>. It includes&nbsp;<code>MCE::Hobo</code>&nbsp;for running code asynchronously.</p>
<ul>
<li>
<p><a href="https://metacpan.org/pod/MCE::Shared">MCE::Shared</a></p>
</li>
<li>
<p><a href="https://metacpan.org/pod/MCE::Hobo">MCE::Hobo</a></p>
</li>
</ul><p>Address of the bookmark: <a href="https://github.com/marioroy/mce-examples" rel="nofollow">https://github.com/marioroy/mce-examples</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30825/open-positions-in-pasini%E2%80%99s-lab</guid>
  <pubDate>Sat, 04 Feb 2017 08:17:18 -0600</pubDate>
  <link></link>
  <title><![CDATA[Open Positions in Pasini’s lab]]></title>
  <description><![CDATA[
<p>Computational Biologists<br />Open to PhD-student and Post-doc candidates<br />We are looking for wet and computational biologists to work on an ERC funded project in our<br />laboratory located at the Department of Experimental Oncology of the European Institute of<br />Oncology in Milan (Italy). The project will focus on different aspects of the function of Polycomb<br />Group proteins and other chromatin modifying activities in relation to their role in regulating cellular<br />identity in the development of adult tissues.<br />The candidates will be in charge of computational analysis and data management related to the<br />project. She/he will directly interact with the wet scientists working in our laboratory while working<br />embedded in the community of computational biologists present at our institution. The work will<br />involve the analysis of sequencing data produced with cutting edge technologies to study gene<br />expression and chromatin environment including data produced on rare cell populations and single<br />cells. The applicants must have a good knowledge of programming in python/perl/java along with<br />strong statistical background and performing analysis in R platform. A biological background is<br />also recommended however it’s not mandatory for application.<br />Each applicant should submit a full CV (with a detailed description of her/his background,<br />expertise, achievements and publication records) together with a letter of intent and at least two<br />contacts for recommendations (for a post-doc position). Competitive salary will be offered based<br />on the experience of the candidate. Non Italian as well as Italian applicants that have been working<br />outside Italy (&gt;3yrs.) will have the opportunity to benefit of a full tax deduction for the first three<br />years of contract.<br />Applications should be submitted as single PDF to diego.pasini@ieo.it</p>

<p>Lab https://www.ieo.it/en/RESEARCH/People/Researchers/Pasini-Diego/</p>
]]></description>
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