<?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/30550?offset=1260</link>
	<atom:link href="https://bioinformaticsonline.com/related/30550?offset=1260" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/22569/reverse-complement-problem-solved-with-perl</guid>
	<pubDate>Tue, 09 Jun 2015 23:37:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/22569/reverse-complement-problem-solved-with-perl</link>
	<title><![CDATA[Reverse Complement Problem Solved with Perl]]></title>
	<description><![CDATA[<p>Question at http://rosalind.info/problems/1b/</p><p>#Find the reverse complement of a DNA string.<br />#Given: A DNA string Pattern.<br />#Return: Pattern, the reverse complement of Pattern.<br /><br />use strict;<br />use warnings;<br /><br />my $string="AAAACCCGGT";<br />my $finalString="";<br />my %hash = (<br />&nbsp;&nbsp; &nbsp;"C" =&gt; "G", <br />&nbsp;&nbsp; &nbsp;"A" =&gt; "T", <br />&nbsp;&nbsp; &nbsp;"T" =&gt; "A", <br />&nbsp;&nbsp; &nbsp;"G" =&gt; "C",<br />);<br /><br />for (my $aa=0; $aa&lt;=(length($string)-1); $aa++) {<br />&nbsp;&nbsp; &nbsp;my $char=substr $string, $aa, 1;<br />&nbsp;&nbsp; &nbsp;#print $hash{$char};<br />&nbsp;&nbsp; &nbsp;$finalString="$hash{$char}"."$finalString";<br />}<br /><br />print $finalString;<br />print "\n";</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38004/vcfr-a-package-to-manipulate-and-visualize-vcf-data-in-r</guid>
	<pubDate>Thu, 25 Oct 2018 09:05:59 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38004/vcfr-a-package-to-manipulate-and-visualize-vcf-data-in-r</link>
	<title><![CDATA[vcfR:  a package to manipulate and visualize VCF data in R]]></title>
	<description><![CDATA[<p><span>VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file or converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and the R environment connecting familiar software with genomic data.</span></p><p>Address of the bookmark: <a href="https://github.com/knausb/vcfR" rel="nofollow">https://github.com/knausb/vcfR</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22580/appointment-of-two-traineeships-and-two-studentships-in-bioinformatics</guid>
  <pubDate>Wed, 10 Jun 2015 10:19:07 -0500</pubDate>
  <link></link>
  <title><![CDATA[Appointment of two traineeships and two studentships in Bioinformatics]]></title>
  <description><![CDATA[
<p>Jawaharlal Nehru<br />TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE<br />An organization under the Kerala State Council for Science, Technology and Environment and<br />National Centre of Excellence, Government of India<br /> <br />Applications are invited for the appointment of two traineeships and two studentships in Bioinformatics for a period of six months sponsored by Department of Biotechnology, Government of India in the Bioinformatics Sub-DIC, Saraswathy Thangavelu Centre, JNTBGRI, Puthenthope, Thiruvananthapuram 695 586. The required qualifications and other details are given below.</p>

<p>Monthly fellowship (in rupee): 5,000/-<br />	<br />Traineeship<br />	<br />First Class M.Sc Bioinformatics/ Biotechnology/ Botany<br />	<br />Studentship: 5,000/-<br />	<br />M.Phil/M.Tech Bioinformatics/ Biotechnology/ any branch of Life Science students for doing their thesis work in the area of Bioinformatics.</p>

<p>Age limit as on 1.1.2015, 28 years. Age relaxation will be provided for SC, ST, OBC candidates as per Govt. norms.</p>

<p>Interested candidates may appear for walk-in-interview on 16th June 2015 at 10.30 am at JNTBGRI, Palode, Thiruvananthapuram. The candidate should report to the Office at Palode before 10.00 am</p>

