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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/31881?offset=980</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30747/11th-international-joint-conference-on-biomedical-engineering-systems-and-technologies</guid>
  <pubDate>Wed, 01 Feb 2017 17:39:27 -0600</pubDate>
  <link></link>
  <title><![CDATA[11th International Joint Conference on Biomedical Engineering Systems and Technologies]]></title>
  <description><![CDATA[
<p>BIOSTEC, the 11th International Joint Conference on Biomedical Engineering Systems and Technologies.<br /> Registration to BIOINFORMATICS allows free access to all other BIOSTEC conferences. </p>

<p>Upcoming Deadlines<br />Regular Paper Submission: July 31, 2017 <br />Regular Paper Authors Notification: October 16, 2017 <br />Regular Paper Camera Ready and Registration: October 30, 2017 </p>

<p>The purpose of the International Conference on Bioinformatics Models, Methods and Algorithms is to bring together researchers and practitioners interested in the application of computational systems, algorithmic concepts and information technologies to address challenging problems in Biomedical research with a particular focus on the emerging problems in Bioinformatics and computational biology. There is a tremendous need to explore how mathematical, statistical and computational models can be used to better understand biological processes and systems, while developing new methodologies and tools to analysis the massive currently-available biological data. Areas of interest to this community include systems biology, sequence analysis, biostatistics, image analysis, network and graph models, scientific data management and data mining, machine learning, pattern recognition, computational evolutionary biology, computational genomics and proteomics, and related areas.</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30831/fsa-fast-statistical-alignment</guid>
	<pubDate>Mon, 06 Feb 2017 04:26:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30831/fsa-fast-statistical-alignment</link>
	<title><![CDATA[FSA: Fast Statistical Alignment]]></title>
	<description><![CDATA[<p><span>FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise comparisons, developed by Ariel Schwartz in&nbsp;</span><a href="http://www.eecs.berkeley.edu/Pubs/TechRpts/2007/EECS-2007-39.html">"Posterior Decoding Methods for Optimization and Control of Multiple Alignments</a><span>."</span></p>
<p>FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments:</p>
<ul>
<li>FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This "query-specific learning" alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints.</li>
<li>FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy.</li>
<li>FSA can quickly align very long sequences using the "anchor annealing" technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above.</li>
<li>The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned (see the picture and&nbsp;<a href="http://fsa.sourceforge.net/images/Suchard_SIV.fsa.mov">movie</a>&nbsp;at the top of the page).</li>
</ul>
<p><span>You can see more information on the&nbsp;</span><a href="http://fsa.sourceforge.net/FAQ.html">FAQ</a><span>.&nbsp;</span></p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="http://fsa.sourceforge.net/" rel="nofollow">http://fsa.sourceforge.net/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30897/finestructure-v2-globetrotter</guid>
	<pubDate>Mon, 13 Feb 2017 08:40:23 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30897/finestructure-v2-globetrotter</link>
	<title><![CDATA[fineSTRUCTURE v2 &amp; GLOBETROTTER]]></title>
	<description><![CDATA[<p>Software available at this site</p>
<div>
<ul>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructure_info.html">FineSTRUCTURE version 2</a>, a pipeline for running ChromoPainter and FineSTRUCTURE for population inference. A GUI is available for interpretation. Download from the <a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructure.html">Downloads</a> page.</li>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructureR.html">FineSTRUCTURE R scripts</a>, a facility for exploring the results when the GUI is unavailable.</li>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/globetrotter.html">GLOBETROTTER</a>, the admixture dating method based on ChromoPainter. Download from the <a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructure.html">Downloads</a> page.</li>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/admixture.html">AdmixturePainting</a>, A set of R tools to inmterpret the results of ADMIXTURE and STRUCTURE-like mixture models.</li>
<li><a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/radpainter.html">RADpainter</a>, finestructure and ChromoPainter for RAD tag data used for non-model organisms.</li>
<li>Scripts to perform many types of conversion. Included in the main software download from the <a href="https://people.maths.bris.ac.uk/%7Emadjl/finestructure/finestructure.html">Downloads</a> page.</li>
</ul>
What this page is This page provides information about and downloads for <strong>methodology for Chromosome Painting</strong>. It is not a facility to analyse your genome. Sorry if you were misled by the punchy name!<br> About Chromosome Painting Painting is an efficient way of identifying important haplotype information from dense genotype data. It describes ancestry in an efficient way suitable for a range of further analyses, including population identification and admixture dating.</div><p>Address of the bookmark: <a href="http://paintmychromosomes.com/" rel="nofollow">http://paintmychromosomes.com/</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31207/laj-viewing-and-manipulating-the-output-from-pairwise-alignment-programs</guid>
	<pubDate>Wed, 01 Mar 2017 08:35:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31207/laj-viewing-and-manipulating-the-output-from-pairwise-alignment-programs</link>
	<title><![CDATA[Laj: viewing and manipulating the output from pairwise alignment programs]]></title>
	<description><![CDATA[<p>Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as <a href="http://bio.cse.psu.edu/">blastz</a>. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.</p>
<p>The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for "Local Alignments with Java". Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.</p><p>Address of the bookmark: <a href="http://www.bx.psu.edu/~ratan/" rel="nofollow">http://www.bx.psu.edu/~ratan/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/87/linux-cheat-sheet</guid>
	<pubDate>Tue, 09 Jul 2013 17:30:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/87/linux-cheat-sheet</link>
	<title><![CDATA[Linux Cheat Sheet]]></title>
	<description><![CDATA[<p><span>In an attempt to find a good Linux reference for bioinformatician and BOL readers, I was unsuccessful at finding a decent one on the Internet. So, we decided to make a cheat sheet for biological programmers.</span></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/87" length="81260" type="application/pdf" />
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/31520/research-associate-openings-at-iasri-india</guid>
  <pubDate>Fri, 10 Mar 2017 03:53:03 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Associate openings at IASRI, India]]></title>
  <description><![CDATA[
<p>Research Associate (RA) Two (2) </p>

