<?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/26972?offset=1080</link>
	<atom:link href="https://bioinformaticsonline.com/related/26972?offset=1080" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/38815/research-opening-ibab-bengaluru</guid>
  <pubDate>Mon, 28 Jan 2019 17:45:54 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research opening @ IBAB, Bengaluru]]></title>
  <description><![CDATA[
<p>Applications are invited for the position of Project Assistant in Bio-IT centre at IBAB, Electronic city, Bengaluru. The successful candidate will work in the next-generation sequencing (NGS) facility to perform nucleic acid isolations, quality and quantity analyses, NGS library preparations, and maintenance of sequencing related instruments and other related lab equipment. In addition, the candidate is expected to assist in various administrative matters including procurement, maintaining inventory of laboratory consumables etc. The person will have opportunity to get expertise in entire pipeline of NGS. After sufficient training, the person will act as a demonstrator in the workshops conducted by Bio-IT centre.<br />Essential Qualifications, Experiences, and Skills:</p>

<p>1. MSc. or B. Tech. or equivalent degree in Biotechnology or related life sciences discipline.<br />2. Strong aptitude for laboratory work and should be detail-oriented person.<br />3. Hands-on experience in basic molecular biology techniques.<br />4. Prior experience in working in a research laboratory or industry.<br />5. Basic IT skills that include familiarity with Microsoft Office packages.<br />6. Ability to carry out basic maintenance of general lab equipments and laboratory resources.<br />7. Ability to maintain accurate records of laboratory work.<br />8. Willingness to learn, and should be a team player.<br />Desirable Experience and Skills:<br />1. Familiarity with NGS technology.<br />2. Experience in preparation of NGS libraries.<br />3. Familiarity with Sanger sequencing technology (capillary electrophoresis based)</p>

<p>Remuneration: Remuneration will commensurate with expertise and experience.</p>

<p>How to Apply: Interested applicants fulfilling the criteria may send their detailed CV and a cover letter that explains their suitability for this position, in a single PDF, to Dr. Sreekanth Reddy at careers_bioit@ibab.ac.in. Last date for submission of application is 23rd February 2019. Please mention the position applying for in the subject line of the email.</p>

<p>About IBAB: The Bio-IT Centre at IBAB has state-of-art sequencing facility with the HiSeq 2500 and accessories such as Qubit, Covaris, Agilent 2200 TapeStation, Stratagene Mx 3000 for next generation sequencing, 3500 Dx Genetic Analyzer for capillary electrophoresis based sequencing, and HiScan for microarray imaging. The facility is fully operational and providing services to the scientific community. The Institute of Bioinformatics and Applied Biotechnology (IBAB) is a unique institute engaged in education, research and entrepreneur support programs and is based at Electronic City, Bangalore. IBAB’s mission is to catalyze the growth of the biotechnology and bioinformatics industries in India. To know more please visit: http://www.ibab.ac.in/index.php/bioit/</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/9039/postdoc-position-in-computational-biology</guid>
  <pubDate>Fri, 14 Mar 2014 01:38:49 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoc Position in Computational Biology]]></title>
  <description><![CDATA[
<p>The Computational Biology Group of Interdisciplinary Center for<br />Clinical Research (IZKF) Aachen, RWTH Aachen University Hospital,<br />Aachen, invites applicants for PhD candidate or postdoctoral position<br />in computational biology in one of the following topics:</p>

<p>1) Statistical machine learning methods for the analysis of medical<br />epigenomics data.</p>

<p>2) Sequence analysis algorithms for detection of RNA-DNA interactions.</p>

<p>Applicants should hold a M.Sc . or PhD in Computer Science or related<br />areas. Experience in the analysis of biological sequences, gene<br />expression and gene regulation is desirable. The candidate should have<br />solid programming skills (C, Python and/or R) and acquaintance with<br />Linux. Experience with high performance computing is a plus. The<br />working language of the group is English.</p>

<p>The position is based on the German TV-L 13 salary scale, including<br />all German social benefits (health insurance and pension scheme). The<br />expected starting date is September 2014. Interested candidates should<br />send a CV, statement of research interests and the names of three<br />references to jobs@costalab.org.</p>

