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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/26380?offset=240</link>
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	<description><![CDATA[]]></description>
	
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4081/csir-institute-of-genomics-integrative-biology</guid>
  <pubDate>Thu, 29 Aug 2013 05:22:03 -0500</pubDate>
  <link></link>
  <title><![CDATA[CSIR-INSTITUTE OF GENOMICS &amp; INTEGRATIVE BIOLOGY]]></title>
  <description><![CDATA[
<p>CSIR-INSTITUTE OF GENOMICS &amp; INTEGRATIVE BIOLOGY, Mall Road, Delhi 110007</p>

<p>POSITIONS OPEN FOR TEMPORARY RESEARCH PROJECT POSTS</p>

<p>(Date of interview 23rd September 2013 at 10:30 AM)</p>

<p>CSIR-Institute of Genomics &amp; Integrative Biology (IGIB), desires to engage qualified incumbents on purely temporary basis as detailed below:</p>

<p>Project Code/Title (Project Code BSC0123)</p>

<p>Genome dynamics in Cellular Organization, Differentiation and Enantiostasis (GENCODE)</p>

<p>Project Fellow<br />	<br />First Class M.Sc./M.Tech in bioinformatics/Human Genetics/Genomics</p>

<p>Rs. 16,000/- + 30 % HRA per month</p>

<p>Sr. Project Fellow	</p>

<p>First Class M.Sc./M.Tech in bioinformatics/Human Genetics/Genomics</p>

<p>With two years of experience in NGS data analysis.</p>

<p>Rs. 18,000/- + 30 % HRA per month</p>

<p>Age relaxation as per Govt. of India instructions.</p>

<p>Engagement is for the project and on behalf of the funding agency and the tenure shall be as mentioned above. The duration of the post is initially for One year or till the closing date of the project, whichever is earlier. Tenure may be extendable up to project duration. Contract may be terminated at any time by giving one-month notice by either side. The applicants will have no claim implicit or explicit for consideration against any CSIR/IGIB post.</p>

<p>How to Apply:</p>

<p>It is mandatory for eligible applicants to apply by both the processes as given below:</p>

<p>1.    Sending the resume in MS Word format directly to hrd@igib.res.in (Mentioning the Project Code-Post Code in the Subject Line of the email example:GAP0059-1)</p>

<p>2.    They also need to fill up proforma by clicking on the following link HR Online Form.</p>

<p>3.    Candidate cannot apply for more than two posts.</p>

<p>Last date of receiving application is 02-09-2013.</p>

<p>No application would be entertained with result awaited status or after due date.</p>

<p>The email will be sent to the short listed candidates.</p>

<p>No TA/DA will be paid to the candidates to attend the interview. The engagement shall be as per guidelines of CSIR/Funding agency. Candidates will have an option to give reply in Hindi.</p>

<p>Note: The shortlisted candidates, who will receive the email for interview, have to report at 09:00 AM on the day of interview along with any Photo ID card and original certificates for entry purpose. Entry will be closed by 10:00 AM.</p>

<p>More @ http://www.igib.res.in/sites/default/files/23092013.htm</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/39612/bioclues-and-pine-biotech-join-forces-to-advance-bioinformatics-in-india</guid>
	<pubDate>Fri, 14 Jun 2019 10:20:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/39612/bioclues-and-pine-biotech-join-forces-to-advance-bioinformatics-in-india</link>
	<title><![CDATA[Bioclues and Pine Biotech join forces to advance Bioinformatics in India]]></title>
	<description><![CDATA[<p><img src="https://edu.t-bio.info/wp-content/uploads/2019/06/PineBio-Bioclues.jpg" alt="Bioclues and Pine Biotech join forces" width="1280" height="720" style="border: 0px; border: 0px;">&nbsp;As a collaborative effort, the two organizations will help implement best practices in bioinformatics education across universities in Inida that have little to no experience in bioinformatics. The collaboration comes as Pine Biotech starts registrations for it's pilot program at Amity University in Kolkata, India.</p><p>To read more about this collaboration, visit:&nbsp;https://edu.t-bio.info/pine-biotech-joins-forces-with-the-bioclues-organization-to-promote-bioinformatics/</p>]]></description>
	<dc:creator>eliabrodsky</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/3013/python-and-biopython-tutorial</guid>
	<pubDate>Fri, 23 Aug 2013 06:47:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/3013/python-and-biopython-tutorial</link>
	<title><![CDATA[Python and BioPython Tutorial]]></title>
	<description><![CDATA[<p>A quickstart tutorial that allows to become familiar with the Python language. The exercises expect knowledge of basic concepts of programming. A group of 2nd year computer science students with no previous Python knowledge required 60'-90' to complete the exercises. With about 3 hours time, the exercise is suitable for non-programmers as well.</p><p>Address of the bookmark: <a href="http://www.biotnet.org/training-materials/python-programmers" rel="nofollow">http://www.biotnet.org/training-materials/python-programmers</a></p>]]></description>
	<dc:creator>Manshi Raghubanshi</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/40881/liu-lab</guid>
  <pubDate>Tue, 04 Feb 2020 06:27:02 -0600</pubDate>
  <link></link>
  <title><![CDATA[Liu Lab]]></title>
  <description><![CDATA[
<p>Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.</p>