<p>Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements. </p>

<p>Knowledge in System Biology/ Statistical and computational Genomics/ Bioinformatics <br />Knowledge in computer programming, LINUX OS. <br />Expertise in use of R/other Bioinformatics software </p>

<p>More at http://iasri.res.in/employment/2017/cabin_advertisement_RA_SRF_YP_Mar2017.pdf</p>

<p>Phenomics of Moisture Deficit Stress Tolerance and Nitrogen Use December 31, 2019 </p>

<p>Research Associate (RA) Two (2) </p>

<p>Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or System Administrator/ Computer expert for database development, development of phenome data bank and virtual phenomics facility, data archiving and Efficiency in Rice and Wheat-Phase II (Funded by National Agricultural Science Fund, ICAR) Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements. maintenance; Development of image analysis algorithms, APIs and IAPs. </p>

<p>Knowledge in System Biology/ Statistical and computational Genomics/ Bioinformatics <br />Knowledge of programming in LINUX/R/Perl/JAVA/PHP/JSP and use of various software &amp; tools. <br />December 31, 2019 </p>

<p>Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science / Computer Application or equivalent or Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements. </p>

<p>Knowledge of Statistical and Computational Genomics/ Bioinformatics. <br />Knowledge of programming in LINUX/R/Perl/JAVA/PHP/JSP and use of various software &amp; tools. <br />March 31, 2020</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/396/bioinformatics-introduction-to-perl</guid>
	<pubDate>Thu, 11 Jul 2013 09:49:37 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/396/bioinformatics-introduction-to-perl</link>
	<title><![CDATA[Bioinformatics: Introduction to PERL]]></title>
	<description><![CDATA[<p>This course is aimed at those new to programming and provides an introduction to programming using <strong>Perl</strong>. By the end of this course, attendees should be able to write simple <strong>Perl</strong> programs and to understand more complex <strong>Perl</strong> programs written by others. The course will be taught using the online <a href="http://sofiarobb.com/learning-perl-toc/" title="http://sofiarobb.com/learning-perl-toc/">Learning Perl</a> materials created by <a href="http://stajich.bioinformatics.ucr.edu/members/sofia-robb" title="http://stajich.bioinformatics.ucr.edu/members/sofia-robb">Sofia Robb</a> of the <a href="http://www.ucr.edu/" title="http://www.ucr.edu/">University of California Riverside</a>. Further information is <a href="http://ruddles.bio.cam.ac.uk/%7Edpjudge/Descriptions/PERL.php" title="http://ruddles.bio.cam.ac.uk/~dpjudge/Descriptions/PERL.php">available</a>.</p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/842/ngs-bioinformatics-summit-europe</guid>
  <pubDate>Sat, 13 Jul 2013 17:02:34 -0500</pubDate>
  <link></link>
  <title><![CDATA[NGS &amp; Bioinformatics Summit Europe]]></title>
  <description><![CDATA[
<p>NGS &amp; Bioinformatics Summit Europe </p>

<p>Conference </p>

<p>7th   to  8th October 2013 <br />Berlin, Germany </p>

<p>Website: https://www.gtcbio.com/conference/ngseurope-overview <br />Contact person: Kristen Starkey </p>

<p>We welcome you to join us at GTC’s NGS &amp; Bioinformatics Summit Europe on October 7-8, 2013 in Berlin, Germany. </p>

<p>Organized by: GTC <br />Deadline for abstracts/proposals: 7th September 2013</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32011/fools-guide</guid>
	<pubDate>Sun, 02 Apr 2017 14:31:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32011/fools-guide</link>
	<title><![CDATA[Fools guide]]></title>
	<description><![CDATA[<p><span>This website and accompaning documents are intended as a tool to help researchers dealing with non-model organisms acquire and process transcriptomic high-throughput sequencing data without having to learn extensive bioinformatics skills. It covers all steps from tissue collection, sample preparation and computer setup, through addressing biological questions with gene expression and SNP data.</span></p>
<p>http://sfg.stanford.edu/denovo.html</p>
<p>http://sfg.stanford.edu/sequencing.html</p>
<p>http://sfg.stanford.edu/BLAST.html</p>
<p>http://sfg.stanford.edu/denovo.html&nbsp;</p><p>Address of the bookmark: <a href="http://sfg.stanford.edu/guide.html" rel="nofollow">http://sfg.stanford.edu/guide.html</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/859/boku-chair-of-bioinformatics</guid>
  <pubDate>Sun, 14 Jul 2013 12:37:23 -0500</pubDate>
  <link></link>
  <title><![CDATA[Boku Chair of Bioinformatics]]></title>
  <description><![CDATA[
<p>The Bioinformatics group at Boku University has two main areas of interest, underpinning a common goal, the study of complex systems in living organisms. To overcome the engineered redundancies and combinatorial effects prevalent in higher eukaryotes, novel views augmenting the classical gene by gene approaches are required. We combine<br />Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and<br />Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)</p>

<p>Link @ http://bioinf.boku.ac.at/</p>
]]></description>
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