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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/28566?offset=400</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28200/machine-learning</guid>
	<pubDate>Fri, 01 Jul 2016 12:57:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28200/machine-learning</link>
	<title><![CDATA[Machine Learning !!!]]></title>
	<description><![CDATA[<p>In machine learning, computers apply&nbsp;<strong>statistical learning</strong>&nbsp;techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.</p>
<p><em>Keep scrolling.</em>&nbsp;Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.</p><p>Address of the bookmark: <a href="http://www.r2d3.us/visual-intro-to-machine-learning-part-1/" rel="nofollow">http://www.r2d3.us/visual-intro-to-machine-learning-part-1/</a></p>]]></description>
	<dc:creator>Gudiya Pal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28303/fancy-oneliner-for-bioinformatics</guid>
	<pubDate>Thu, 07 Jul 2016 12:05:50 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28303/fancy-oneliner-for-bioinformatics</link>
	<title><![CDATA[Fancy Oneliner for Bioinformatics !!]]></title>
	<description><![CDATA[<p><span>This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are sharing these codes with the intention that if they are useful and help you in your analyses, then we will be appropriately credited as considerable effort has been put into devising them.</span></p><p>Address of the bookmark: <a href="http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html" rel="nofollow">http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/28439/binc-exam-preparation-tips</guid>
	<pubDate>Fri, 15 Jul 2016 20:53:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/28439/binc-exam-preparation-tips</link>
	<title><![CDATA[BINC exam preparation tips !!]]></title>
	<description><![CDATA[<p>How to prepare for <span>BINC (BioInformatics National Certification)</span>&nbsp;exam? What are the expected questions?</p><p>These are just a scant few of the common questions asked by bioinformatics students as they ready themselves for the next exam sitting. If you read the entire <a href="http://bioinformaticsonline.com/bookmarks/view/2334/binc-bioinformatics-national-certification-website-address">Syllabus</a> (and I know that everyone does), you will see a section devoted to study and exam techniques. The section discusses such broad concepts as motivation, scheduling, and retention. Upon reading this section, however, I find the "hints" to be too general. Much of the advice boils down to read, study, understand, and memorize the material. The techniques mentioned apply to everyone and thus the overall advice ends up as a broad overview of the learning process.</p><p>The idea behind this article is to give students ideas on different approaches and techniques in the preparation for exams. By providing various ways to prepare for the exam process, fascinated readers may gain some additional insight to help complement their studying methodology. There are, of course, many common themes expressed in this small empirical sample of students' study habits. The idea of note cards, memorization, and problem solving are frequently mentioned by all students. No matter what technique a candidate uses, it always takes a significant amount of time and personal resources to successfully complete the examination process.</p><p>1 Explain it in your own word</p><p>Your teacher or lecturer can explain something to you, you can learn it from a text book, your friends can study with you, even your own notes can explain it to you but all these explanations are of little use if, by the end, you can&rsquo;t explain what you have learned to yourself. The BINC exam looking for ability to write and explain the concept in your own word. You, therefore, need to illustrate in an exam to get top exam results, then you won&rsquo;t be happy with your end exam result. So don&rsquo;t just memorise and tick off the list &ndash; make sure you understand your theory.</p><p>2 Be an examiner yourself</p><p>Of course, depending on what you&rsquo;re studying, it may be quite difficult to get into a position to understand a concept, theory or other information you need to learn. Ask &lsquo;stupid&rsquo; question to yourself and train yourself for the worst! Embrace your curiosity, for as William Arthur Ward said: &ldquo;Curiosity is the wick in the candle of learning.&rdquo; Doing so will allow you to fill in the blanks and better prepare you for exams.</p><p>3 Quiz yourself</p><p>Once you feel you understand topic, it is important to test yourself regularly. Try yourself to replicate exam conditions as much as possible: turn your phone off, don&rsquo;t talk, time yourself etc. You can set yourself a study quiz or practice exam questions and, so long as you approach it with the right mindset, you can get a very good idea of how much you know. You gain a greater insight into where you stand in relation to what you&rsquo;ve studied so far.</p><p>4 Online study</p><p>Keeping the fact that, bioinformatics is ever changing subject, you might need to update yourself on timely basis. Don&rsquo;t feel obliged to just sit in front of a book with a highlighter; there are many different ways to improve your bioinformatics knowledge. Login and check almost all web servers and keep yourself updated, like how many genomes sequenced, sizes, techniques used, software names etc.</p><p>5 Study plan</p><p>In order to achieve exam success, you need to know what you want to achieve and focus on. That&rsquo;s why it is extremely important to set your Study Goals now and outline to yourself what you need to do. With your study goals in mind, you properly need to attention all subjects. It should be broad enough to allow you to add and change aspects but concise enough so you know you&rsquo;re covering each subject/topic as best you can at this point.</p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28554/megan6</guid>
	<pubDate>Mon, 25 Jul 2016 05:45:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28554/megan6</link>
	<title><![CDATA[MEGAN6]]></title>
	<description><![CDATA[<p>Microbiome analysis using a single application</p>
<p>MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.</p>
<ul>
<li>Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA</li>
<li>Functional analysis using InterPro2GO, SEED, eggNOG or KEGG</li>
<li>Bar charts, word clouds, Voronoi tree maps and many other charts</li>
<li>PCoA, clustering and networks</li>
<li>Supports metadata</li>
<li>MEGAN parses many different types of input</li>
</ul>
<p>Why use MEGAN6?</p>
<div>&nbsp;The software is:</div>
<div><ol>
<li>Easy to use. MEGAN6 is a single application and all features are available through menus, toolbars and graphics. No scripting skills required.</li>
<li>Powerful. MEGAN6 allows you to work with hundreds of samples containing&nbsp;hundreds of millions of sequencing reads. Blast-like analysis can be performed using DIAMOND.</li>
<li>Comprehensive. MEGAN6 offers a large range of analysis tools, and is under active development.</li>
</ol></div><p>Address of the bookmark: <a href="https://ab.inf.uni-tuebingen.de/software/megan6" rel="nofollow">https://ab.inf.uni-tuebingen.de/software/megan6</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/28818/senior-manager-bioinformatics-operations-at-rgcb-india</guid>
  <pubDate>Wed, 17 Aug 2016 03:19:05 -0500</pubDate>
  <link></link>
  <title><![CDATA[Senior Manager (Bioinformatics Operations) at RGCB, India]]></title>
  <description><![CDATA[
<p>No. RGCB/ADVT/ADMN&amp;TECH/01/2016</p>