<p>More at http://costalab.org/wp/phd-and-postdoc-position-in-computational-biology/</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42418/scientist-b-bioinformatics-at-aiims-delhi</guid>
  <pubDate>Sun, 20 Dec 2020 04:34:55 -0600</pubDate>
  <link></link>
  <title><![CDATA[Scientist-B (Bioinformatics) at AIIMS, Delhi]]></title>
  <description><![CDATA[
<p>Name of the Project: “Artificial intelligence in Oncology, Harnessing big data and advanced computing to provide personalized diagnosis and treatment for Cancer patients”</p>

<p>Age Limit: 35</p>

<p>How to Apply for the AIIMS Life Science Job:</p>

<p>Interested applicants are asked to send out a detailed CV to Dr Ashok Sharma (aioncoaiims@gmail.com). Laboratory of Chromatin and also Cancer Epigenetics, Department of Biochemistry with the subject line “Application for Scientist-B position for MeitY project” latest by January 01st, 2021.<br />Complete Information of the year of passing, experience, marks, etc. ought to be mentioned in the CV Incomplete. applications will certainly be rejected Just shortlisted applicants will be called for interview. Chosen candidates will certainly be intimated by email/phone.<br />No TA/DA will certainly be paid for appearing in the interview.<br />Note, The institute reserved the right to fill up or not to fill up the post advertised.</p>

<p>Emoluments: Rs. 56,000/- plus 24 percent HRA</p>

<p>Eligibility:<br />2nd class Master’s Degree with a PhD in a pertinent subject (Bioinformatics) from.a recognized University<br />1st class Master’s degree in Life Sciences (Bioinformatics) from a recognized university OR.<br />Bachelor’s Degree in Engineering or-Technology with minimal 60% marks from a recognized University or equivalent.</p>

<p>Desirable Qualifications:<br />Experience in Bioinformatics/NGS data. Analysis/System Biology/Computer Science/ statistics with experience in Machine learning/Al project.<br />Experience of Deep learning applications in biological data ( image/text).<br />Proficient in Rf Python machine learning libraries.<br />Prior experience in the cancer-related project (ML-based) will be advantageous.<br />Experience with PyTorch/TensorFlow will certainly be very desirable.<br />Applicant should have strong scientific writing as well as. verbal abilities.<br />Papers in sci-indexed journals demonstrating ML skill sets.<br />Database handling will certainly be plus yet not required.</p>

<p>More detail at https://www.aiims.edu/images/pdf/recruitment/advertisement/biochem-16-12-20.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/fun/view/9207/biogeek-fun</guid>
	<pubDate>Sun, 16 Mar 2014 06:33:31 -0500</pubDate>
	<link>https://bioinformaticsonline.com/fun/view/9207/biogeek-fun</link>
	<title><![CDATA[BioGeek Fun]]></title>
	<description><![CDATA[<p>1. A futuristic computational biology student was told to write "It is in my gene!!!" on the board 100 times as a punishment. here's his response -<br /><br />use warnings;<br />for ($count=1; $count &lt;=100; $count++) { print "It is in my gene!!!";}<br /><br />I guess, he is gonna to be a real biogeek. Nice try though. Smart kid.</p><p>&nbsp;</p><p>2. In some perl script I found this <br />&nbsp;. . . . . .<br />&nbsp;. . . . . .<br /># It works for me, only God understood how it is working<br />while (/(&lt;\/[^&gt;]+&gt;)|(&lt;[^&gt;]+&gt;)|(&lt;[^&gt;]+&gt;)$|([^&gt;&lt;]+)/go) {<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $startGene=$1;<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $beginChromosome=$2;<br />&nbsp;&nbsp; &nbsp;<br />. . . . . .<br />&nbsp;.. . . . . .<br />}</p><p>&nbsp;</p><p>3. One more interesting message in Perl found &hellip;. It will must tickle you bone :) <br />open(my $fh, "&lt;", "gene.txt")&nbsp;&nbsp; &nbsp;or kill " Me if you think this is a mistake :$!";<br /><br /></p><p>&nbsp;</p><p>4. From the Perl <br /><br />&nbsp; while () {&nbsp; # "The Mothership Connection is here!"<br />&nbsp;&nbsp; &nbsp;print &ldquo;$_\n&rdquo;; # Printing the offspring :)</p><p>&nbsp;</p><p>5. Perl message<br />if ($1) { print &ldquo;Just found a the error in chromosome !!!, yahoo&hellip;&rdquo;; else { &ldquo;That is not error, but mutation you moron!&rdquo;;</p><p>&nbsp;</p><p>6. One genome database curator walk in wine bar asked the bartender:<br />CREATE TABLE gene IF NOT EXISTS SexOnTheBeach;</p>]]></description>
	<dc:creator>Jit</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/researchlabs/view/9327/jarvis%E2%80%99-laboratory</guid>
  <pubDate>Tue, 18 Mar 2014 18:53:47 -0500</pubDate>
  <link></link>
  <title><![CDATA[Jarvis’ laboratory]]></title>
  <description><![CDATA[
<p>Dr. Jarvis’ laboratory studies the neurobiology of vocal communication. We want to know how the brain generates, perceives, and learns behavior. We use vocal communication as a model behavior. Emphasis is placed on the molecular pathways involved in the perception and production of learned vocalizations. We use an integrative approach that combines behavioral, anatomical, electrophysiological, and molecular biological techniques. The main animal model used is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations. The overall goal of the research is to advance knowledge of the neural mechanisms for vocal learning and basic mechanisms of brain function.</p>