<p>More at http://www.jntbgri.in/jntbgri/news/File0001.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41487/tinycov-standalone-command-line-utility-written-in-python-to-plot-coverage-from-a-bam-file</guid>
	<pubDate>Mon, 23 Mar 2020 06:22:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41487/tinycov-standalone-command-line-utility-written-in-python-to-plot-coverage-from-a-bam-file</link>
	<title><![CDATA[tinycov: standalone command line utility written in python to plot coverage from a BAM file]]></title>
	<description><![CDATA[<p>Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by&nbsp;<a href="https://github.com/matted/genome_coverage_plotter">Matt Edwards' genome coverage plotter</a>.</p>
<p>To install the stable version:&nbsp;<code>pip3 install --user tinycov</code></p>
<p>To install the development version:</p>
<pre><code>git clone https://github.com/cmdoret/tinycov.git
cd tinycov
pip install .</code></pre><p>Address of the bookmark: <a href="https://github.com/cmdoret/tinycov" rel="nofollow">https://github.com/cmdoret/tinycov</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22778/sr-research-fellow-technical-asst-at-indian-institute-of-maize-research-india</guid>
  <pubDate>Wed, 17 Jun 2015 18:47:51 -0500</pubDate>
  <link></link>
  <title><![CDATA[Sr Research Fellow &amp; Technical Asst at Indian Institute of Maize Research - India]]></title>
  <description><![CDATA[
<p>Indian Institute of Maize Research Jobs 2015 –</p>

<p>Sr Research Fellow &amp; Technical Asst Posts: Indian Institute of Maize Research (IIMR), New Delhi has advertised a notification for the recruitment of Senior Research Fellow &amp; Technical Assistant vacancies for the project titled “Genetic modifications to improve biological nitrogen fixation for augmenting nitrogen needs of cereals” on contractual basis. Eligible candidates may apply in prescribed application format on or before 25-06-2015. Other details like age, educational qualification, selection process, how to apply are given below…</p>

<p>Indian Institute of Maize Research Vacancy Details:<br />Total No. of Posts: 03<br />Name of the Posts :<br />1. Senior Research Fellow: 02 Posts<br />2. Technical Assistant: 01 Post</p>

<p>Age Limit: Candidates age should be 35 years for Senior Research Fellow, Minimum 21 years and maximum 45 years for Technical Assistant as on the closing date of the application. Age relaxation is 5 years to SC/ST and women candidates and 3 years to OBC candidates as per ICAR rules.</p>

<p>Educational Qualification: Candidates should possess Post graduate degree in Biotechnology/ Molecular Biology/ Bioinformatics/ Plant physiology for Senior Research fellow, Graduate degree in Agriculture/ Biotechnology/ any discipline of life sciences for Technical Assistant with relevant experience.</p>

<p>Selection Process: Candidates will be selected based on their performance in interview.</p>

<p>How to Apply: Eligible candidates can send their application in prescribed format along with bio-data to Dr. Pranjal Yadava, Principal Investigator, ICAR Indian Institute of Maize Research, Pusa Campus, New Delhi-110012 or mail to pranjal.yadava@gmail.com on or before 25-06-2015 &amp; attend the interview along with application in the attached format at the time of interview, one passport size photograph, self attested copies of certificates for age, and qualifications, reprints of publications and ‘No Objection Certificate’, original documents on 01-07-2015. Venue details are mentioned below.</p>