<p>August 17, 2016</p>

<p>RGCB invites applications for the following positions from Indian citizens with prescribed qualifications. Full details including job description, additional desirable qualifications, etc. are described below.</p>

<p>Code No. 1</p>

<p>Senior Manager (Bioinformatics Operations)</p>

<p>(To download application format, click here )</p>

<p>Scale of Pay</p>

<p>PB-3 Rs.15600-39100 + Grade Pay Rs.6600/-</p>

<p>Number of Positions</p>

<p>1 (General)</p>

<p>Minimum Qualifications</p>

<p>PhD in Bioinformatics, Biotechnology, Life Sciences or Computer Science applied to biological questions.<br />A minimum of 5 years documented experience in national or state government R&amp;D centers or state and central universities.<br />Track record of research funding and peer reviewed publications.<br />Proficiency using statistical analysis software or libraries such as R or Matlab.<br />Experience with a general scripting language such as Python, Ruby, or Pearl<br />Experience working with Next Generation Sequencing data<br />Proficiency with data visualization tools (Spotfire, Tableau, R, Python, etc.)<br />Experience with an object-oriented language such as Java, C++ or C# and familiarity with standard software development best practices: source code control, unit testing, in-code documentation and automated build environments.<br />Excellent listening, time management, organizational and interpersonal skills<br />Excellent communication skills, including the ability to illustrate problems and generate solutions<br />Management skills – demonstrated through the successful management of a team or large projects.<br />Broad and deep knowledge of computational methods for high-throughput sequence analysis and interpretation.<br />Extensive experience in delivering bioinformatics as a service and conducting training programs.<br />Experience of working with a production, customer-focused environment and business development projects.<br />Experience with management of funding and financial sustainability.<br />Demonstrated ability to work in a team environment and ability to lead and motivate an effective team, and also work as a good team player.<br />Good problem solver, able to logically identify solutions to technical problems.<br />Able to see the bigger picture and contribute towards strategic direction of Platforms and Pipelines teams.<br />Responsibilities</p>

