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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30242?offset=1050</link>
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	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35883/arcs-scaffolding-genome-drafts-with-linked-reads</guid>
	<pubDate>Tue, 06 Mar 2018 16:35:26 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35883/arcs-scaffolding-genome-drafts-with-linked-reads</link>
	<title><![CDATA[ARCS: scaffolding genome drafts with linked reads]]></title>
	<description><![CDATA[<p><span>ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS&nbsp;</span><em>H.sapiens</em><span>genome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.</span></p><p>Address of the bookmark: <a href="https://github.com/bcgsc/ARCS/" rel="nofollow">https://github.com/bcgsc/ARCS/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8123/jrf-manit</guid>
  <pubDate>Sun, 02 Feb 2014 03:07:58 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF @ MANIT]]></title>
  <description><![CDATA[
<p>MAULANA AZAD NATIONAL INSTITUTE OF TECHNOLOGY BHOPAL</p>

<p>No. CSE/14/1038</p>

<p>Walk in Interview for the post of JRF under TEQIP-II</p>

<p>SN Department – Qualification Post Graduation – Time</p>

<p>1 Bio-Informatics &amp; Mathematics M.Tech Bio-informatics/M.Sc.* Maths  10.00 AM</p>

<p>2 Biological Sciences M.Sc.* in any branch of Biological Sciences 10.30 AM</p>

<p>3 Chemical Engineering M.Tech Chemical Engineering 11.00 AM</p>

<p>4 Chemistry M.Sc.* Chemistry 11.30 AM</p>

<p>5 Civil Engineering M.Tech Structure/GeoTech. /Water -Resources/Hydraulics/Environment/Transport 12.00 Noon</p>

<p>6 GIS M.Tech GIS/Civil 12.30 PM</p>

<p>7 Computer Science &amp; Engineering M.Tech CSE/Information Security 01.00 PM</p>

<p>8 Electrical Engineering M.Tech Electrical Derives 01.30 PM</p>

<p>9 Electronics &amp; Communication M.Tech Digital Communication 02.00 PM</p>

<p>10 MSME M.Tech Material Science/ Mechanical/Metallurgy 02.30 PM</p>

<p>11 Physics M.Sc.* Physics 03.00 PM</p>

<p>* M.Sc. with NET/GATE qualified</p>

<p>Resume along with one passport size photograph and relevant documents are required at the time of interview</p>

<p>Amount of Fellowship: Rs 18000/-month+ HRA</p>

<p>Duration: 31st Dec 2014 (End of TEQIP-II project)</p>

<p>Date of Interview: 7th  February 2014</p>

<p>Venue Institute Committee Room</p>

<p>Advertisement:</p>

<p>http://www.manit.ac.in/manitbhopal/Year2014/Recruitment/Advertisement%20JRF.pdf</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36830/crossmap-a-program-for-convenient-conversion-of-genome-coordinates</guid>
	<pubDate>Thu, 31 May 2018 06:00:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36830/crossmap-a-program-for-convenient-conversion-of-genome-coordinates</link>
	<title><![CDATA[CrossMap: a program for convenient conversion of genome coordinates]]></title>
	<description><![CDATA[CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) &lt;&gt; hg19 (GRCh37), Mouse mm9 (MGSCv37) &lt;&gt; mm10 (GRCm38)).

It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

CrossMap is designed to liftover genome coordinates between assemblies. 

It’s not a program for aligning sequences to reference genome.

We do not recommend using CrossMap to convert genome coordinates between species.<p>Address of the bookmark: <a href="http://crossmap.sourceforge.net" rel="nofollow">http://crossmap.sourceforge.net</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8287/post-doc-in-computational-genetics-and-genomics-at-ceinge-biotecnologie-avanzate-naples-italy</guid>
  <pubDate>Tue, 11 Feb 2014 08:06:47 -0600</pubDate>
  <link></link>
  <title><![CDATA[Post doc in Computational Genetics and Genomics at CEINGE Biotecnologie Avanzate, Naples, Italy]]></title>
  <description><![CDATA[
<p>We are seeking one motivated scientist to analyze genomics and transcriptomics data of a large collection of neuroblastoma tumors. The successful candidate will be part of a team of researchers with extensive expertise in genome cancer study. He/she will be involved in the analysis of DNA-seq, RNA-seq, ChIP-seq data using available methods running in R and UNIX environment.</p>

<p>Qualifications</p>

<p>PhD or Post-Graduated Master degree is required. Successful candidates will have some expertise in data analysis of NGS data by using methods running in R and UNIX environment. Familiarity with genome databases and browsers is required.</p>

<p>Application</p>

<p>Candidates should send a CV and a brief personal statement focusing on their skills and interests related to the research project.</p>