<p>Important Dates:<br />Last Date for Receipt of Application: 25-06-2015<br />Date &amp; Time of Interview : 01-07-2015.<br />Venue: IIMR, Pusa Campus, New Delhi</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44284/tools-for-geospatial-data-analysis</guid>
	<pubDate>Wed, 22 Mar 2023 02:10:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44284/tools-for-geospatial-data-analysis</link>
	<title><![CDATA[Tools for Geospatial data analysis !]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Geospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools can help you work with data from a variety of sources, including satellite imagery, GPS data, and other forms of spatial data. They can help you visualize data, perform complex analysis, and even create maps and other visualizations.</p><p>The list includes some of the most popular and widely used geospatial tools available in Python. These tools can help you work with data from a variety of sources and in a variety of formats. Some of the tools are focused on visualization, such as Cartopy, Folium, and Contextily, which allow you to create interactive maps and other visualizations. Other tools are more focused on data manipulation and analysis, such as Fiona, GeoPandas, and Rasterio, which allow you to manipulate and analyze spatial data in a variety of ways.</p><p>The list also includes some tools for working with specific types of geospatial data. For example, the H3 library is designed specifically for working with hexagonal grids, while PySAL is focused on spatial econometrics and spatial analysis. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.</p><p>In summary, this list is an excellent resource for anyone working with geospatial data in Python. It contains a wide range of tools for working with different types of data, and can help you visualize data, perform complex analysis, and create maps and other visualizations. If you're looking to enhance your skills in geospatial analysis, this list is definitely worth checking out.</p></div></div></div><div><p>These tools are:</p><ul>
<li>ArcGIS - <a href="https://lnkd.in/dgC6sKJH" target="_new">https://lnkd.in/dgC6sKJH</a></li>
<li>Cartopy - <a href="https://lnkd.in/dc8ijXRg" target="_new">https://lnkd.in/dc8ijXRg</a></li>
<li>Contextily - <a href="https://lnkd.in/dTdQsmKX" target="_new">https://lnkd.in/dTdQsmKX</a></li>
<li>Descartes - <a href="https://lnkd.in/dCJykxwW" target="_new">https://lnkd.in/dCJykxwW</a></li>
<li>Fiona - <a href="https://lnkd.in/d8sJ3Q5a" target="_new">https://lnkd.in/d8sJ3Q5a</a></li>
<li>Folium - <a href="https://lnkd.in/dfSsE-MB" target="_new">https://lnkd.in/dfSsE-MB</a></li>
<li>GDAL - <a href="https://lnkd.in/dYBJBaAY" target="_new">https://lnkd.in/dYBJBaAY</a></li>
<li>Geohash - <a href="https://lnkd.in/d_NxJ4_M" target="_new">https://lnkd.in/d_NxJ4_M</a></li>
<li>GeoJSON - <a href="https://lnkd.in/daGs2WYq" target="_new">https://lnkd.in/daGs2WYq</a></li>
<li>GeoPandas - <a href="https://lnkd.in/dBTFKKV3" target="_new">https://lnkd.in/dBTFKKV3</a></li>
<li>Geopy - <a href="https://lnkd.in/dfAzR8Xa" target="_new">https://lnkd.in/dfAzR8Xa</a></li>
<li>Gevent - <a href="http://www.gevent.org/" target="_new">http://www.gevent.org</a></li>
<li>H3 - <a href="https://h3geo.org/docs/" target="_new">https://h3geo.org/docs/</a></li>
<li>OSMnx - <a href="https://lnkd.in/dm3pHgUS" target="_new">https://lnkd.in/dm3pHgUS</a></li>
<li>PyQGIS - <a href="https://lnkd.in/dShWyWVr" target="_new">https://lnkd.in/dShWyWVr</a></li>
<li>PySAL - <a href="https://pysal.org/" target="_new">https://pysal.org</a></li>
<li>Pydeck - <a href="https://lnkd.in/dGBFu-iw" target="_new">https://lnkd.in/dGBFu-iw</a></li>
<li>Pyproj - <a href="https://lnkd.in/dNG9fdkm" target="_new">https://lnkd.in/dNG9fdkm</a></li>
<li>RTree - <a href="https://lnkd.in/dURMiYpU" target="_new">https://lnkd.in/dURMiYpU</a></li>
<li>Rasterio - <a href="https://lnkd.in/dEMC6ve6" target="_new">https://lnkd.in/dEMC6ve6</a></li>
<li>Scikit-mobility - <a href="https://lnkd.in/dpHhaX2J" target="_new">https://lnkd.in/dpHhaX2J</a></li>
<li>Shapely - <a href="https://lnkd.in/d568datK" target="_new">https://lnkd.in/d568datK</a></li>
</ul><p>These tools offer a wide range of capabilities for working with geospatial data, from visualizing and manipulating data to performing complex analysis and modeling. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.</p></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22787/senior-technical-assistant-at-pondicherry-university</guid>
  <pubDate>Wed, 17 Jun 2015 20:46:12 -0500</pubDate>
  <link></link>
  <title><![CDATA[Senior Technical Assistant at Pondicherry University]]></title>
  <description><![CDATA[
<p>Senior Technical Assistant</p>

<p>Eligibility : BE/B.Tech(CSE, ECE, IT)</p>

<p>Location : Pondicherry</p>

<p>Last Date : 26 Jun 2015</p>

<p>Hiring Process : Face to Face Interview<br />Pondicherry University - Job DetailsDate of posting:19 May 15</p>

<p>Senior Technical Assistant Job position in Pondicherry University on temporary basis  </p>

<p>Project Title : "Bioinformatics National Certification (BINC) for certifying quality human resource in Bioinformatics"</p>

<p>Qualification : i) B.E/ B.Tech Computer Science/ Electronics &amp; Communication Engineering/ Information Technology with 55% or equivalent marks. ii) One year Experience in relevant field in Government/ Public Sector or reputed Private Organizations. Desirable : Working experience in JSP and ASP/PHP</p>