<p>This position will involve cross-functional teamwork to build and develop bioinformatics tools and provide analysis for ongoing clinical trials.<br />Collaborate with biomarker scientists, clinical investigators and pipeline teams to build analytical tools.<br />Implement and evaluate new algorithms for R&amp;D.<br />Support Research and Development teams by analyzing NGS data to identify predictive response markers<br />Lead training programs in Computational Biology and Bioinformatics.</p>

<p>More at http://rgcb.res.in/positions.php</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29103/genome-strip</guid>
	<pubDate>Tue, 06 Sep 2016 03:58:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29103/genome-strip</link>
	<title><![CDATA[Genome STRiP]]></title>
	<description><![CDATA[<p><strong>Genome STRiP</strong><span>&nbsp;(Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.</span><br><br><span>Genome STRiP looks both across and within a set of sequenced genomes to detect variation. The methods are adaptive and support heterogeneous data sets, including variations in sequencing depth, read lengths and mixtures of paired and single-end reads. A minimum of 20 to 30 genomes are required to get acceptable results, but the method gains power across genomes and processing more genomes provide better results.</span><br><br><span>To run discovery or genotyping on a single sequenced genome or a small set of genomes, you need to call your data against a background population, such as a set of genomes from the 1000 Genomes Project.&nbsp; The background population does not need to be matched to the target individuals.</span></p><p>Address of the bookmark: <a href="http://software.broadinstitute.org/software/genomestrip/" rel="nofollow">http://software.broadinstitute.org/software/genomestrip/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29018/crossmap</guid>
	<pubDate>Mon, 05 Sep 2016 04:07:38 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29018/crossmap</link>
	<title><![CDATA[CrossMap]]></title>
	<description><![CDATA[<ul>
<li>CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between&nbsp;<em>different assemblies</em>&nbsp;(such as Human&nbsp;<a href="http://www.ncbi.nlm.nih.gov/assembly/2928/">hg18 (NCBI36)</a>&nbsp;&lt;&gt;&nbsp;<a href="http://www.ncbi.nlm.nih.gov/assembly/2758/">hg19 (GRCh37)</a>, Mouse&nbsp;<a href="http://www.ncbi.nlm.nih.gov/assembly/165668/">mm9 (MGSCv37)</a>&nbsp;&lt;&gt;&nbsp;<a href="http://www.ncbi.nlm.nih.gov/assembly/327618/">mm10 (GRCm38)</a>).</li>
<li>It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.</li>
<li>CrossMap is designed to liftover genome coordinates between assemblies. It&rsquo;s&nbsp;<em>not</em>&nbsp;a program for aligning sequences to reference genome.</li>
<li>We&nbsp;<em>do not</em>&nbsp;recommend using CrossMap to convert genome coordinates between species.</li>
</ul><p>Address of the bookmark: <a href="http://crossmap.sourceforge.net/" rel="nofollow">http://crossmap.sourceforge.net/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28807/organellargenomedraw</guid>
	<pubDate>Tue, 16 Aug 2016 08:13:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28807/organellargenomedraw</link>
	<title><![CDATA[OrganellarGenomeDRAW]]></title>
	<description><![CDATA[<p><span>O</span><span>rganellar</span><span>G</span><span>enome</span><span>DRAW</span><span>&nbsp;is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file format, whereas the output format can be chosen among several formats. The application is especially optimized and adapted for the creation of high-quality, detailed circular maps of organellar genomes like the plastid genome (plastome) or the mitochondrial genome (chondriome). Nevertheless, you can upload any GenBank entry. The workflow is devided into three steps.&nbsp;</span></p>
<p><span>More at&nbsp;http://ogdraw.mpimp-golm.mpg.de/cgi-bin/ogdraw.pl</span></p><p>Address of the bookmark: <a href="http://ogdraw.mpimp-golm.mpg.de/index.shtml" rel="nofollow">http://ogdraw.mpimp-golm.mpg.de/index.shtml</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28844/teannot</guid>
	<pubDate>Thu, 18 Aug 2016 10:02:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28844/teannot</link>
	<title><![CDATA[TEannot]]></title>
	<description><![CDATA[<p>We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the project name is "DmelChr4".</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto" rel="nofollow">https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28870/genemania</guid>
	<pubDate>Mon, 22 Aug 2016 09:55:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28870/genemania</link>
	<title><![CDATA[GeneMANIA]]></title>
	<description><![CDATA[<p>Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function prediction.</p><p>Address of the bookmark: <a href="http://genemania.org/" rel="nofollow">http://genemania.org/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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