<p>Lab page: http://jarvislab.net/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43892/choosing-the-right-ngs-sequencing-instrument-for-your-study</guid>
	<pubDate>Wed, 15 Jun 2022 00:37:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43892/choosing-the-right-ngs-sequencing-instrument-for-your-study</link>
	<title><![CDATA[Choosing the Right NGS Sequencing Instrument for Your Study]]></title>
	<description><![CDATA[<p>The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared metrics for each of the instruments available. If you&rsquo;re new to high-throughput sequencing and have questions about how you should design your sequencing run, fill out our&nbsp;<a href="https://genohub.com/ngs-consultation/"><span>free consultation form</span></a>&nbsp;and we'll get in touch with you to help.</p>
<p>More at&nbsp;https://genohub.com/ngs-instrument-guide/</p><p>Address of the bookmark: <a href="https://genohub.com/ngs-instrument-guide/" rel="nofollow">https://genohub.com/ngs-instrument-guide/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/9518/professor-and-associate-professors-pb-iv-assistant-professors-pb-iii-job-at-iiit-allahabad</guid>
  <pubDate>Mon, 31 Mar 2014 08:09:07 -0500</pubDate>
  <link></link>
  <title><![CDATA[Professor and Associate Professors (PB-IV) Assistant Professors (PB-III) Job at IIIT, Allahabad]]></title>
  <description><![CDATA[
<p>Indian Institute of Information Technology, Allahabad <br />Devghat, Jhalwa, Allahabad – 211012, Uttar Pradesh, India <br />E-mail: contact@iiita.ac.in, faculty.applications@iiita.ac.in <br />Web: www.iiita.ac.in Phone : 0532-2922031/27/67 </p>

<p>Applications are invited on prescribed format along with self attested copies of the certificates for Faculty Positions in the following areas:  <br />Sciences – Systems Biology, Computer Aided Drug Designing, Statistics, Applied Mathematics, Applied Physics. BioMedical Engineering – BioMechanics, BioMedical Instrumentation.  </p>

