<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32152?offset=1220</link>
	<atom:link href="https://bioinformaticsonline.com/related/32152?offset=1220" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/7212/bioinformatics-group-at-boku-university</guid>
  <pubDate>Thu, 12 Dec 2013 17:53:10 -0600</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics group at Boku University]]></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</p>

<p>1. Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and<br />2. Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)</p>

<p>Lab page @ http://bioinf.boku.ac.at/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39947/radar-charts-with-ggplot2</guid>
	<pubDate>Tue, 17 Sep 2019 23:01:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39947/radar-charts-with-ggplot2</link>
	<title><![CDATA[radar charts with ggplot2]]></title>
	<description><![CDATA[<p><code>ggradar</code>&nbsp;allows you to build radar charts with ggplot2. This package is based on&nbsp;<a href="http://rstudio-pubs-static.s3.amazonaws.com/5795_e6e6411731bb4f1b9cc7eb49499c2082.html">Paul Williamson&rsquo;s</a>&nbsp;code, with new aesthetics and compatibility with ggplot2 2.0.</p>
<p>It was inspired by&nbsp;<a href="http://www.buildingwidgets.com/blog/2015/12/9/week-49-d3radarr">d3radaR</a>, an htmlwidget built by&nbsp;<a href="https://github.com/timelyportfolio">timelyportfolio</a>.</p><p>Address of the bookmark: <a href="https://github.com/ricardo-bion/ggradar" rel="nofollow">https://github.com/ricardo-bion/ggradar</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books</guid>
	<pubDate>Thu, 12 Dec 2013 19:38:34 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/7216/free-math-books</link>
	<title><![CDATA[Free math books]]></title>
	<description><![CDATA[<p>Bioinformatics require some match skills, therefore I decided to provide this wonderful math eBooks links to the BOL community.</p>
<p>Please add ur links/bookmarks in comment section.</p><p>Address of the bookmark: <a href="http://physicsdatabase.com/free-math-books/" rel="nofollow">http://physicsdatabase.com/free-math-books/</a></p>]]></description>
	<dc:creator>Manisha Mishra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40583/trelliscope-flexibly-visualize-large-complex-data-in-great-detail-from-within-the-r-statistical-programming-environment</guid>
	<pubDate>Tue, 21 Jan 2020 04:22:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40583/trelliscope-flexibly-visualize-large-complex-data-in-great-detail-from-within-the-r-statistical-programming-environment</link>
	<title><![CDATA[Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical programming environment.]]></title>
	<description><![CDATA[<p>Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the<span>&nbsp;</span><a href="http://deltarho.org/docs-trelliscope/deltarho.org">DeltaRho</a><span>&nbsp;</span>environment.</p>
<p>For those familiar with<span>&nbsp;</span><a href="http://cm.bell-labs.com/cm/ms/departments/sia/project/trellis/">Trellis Display</a>,<span>&nbsp;</span><a href="http://docs.ggplot2.org/0.9.3.1/facet_wrap.html">faceting in ggplot</a>, or the notion of<span>&nbsp;</span><a href="http://en.wikipedia.org/wiki/Small_multiple">small multiples</a>, Trelliscope provides a scalable way to break a set of data into pieces, apply a plot method to each piece, and then arrange those plots in a grid and interactively sort, filter, and query panels of the display based on metrics of interest. With Trelliscope, we are able to create multipanel displays on data with a very large number of subsets and view them in an interactive and meaningful way.</p><p>Address of the bookmark: <a href="http://deltarho.org/docs-trelliscope/#introduction" rel="nofollow">http://deltarho.org/docs-trelliscope/#introduction</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era</guid>
	<pubDate>Sun, 22 Dec 2013 17:31:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era</link>
	<title><![CDATA[Bioinformatics software for biologists in the genomics era]]></title>
	<description><![CDATA[<p>The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.</p><p>Address of the bookmark: <a href="http://bioinformatics.oxfordjournals.org/content/23/14/1713.full" rel="nofollow">http://bioinformatics.oxfordjournals.org/content/23/14/1713.full</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41043/postdoctoral-scientist-genome-analytics-genome-bioinformatics-mf</guid>
  <pubDate>Sun, 16 Feb 2020 02:57:40 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral scientist genome analytics/ genome bioinformatics (m/f/*)]]></title>
  <description><![CDATA[
<p>https://www.uksh.de/jobs/Stellenangebote-nr-20190570-p-8.html<br />Your profile:<br />Degree in bioinformatics, biostatistics, or equivalent<br />Experience in the processing and analysis of large-scale genomics data using compute clusters / high-performance computing<br />Strong competence in working in Unix/Linux environments (shell)<br />Strong programming skills (in particular: Python, R, Perl)<br />Experience with using git and snakemake<br />Fluent English language skills, both spoken and written<br />Strong communication skills and motivation to work in a young, interdisciplinary, dynamic team</p>