<p>No. of Post : 01</p>

<p>Department : Biotechnology</p>

<p>Pay : Rs. 27,800/- </p>

<p>Age Limit : 30 Yrs<br />How to apply</p>

<p>Both above-mentioned posts are purely on temporary basis, extended by one year based on performance and will be terminated with the completion of BINC Program at Pondicherry University. Interested Candidates may send their application in the prescribed format with self-attested copies of all mark sheets and certificates to Dr. Basant K. Tiwary, Coordinator (BINC), Centre for Bioinformatics, Pondicherry University, Puducherry-605 014 before June 26, 2015.</p>

<p>Click Here http://www.pondiuni.edu.in/news/requirement-post-one-senior-technical-assistant-one-computer-assistant-–-dept-biotechnologygove</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34172/orthodotter-synteny-plots-oxford-grid</guid>
	<pubDate>Wed, 09 Aug 2017 07:16:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34172/orthodotter-synteny-plots-oxford-grid</link>
	<title><![CDATA[orthodotter: Synteny plots (oxford grid)]]></title>
	<description><![CDATA[<pre><code>orthodotter -h
--------------------------------------------------------------------------------
orthodotter - Plot orthologous genes on an oxford grid.
       -f &lt;file&gt;     : input file, containing orthologous genes, default is stdin
                       species chr-name start end species chr-name start end
       -toPlot &lt;arg&gt; : give the x and y sets and the color separated by double-dots,
                       for example set1:set2:red will plot set1 on x, set2 on y with
                       red points. Could give several -toPlot arguments.
                       To launch the clustering of dots, use extra-option 1=dist,min_nb_genes
                       where dist is the minimal distance (euclidian) between two points and min_nb_genes the minimal
                       number of genes in a cluster to be valid.
       -o &lt;file&gt;     : output file, default is stdout
       -x &lt;int&gt;      : resolution of x axis, default is 600
       -y &lt;int&gt;      : resolution on y axis, default is 600
       -r &lt;int&gt;      : radius of circle representing orthologous genes
       -format       : could be png, gif, jpg, pdf or ps. Default is png.
       -fg           : foreground color, default is black
       -bg           : background color, default is transparent
       -fSize &lt;int&gt;  : fontSize, default is 1
       -filter       : check chromosome names
       -h            : help
--------------------------------------------------------------------------------
orthodotter -f Vigne_Banane.ortho -toPlot Vigne:Banane:black:1=10,5 -x 1200 -y 1200 -bg white -o Vigne_vs_Banane.png &gt; Vigne_vs_Banane.clusters
--------------------------------------------------------------------------------</code></pre><p>Address of the bookmark: <a href="https://github.com/institut-de-genomique/orthodotter" rel="nofollow">https://github.com/institut-de-genomique/orthodotter</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/poll/view/22920/how-long-have-you-been-a-bioinformatics-scientist-for</guid>
	<pubDate>Tue, 23 Jun 2015 10:55:33 -0500</pubDate>
	<link>https://bioinformaticsonline.com/poll/view/22920/how-long-have-you-been-a-bioinformatics-scientist-for</link>
	<title><![CDATA[How long have you been a bioinformatics scientist for?]]></title>
	<description><![CDATA[<p>Most of the researcher have been a scientist whole life, but infact they actually started paying&nbsp; it with at certain time.So, how long have you been in bioinformatics domain now?</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34038/quota-synteny-alignment</guid>
	<pubDate>Mon, 31 Jul 2017 04:11:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34038/quota-synteny-alignment</link>
	<title><![CDATA[Quota synteny alignment]]></title>
	<description><![CDATA[<p><span>Typically in comparative genomics, we can identify anchors, chain them into syntenic blocks and interpret these blocks as derived from a common descent. However, when comparing two genomes undergone ancient genome duplications (plant genomes in particular), we have large number of blocks that are not orthologous, but are paralogous. This has forced us sometimes to use&nbsp;</span><em>ad-hoc</em><span>&nbsp;rules to screen these blocks. So the question is:&nbsp;</span><span>given the expected depth (quota) along both x- and y-axis, select a subset of the anchors with maximized total score</span><span>.</span></p><p>Address of the bookmark: <a href="https://github.com/tanghaibao/quota-alignment" rel="nofollow">https://github.com/tanghaibao/quota-alignment</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

</channel>
</rss>