<p> Last Date : May 10, 2014 </p>

<p>Details are available on our website : http://www.iiita.ac.in</p>

<p>http://www.iiita.ac.in/downloads/announcements/uploads/FACULTY_Advertisement_NO-FS-01_2014130.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44229/common-steps-for-reads-mapping</guid>
	<pubDate>Thu, 09 Mar 2023 02:48:02 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44229/common-steps-for-reads-mapping</link>
	<title><![CDATA[Common steps for reads mapping !]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Mapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis. Here are some general steps to follow for mapping reads to a genome:</p><ol>
<li>
<p>Choose a read mapper: There are many read mappers available, such as BWA, Bowtie, and HISAT2. Choose a mapper that is appropriate for your type of data and research question.</p>
</li>
<li>
<p>Index the reference genome: Before mapping reads, the reference genome needs to be indexed. This involves creating an index of the genome sequence that allows the mapper to quickly find matches to the reads. Most mappers have their own indexing tools.</p>
</li>
<li>
<p>Prepare the read data: The reads should be in a format that is compatible with the mapper. Most mappers accept FASTQ or BAM files. Depending on the quality of the data, it may need to be filtered or trimmed before mapping.</p>
</li>
<li>
<p>Run the mapper: The mapper is run with the command-line interface or using a graphical user interface. The specific command depends on the mapper being used, but typically involves specifying the input data, reference genome, and output file format.</p>
</li>
<li>
<p>Evaluate the mapping results: After the mapping is complete, the results should be evaluated. This includes assessing the quality of the mapping, such as the mapping rate, the number of mapped reads, and the mapping quality score.</p>
</li>
<li>
<p>Post-processing: Depending on the analysis being performed, post-processing of the mapped reads may be necessary. This can include filtering reads based on quality, removing duplicate reads, and calling variants.</p>
</li>
</ol><p>Overall, mapping reads to a reference genome is a complex process that requires careful consideration of the type of data, the research question, and the specific mapper being used.</p></div></div></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/9639/find-certain-filesdocuments-in-linux-os</guid>
	<pubDate>Sun, 06 Apr 2014 23:56:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/9639/find-certain-filesdocuments-in-linux-os</link>
	<title><![CDATA[Find certain files/documents in Linux OS]]></title>
	<description><![CDATA[<p>As bioinformatician I know the fact that we usually handle the large dataset and lost in the huge numbers of files and folders. In order to search the missing file a strong search command is required. The Linux Find Command is one of the most important and much used command in Linux sytems. Find command used to search and locate list of files and directories based on conditions you specify for files that match the arguments. Find can be used in variety of conditions like you can find files by permissions, users, groups, file type, date, size and other possible criteria.<br /><br />Through this article we are sharing our day-to-day Linux find command experience and its usage in the form of examples. In this article we will show you the most used 35 Find Commands examples in Linux. We have divided the section into Five parts from basic to advance usage of find command.</p><p><strong>Part I &ndash; Basic Find Commands for Finding Files with Names</strong><br />1. Find Files Using Name in Current Directory<br /><br />Find all the files whose name is gene.txt in a current working directory.<br /><br /># find . -name gene.txt<br /><br />./gene.txt<br /><br />2. Find Files Under Home Directory<br /><br />Find all the files under /home directory with name gene.txt.<br /><br /># find /home -name gene.txt<br /><br />/home/gene.txt<br /><br />3. Find Files Using Name and Ignoring Case<br /><br />Find all the files whose name is gene.txt and contains both capital and small letters in /home directory.<br /><br /># find /home -iname gene.txt<br /><br />./gene.txt<br />./Gene.txt<br /><br />4. Find Directories Using Name<br /><br />Find all directories whose name is Gene in / directory.<br /><br /># find / -type d -name Gene<br /><br />/Gene<br /><br />5. Find fasta Files Using Name<br /><br />Find all php files whose name is gene.fasta in a current working directory.<br /><br /># find . -type f -name gene.fasta<br /><br />./gene.fasta<br /><br />6. Find all PHP Files in Directory<br /><br />Find all fasta files in a directory.<br /><br /># find . -type f -name "*.fasta"<br /><br />./gene.fasta<br />./cancer.fasta<br />./allgene.fasta<br /><br /><strong>Part II &ndash; Find Files Based on their Permissions</strong><br />7. Find Files With 777 Permissions<br /><br />Find all the files whose permissions are 777.