<p>Additional Information:</p>

<p>If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).</p>

<p>Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).</p>

<p>Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.</p>

<p>Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7753/jrf-pondicherry-university</guid>
  <pubDate>Fri, 03 Jan 2014 16:48:56 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF @ PONDICHERRY UNIVERSITY]]></title>
  <description><![CDATA[
<p>PONDICHERRY UNIVERSITY</p>

<p>CENTRE FOR BIOINFORMATICS</p>

<p>PUDUCHERRY</p>

<p>Applications are invited for one Project Assistant to work in the UGC sponsored Research Award "Molecular Docking and Dynamics studies to understand the interacting mechanism of oncogenic 101 protein with its cellular proteins".</p>

<p>The duration for the fellowship is 12months only with consolidated pay ofRs. 5,000 per month.</p>

<p>Application on plain paper with following details: Name, Address, Data of Birth, Father's Name, Nationality, Educational Qualification (SSLC onwards-enclose attested copies of certificate) and Researcb Experience may be addressed to Dr. R. Krishna, Principle Investigator (PI), UGC Research Award, Centre for Bioinformatics, Pondicherry University, Pondicherry - 605 014.</p>

<p>Application should reach in January 261h , 2013.</p>

<p>Essential Qualification: M.Sc. in Bioinformatics/Biophysics with good academic record.</p>

<p>Qualification for Project Fellow:</p>

<p>M.Sc in Bioinformatics/Biophysics.</p>

<p>The person to be considered for appointment as Project Fellow must have second class master degree with a minimum of 55% marks in the subject concerned or a related subject.</p>

<p>The candidate to be appointed as Project Fellows should be below thc age of40 years at the time of appointment.</p>

<p>Desirable Qualification for this Project: Research Experience in Small/Macromolecule Crystallography and Structural Bioinformatics.</p>

<p>For more details, refer the web site: www.pondiuni.edu.in/sites/default/files/BIC-311213.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/41496/new-machine-learning-packages-in-r</guid>
	<pubDate>Fri, 27 Mar 2020 12:11:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/41496/new-machine-learning-packages-in-r</link>
	<title><![CDATA[New Machine Learning Packages in R]]></title>
	<description><![CDATA[<h3 id="machine-learning">Machine Learning</h3><p><a href="https://cran.r-project.org/package=autokeras">autokeras</a>&nbsp;v1.0.1: Implements an interface to&nbsp;<a href="https://autokeras.com/">AutoKeras</a>, an open source software library for automated machine learning. See&nbsp;<a href="https://cran.r-project.org/web/packages/autokeras/readme/README.html">README</a>&nbsp;for an example.</p><p><a href="https://cran.r-project.org/package=MTPS">MTPS</a>&nbsp;v0.1.9: Implements functions to predict simultaneous multiple outcomes based on revised stacking algorithms as described in&nbsp;<a href="denied:doi:10.1093/bioinformatics/btz531">Xing et al. (2019)</a>. See the&nbsp;<a href="https://cran.r-project.org/web/packages/MTPS/vignettes/Guide.html">vignette</a>&nbsp;to get started.</p><p><a href="https://cran.r-project.org/package=quanteda.textmodels">quanteda.textmodels</a>&nbsp;v0.9.1: Implements methods for scaling models and classifiers based on sparse matrix objects representing textual data. It includes implementations of the&nbsp;<a href="denied:doi:10.1017/S0003055403000698">Laver et al. (2003)</a>&nbsp;wordscores model, the&nbsp;<a href="denied:arxiv:1710.08963">Perry &amp; Benoit&rsquo;s (2017)</a>&nbsp;class affinity scaling model, and the&nbsp;<a href="denied:doi:10.1111/j.1540-5907.2008.00338.x">Slapin &amp; Proksch (2008)</a>&nbsp;wordfish model. See the&nbsp;<a href="https://cran.r-project.org/web/packages/quanteda.textmodels/vignettes/textmodel_performance.html">vignette</a>&nbsp;to get started.</p><p><a href="https://cran.r-project.org/package=SeqDetect">SeqDetect</a>&nbsp;v1.0.7: Implements the automaton model found in&nbsp;<a href="https://ieeexplore.ieee.org/document/8910574">Krleža, Vrdoljak &amp; Brčić (2019)</a>&nbsp;to detect and process sequences. See the&nbsp;<a href="https://cran.r-project.org/web/packages/SeqDetect/vignettes/SequentialDetector.pdf">vignette</a>&nbsp;for examples and theory.</p><p><a href="https://cran.r-project.org/package=studyStrap">studyStrap</a>&nbsp;v1.0.0: Implements multi-Study Learning algorithms such as Merging, Study-Specific Ensembling (Trained-on-Observed-Studies Ensemble), the Study Strap, and the Covariate-Matched Study Strap. and offers over 20 similarity measures. See&nbsp;<a href="denied:doi:10.1101/856385">Kishida, et al. (2019)</a>&nbsp;for background and the&nbsp;<a href="https://cran.r-project.org/web/packages/studyStrap/vignettes/vignette.html">vignette</a>&nbsp;for how to use the package.</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7998/faculty-positions-at-iiit-allahabad</guid>
  <pubDate>Thu, 23 Jan 2014 06:19:34 -0600</pubDate>
  <link></link>
  <title><![CDATA[FACULTY POSITIONS AT IIIT-ALLAHABAD]]></title>
  <description><![CDATA[
<p>OPENINGS OF FACULTY POSITIONS AT IIIT-ALLAHABAD</p>