<p>Contacts</p>

<p>Start date: 1° April 2014<br />Salary on grant: 25,000 euros per year.<br />Contact Person (Referent): Mario Capasso<br />Ref. Email: mario.capasso@unina.it and achille.iolascon@unina.it<br />Tel: +39 081 3737889</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/36952/getoptspl-file</guid>
	<pubDate>Fri, 15 Jun 2018 04:43:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/36952/getoptspl-file</link>
	<title><![CDATA[getopts.pl file]]></title>
	<description><![CDATA[
<p>SSPACE_longread complain for getopts.pl file. </p>

<p>To resolve this, download and have in SSPACED-Longreads folder. </p>

<p>Cheers :)</p>
]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/36952" length="942" type="text/plain" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/8317/new-version-of-modeller-913</guid>
	<pubDate>Thu, 13 Feb 2014 09:07:57 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/8317/new-version-of-modeller-913</link>
	<title><![CDATA[New version of Modeller, 9.13]]></title>
	<description><![CDATA[<p>The new version of Modeller, 9.13, is now available for download! Please see the download page at <a href="http://www.facebook.com/l.php?u=http%3A%2F%2Fsalilab.org%2Fmodeller%2F&amp;h=mAQG5wo_Z&amp;enc=AZOoq2B7BxT95AT3Mw3za3VlbmRFke43YMI5vAjCAbBlIcf3bptn8pmFC1Idxrssy98117S03IgdcNmEWcQBi9bmi8Or_ut1D1yybt1ZonvPoCT3_LOglcYV7o6bEaa442_6LhbjefEaelkq0aq6dl0w&amp;s=1" target="_blank">http://salilab.org/modeller/</a> for more information.</p><p><img src="http://salilab.org/modeller/gifs/modeller.jpg" alt="image" width="848" height="272" style="border: 0px; border: 0px;"><br /> <br /> If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.13 - the same license key will work. (It won't <span>do any harm to reregister if you want to, though!)<br /> <br /> 9.13 is primarily a bugfix release relative to the last public release(9.12). Major user-visible changes include:<br /> <br /> # Modeller now includes a variety of SOAP (statistically optimized atomic potential) scores for assessing proteins, loops, and interfaces.<br /> <br /> # The Lennard-Jones interaction energy is now artificially truncated at very short distance; this makes simulations with poor starting conditions much less likely to 'blow up'.<br /> <br /> # model.get_insertions(), model.get_deletions() and model.loops() now have an include_termini option; if False, residue ranges that include chain termini are excluded from the output.<br /> <br /> See the Modeller manual for a full change log: <a href="http://salilab.org/modeller/9.13/manual/node39.html" target="_blank">http://salilab.org/modeller/9.13/manual/node39.html</a><br /> <br /> If you encounter bugs in Modeller 9.13, please see <a href="http://salilab.org/modeller/9.13/manual/node10.html" target="_blank">http://salilab.org/modeller/9.13/manual/node10.html</a> for information on how to report them.</span></p><p><span>Reference:</span></p><p><span>http://salilab.org/modeller/</span></p>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/fun/view/8509/the-best-bioinformatics-computational-biology-quotes</guid>
	<pubDate>Wed, 26 Feb 2014 17:50:59 -0600</pubDate>
	<link>https://bioinformaticsonline.com/fun/view/8509/the-best-bioinformatics-computational-biology-quotes</link>
	<title><![CDATA[The Best Bioinformatics / Computational Biology Quotes]]></title>
	<description><![CDATA[<p><img src="http://bioinformaticsonline.com/mod//photo/hahaha.png" style="border: 0; border: 0px;" alt="image"></p><p>Bioinformatician are not anti-social; We are just genome friendly.</p><p>Bioinformatician would love to change the biological world, but they won't give us the genetic code :P</p><p>If at first you don't succeed; call it version 1.0</p><p>The glass is neither half-full nor half-empty: it's actually have several genomes.</p><p>I'm BioGeek.</p><p>Fedup with LIPS, try God script.</p><p>Idiot, Go ahead, make my data!</p><p>Thank god, my genome just compiled.</p><p>Error message: "Out of space on genome drive:"</p><p>Shut up mobile elements, or i'll flush you out.</p><p>Never underestimate the internet bandwidth, u gotta incomplete.</p><p>Applied fuzzy logic to understand God's logic?</p><p>Warning! Overflow, delete chromosome !</p><p>Be nice to the BioGeek, for all you know they might be the next curator!</p><p>Beware of computational biologist they screw genes and protein.</p><p>Warning! Your genome is full of garbage, delete it !</p><p>Bad or missing mouse genome. Spank the cat? (Y/N)</p><p>Genome make very fast, very accurate mistakes.</p><p>Let's BLAST it.</p><p>Some genome never has transposons. It just develops random features.</p><p>Go watch CINEMA and have BLAST.</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37650/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</guid>
	<pubDate>Fri, 07 Sep 2018 05:19:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37650/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</link>
	<title><![CDATA[P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads]]></title>
	<description><![CDATA[<p><span>P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or other Protein-based approaches (for instance,&nbsp;</span><a href="http://www.fishbrowser.org/software/PEP_scaffolder/">PEP_scaffolder&nbsp;</a><span>) for scaffolding genome sequences. The most important feature of this method is to improve the completeness of gene regions and long-coding gene regions (for instance,&nbsp;</span><a href="http://circrna.org/">circRNA</a><span>).</span></p><p>Address of the bookmark: <a href="http://www.fishbrowser.org/software/P_RNA_scaffolder/#" rel="nofollow">http://www.fishbrowser.org/software/P_RNA_scaffolder/#</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/8987/the-dna-of-a-successful-bioinformatician-decoded</guid>