<br /><br /># find . -type f -perm 0777 -print<br /><br />8. Find Files Without 777 Permissions<br /><br />Find all the files without permission 777.<br /><br /># find / -type f ! -perm 777<br /><br />9. Find SGID Files with 644 Permissions<br /><br />Find all the SGID bit files whose permissions set to 644.<br /><br /># find / -perm 2644<br /><br />10. Find Sticky Bit Files with 551 Permissions<br /><br />Find all the Sticky Bit set files whose permission are 551.<br /><br /># find / -perm 1551<br /><br />11. Find SUID Files<br /><br />Find all SUID set files.<br /><br /># find / -perm /u=s<br /><br />12. Find SGID Files<br /><br />Find all SGID set files.<br /><br /># find / -perm /g+s<br /><br />13. Find Read Only Files<br /><br />Find all Read Only files.<br /><br /># find / -perm /u=r<br /><br />14. Find Executable Files<br /><br />Find all Executable files.<br /><br /># find / -perm /a=x<br /><br />15. Find Files with 777 Permissions and Chmod to 644<br /><br />Find all 777 permission files and use chmod command to set permissions to 644.<br /><br /># find / -type f -perm 0777 -print -exec chmod 644 {} \;<br /><br />16. Find Directories with 777 Permissions and Chmod to 755<br /><br />Find all 777 permission directories and use chmod command to set permissions to 755.<br /><br /># find / -type d -perm 777 -print -exec chmod 755 {} \;<br /><br />17. Find and remove single File<br /><br />To find a single file called gene.txt and remove it.<br /><br /># find . -type f -name "gene.txt" -exec rm -f {} \;<br /><br />18. Find and remove Multiple File<br /><br />To find and remove multiple files such as .fa or .gb, then use.<br /><br /># find . -type f -name "*.fa" -exec rm -f {} \;<br /><br />OR<br /><br /># find . -type f -name "*.gb" -exec rm -f {} \;<br /><br />19. Find all Empty Files<br /><br />To file all empty files under certain path.<br /><br /># find /tmp -type f -empty<br /><br />20. Find all Empty Directories<br /><br />To file all empty directories under certain path.<br /><br /># find /tmp -type d -empty<br /><br />21. File all Hidden Files<br /><br />To find all hidden files, use below command.<br /><br /># find /tmp -type f -name ".*"<br /><br /><strong>Part III &ndash; Search Files Based On Owners and Groups</strong><br />22. Find Single File Based on User<br /><br />To find all or single file called gene.txt under / root directory of owner root.<br /><br /># find / -user root -name gene.txt<br /><br />23. Find all Files Based on User<br /><br />To find all files that belongs to user Rahul under /home directory.<br /><br /># find /home -user rahul<br /><br />24. Find all Files Based on Group<br /><br />To find all files that belongs to group Developer under /home directory.<br /><br /># find /home -group developer<br /><br />25. Find Particular Files of User<br /><br />To find all .txt files of user Rahul under /home directory.<br /><br /># find /home -user rahul -iname "*.txt"<br /><br /><strong>Part IV &ndash; Find Files and Directories Based on Date and Time</strong><br />26. Find Last 50 Days Modified Files<br /><br />To find all the files which are modified 50 days back.<br /><br /># find / -mtime 50<br /><br />27. Find Last 50 Days Accessed Files<br /><br />To find all the files which are accessed 50 days back.<br /><br /># find / -atime 50<br /><br />28. Find Last 50-100 Days Modified Files<br /><br />To find all the files which are modified more than 50 days back and less than 100 days.<br /><br /># find / -mtime +50 &ndash;mtime -100<br /><br />29. Find Changed Files in Last 1 Hour<br /><br />To find all the files which are changed in last 1 hour.<br /><br /># find / -cmin -60<br /><br />30. Find Modified Files in Last 1 Hour<br /><br />To find all the files which are modified in last 1 hour.<br /><br /># find / -mmin -60<br /><br />31. Find Accessed Files in Last 1 Hour<br /><br />To find all the files which are accessed in last 1 hour.<br /><br /># find / -amin -60<br /><br /><strong>Part V &ndash; Find Files and Directories Based on Size</strong><br />32. Find 50MB Files<br /><br />To find all 50MB files, use.<br /><br /># find / -size 50M<br /><br />33. Find Size between 50MB &ndash; 100MB<br /><br />To find all the files which are greater than 50MB and less than 100MB.<br /><br /># find / -size +50M -size -100M<br /><br />34. Find and Delete 100MB Files<br /><br />To find all 100MB files and delete them using one single command.<br /><br /># find / -size +100M -exec rm -rf {} \;<br /><br />35. Find Specific Files and Delete<br /><br />Find all .gb files with more than 10MB and delete them using one single command.<br /><br /># find / -type f -name *.gb -size +10M -exec rm {} \;</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

</channel>
</rss>