<p>(Under Tenure-Track Model)</p>

<p>Open Advt. No IIITA/DIC/16012014</p>

<p>IIIT-Allahabad has several Openings for the Faculty positions at the Assistant Professor level.</p>

<p>It is a regular tenure-track faculty positions for 3-5 years in teaching and research. A regular faculty is expected to engage heavily in research and teaching. The eligibility criteria for regular faculty positions are similar as in IITs. For an Assistant Professor position, a candidate must have a PhD (in IT/Computer Science &amp;/or Engineering/Electrical, Electronics &amp;/or Communication Engineering/etc; for interdisciplinary areas the PhD may be in an appropriate field), plus three years experience. However, for PhDs from a well known University/Institute (e.g. IITs/IISc/TIFR/ISI in India or well known research universities across the world), and a good research/academic record, the 3 years experience requirement may be waived.</p>

<p>The pay scale for faculty is same as in IITs. Other benefits include initiation research grant, travel support, book grant, professional society membership, etc., and personal benefits such as medical/LTC, on campus subsidized family housing with excellent modern infrastructural facilities.</p>

<p>Areas of Interest</p>

<p>IIIT-Allahabad aims to build strong research groups in important and emerging areas in CS/IT/ECE as well as in emerging interdisciplinary areas, and applications are invited in all these areas. Some of the areas of special interest, besides strengthening the existing research areas, are : Software Engineering, Theoretical Computer Science, Cyber Physical Systems, Robotics, Network science, Digital Media, Computational neuroscience, Machine learning, Healthcare informatics, Computational Biology, Communications networks (both at hardware and protocol levels), Circuits (including VLSI, analog, low power, etc), Energy systems and technologies, Biomedical electronics and systems, Computer Architecture, signal/image processing, Embedded and control systems.</p>

<p>Application Process</p>

<p>Interested candidates can apply by sending their detailed CV with list of publications clearly mentioning Journal names and citation index with three references through email entitled “Faculty positions at IIIT Allahabad” to faculty.applications@iiita.ac.in. Do not send your applications in any other email addresses. Applications will be considered regularly, hence there is no deadline for applying.</p>

<p>Important Clarifications on Eligibility</p>

<p>A PhD in CS/IT (or other disciplines, as announced) is the minimum expected requirement for an Assistant Professor.</p>

<p>Advertisement: http://iiita.ac.in/pub/Faculty-Position-IIITA1.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r</guid>
	<pubDate>Fri, 13 Aug 2021 07:44:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r</link>
	<title><![CDATA[QuasR: Quantification and annotation of short reads in R]]></title>
	<description><![CDATA[<p>The <em><a href="https://bioconductor.org/packages/3.14/QuasR">QuasR</a></em> package (short for <em>Qu</em>antify and <em>a</em>nnotate <em>s</em>hort reads in <em>R</em>) integrates the functionality of several <strong>R</strong> packages (such as <em><a href="https://bioconductor.org/packages/3.14/IRanges">IRanges</a></em> <span>(Lawrence et al. 2013)</span> and <em><a href="https://bioconductor.org/packages/3.14/Rsamtools">Rsamtools</a></em>) and external software (e.g.&nbsp;<code>bowtie</code>, through the <em><a href="https://bioconductor.org/packages/3.14/Rbowtie">Rbowtie</a></em> package, and <code>HISAT2</code>, through the <em><a href="https://bioconductor.org/packages/3.14/Rhisat2">Rhisat2</a></em> package). The package aims to cover the whole analysis workflow of typical high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single <strong>R</strong> script can contain all steps of a complete analysis, making it simple to document, reproduce or share the workflow containing all relevant details.</p><p>Address of the bookmark: <a href="https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html" rel="nofollow">https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

</channel>
</rss>