	<pubDate>Wed, 12 Mar 2014 13:41:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/8987/the-dna-of-a-successful-bioinformatician-decoded</link>
	<title><![CDATA[The DNA of a Successful Bioinformatician decoded !!!]]></title>
	<description><![CDATA[<p>Many blogs exist about successful bioinformatician, but this blog so far now is my personal view on characteristics of successful bioinformatician or computational biologist. &nbsp;Hmm &hellip; of course these views are subjective to my own personal experiences and therefore I don't claim that the view listed here is complete. As a human, I don&rsquo;t take them too serious. The success must not be the only target of your work. The target is to work on your own virtues; some of those virtues are the topic of this blog.</p><p><img src="http://bioinformaticsonline.com/mod/photo/genome_decode.png" alt="image" width="509" height="458" style="border: 0px; border: 0px;"><br /> <br /> <strong>1. Update new things continuously<br /></strong>As per my personal experience, it&rsquo;s not always easy to work as a bioinformatician! &nbsp;There are couple of reasons to say that; First computational part of biology make our life&rsquo;s a little harder compared to other professional categories. The fact - for instance - that the technology cycle in the bioinformatics world is very short, the actual knowledge becomes outdated in a few months or years. Therefore, we need to learn continuously - new things get important. Second, to stay on top of things we really need the strong will to be good at our job. That's probably the most important characteristic to bioinformatician. They are usually an excellent knowledge worker with great technical abilities, and have the will to be that over decades!<br /> <br /> <strong>2. Avoid the sentence </strong><strong>"I did not know what to do!"</strong><br /> In our computational biology lab, we generally face lots of technical problems. But as you know, it's impossible to know everything to do the computational biology jobs ( Yup.. because you need diverse and multidisciplinary knowledge to understand biological problems and resolve their respective solutions), therefore it's absolutely necessary that a bioinformatician finds its way through a new topic. How I typically do that is I use google and I talk to other experts in our laboratory or online biostar community to find out what they think. "I did not know what to do!" should not be an argument for us.<strong><br /><br /> <strong>3. To make oneself useful</strong></strong><br /> Several time it does happen, you finished our task earlier than expected; in such cases if you have some time left then: Take a coffee and play chess; reversi, etc. In my case I take a rest. Afterwards I think about what I could do that helps the team to achieve its targets, 'cause some of my team mates probably didn't finish! (at least if I didn't met them at coffee bar !!)</p><p><strong>4. Care for all</strong><br /> During my rigorous research duration; I attended several workshop organized by my University departments. I had a discussion with other research fellow, professors; I generally ask &hellip; what it really takes to make a team successful or to be a successful research leader. They always said: "Well, you need some caring people!" I think there is a lot truth in that statement. If we do not care about quality, timelines, good team culture, respectful communication (!!), clean code, if all this doesn&rsquo;t matter to us, then I believe the probability is higher that we fail in research and analysis. <br /> <br /> <strong>5. Be good with people</strong><br /> Because bioinformatician and computational biologist jobs typically involves to work in a (most wanted J cross-departmental!) team, therefore it's important that we're (more or less) good in dealing with other individuals. Everyone have their own strengths and weaknesses, just like us. It's important to treat all the research team mates with respect, regardless of their technical competence or contributions. Of course, sometimes people deserve a clear statement (!!!), but try to do these things one-on-one. Make sure nobody loses his face. Attend the meetings at the coffee bar; be good at table top soccer and go out once in a while to have a beer with your team. You know what I'm talking about.</p><p>At the end of a week I look back and I ask myself what I have produced. This could be paperwork, community days or (best!!) programming code. Always remember there is always a solution to a problem. Most of the times there are at least three solutions. So, don&rsquo;t just blame, suggest a solution.<br /> <br /> That's it. I am looking forward to your thoughts and comments!</p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38041/synima-a-synteny-imaging-tool-for-annotated-genome-assemblies</guid>
	<pubDate>Tue, 30 Oct 2018 10:49:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38041/synima-a-synteny-imaging-tool-for-annotated-genome-assemblies</link>
	<title><![CDATA[Synima: a Synteny imaging tool for annotated genome assemblies]]></title>
	<description><![CDATA[<p><span>Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima &ndash; and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from&nbsp;</span><a href="https://github.com/rhysf/Synima" target="_blank">https://github.com/rhysf/Synima</a><span>&nbsp;under the MIT License.</span></p><p>Address of the bookmark: <a href="https://github.com/rhysf/Synima" rel="nofollow">https://github.com/rhysf/Synima</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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