<p>https://liulab-dfci.github.io/software/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/3967/research-project-posts-for-csir-project-delhi</guid>
  <pubDate>Tue, 27 Aug 2013 04:31:41 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Project Posts for CSIR Project, Delhi]]></title>
  <description><![CDATA[
<p>Positions Open For Temporary Research Project Posts for CSIR Project, Delhi<br />CSIR is looking for bright young candidates to get involved in building algorithms and platforms for large biological data analyses in the areas of comparative genomics, computational workflows, disease association studies, simulating virtual organelles, etc. Anyone who fulfills the eligibility criteria mentioned below may appear for a walk-in interview on 3rd September 2013 at CSIR Headquarters, Anusandhan Bhawan, 2 Rafi Marg, Delhi – 110001.<br />you can go to link for details or download PDF</p>

<p>http://www.csir.res.in/External/Heads/aboutcsir/announcements/ProjectPost_130813.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41394/ngsymposium-in-computational-biology</guid>
  <pubDate>Mon, 09 Mar 2020 06:00:30 -0500</pubDate>
  <link></link>
  <title><![CDATA[NGSymposium in Computational Biology]]></title>
  <description><![CDATA[
<p>We have a great pleasure to invite you to the NGSymposium in Computational Biology to celebrate the 5th anniversary of the NGSchool Summer Schools. This international conference will make way for exchanging knowledge and experiences between experienced and early-stage researchers as well as bioinformaticians. The meeting will be held on 31.07 - 1.08.2020 in Warsaw. It will be a satellite event to the #NGSchool2020: Statistical Learning in Genomics. It will cover a wide range of topics from basic and applied biomedical sciences: bioinformatics, genomics, transcriptomics, computational biology, Machine Learning.</p>

<p>Registration of active participants will be open from February, 27 12 PM CET to April 17, 23:59 CET. In registration forms you will be asked for providing us with some basic information about yourself. You will also be able to submit your abstract. You can save your registration form after filling it partially and come back later to supply more data e.g. upload an abstract. Your registration will be completed only with the payment of the registration fee reaching our accounts - please make sure to transfer the money in advance!</p>

<p>Registration of passive participants will be open after closing of registration of active participants.</p>

<p>Details an registration: https://ngschool.eu/conference/</p>
]]></description>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials</guid>
	<pubDate>Thu, 29 Aug 2013 09:23:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials</link>
	<title><![CDATA[Bioinformatics Algorithm Demonstrations and Tutorials]]></title>
	<description><![CDATA[<p>Abstract</p>
<p>This project presents demonstrations of selected computer science algorithms important in&nbsp;bioinformatics, implemented in the spreadsheet program Microsoft Excel. Spreadsheets provide an&nbsp;interesting platform for demonstration of algorithms, since various steps of the calculations can be&nbsp;exposed in a manner that is easily comprehensible to users with little programming experience. The&nbsp;algorithms demonstrated include two approaches to approximate string matching (dynamic programming&nbsp;and Shift-AND numeric approximate matching), Hierarchical Clustering (used in phylogenetic studies&nbsp;and microarray analysis of gene expression), a Naive Bayes Classifier for simulated microarray gene&nbsp;expression data, and a simple Neural Network. These demonstrations are designed to serve as&nbsp;instructional aids in bioinformatics courses.</p>
<p>Tutorial @&nbsp;http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsInExcel.zip</p>
<p>One of the best resource for online bioinformatics learning is https://stepic.org/Bioinformatics-Algorithms-2 Enjoy the online learning.</p>
<p>Reference :&nbsp;cybertory</p>
<blockquote>
<p><span>" Please add your favourite bioinformatics algorithms and tutorial links below in the comment section, for the benefit of bioinformatics and computational biology community ".&nbsp;</span></p>
</blockquote><p>Address of the bookmark: <a href="http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsExcelDoc.pdf" rel="nofollow">http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsExcelDoc.pdf</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools</guid>
	<pubDate>Tue, 27 Oct 2020 19:42:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools</link>
	<title><![CDATA[Frequent parameters for bioinformatics tools !]]></title>
	<description><![CDATA[<div><div>Third party executable parameters and options.</div><div>&nbsp;</div><div>Trimmomatic</div><div>&nbsp;</div><div>&ldquo;ILLUMINACLIP:...:2:30:10&rdquo;</div><div>&ldquo;LEADING:15&rdquo;</div><div>&ldquo;TRAILING:15&rdquo;</div><div>&ldquo;SLIDINGWINDOW:4:20&rdquo;</div><div>&ldquo;MINLEN:20&rdquo;</div><div>&ldquo;TOPHRED33&rdquo;</div><div>&nbsp;</div><div>Filtlong</div><div>--min_length 500</div><div>--min_mean_q 85</div><div>--min_window_q 65</div><div>&nbsp;</div><div>FastQ Screen</div><div>--aligner bowtie2' (bwa for PacBio)</div><div>--subset 1000 (for PacBio)</div><div>&nbsp;</div><div>SPAdes</div><div>--careful</div><div>--disable-gzip-output</div><div>--cov-cutoff auto</div><div>--phred-offset 33</div><div>&nbsp;</div><div>HGAP</div><div>Pbalign.task_options.min_accuracy: 70</div><div>Pbalign.task_options.no_split_subreads: false</div><div>Genomic_consensus.task_options.min_confidence: 40</div><div>falcon_ns.task_options.HGAP_GenomeLength_str:</div><div>6000000</div><div>Pbcoretools.task_options.read_length: 0</div><div>Genomic_consensus.task_options.use_score: 0</div><div>Pbalign.task_options.min_length: 50</div><div>Pbalign.task_options.algorithm_options: --minMatch 12</div><div>--bestn 10 --minPctSimilarity 70.0</div><div>Pbalign.task_options.hit_policy: randombest</div><div>Pbcoretools.task_options.other_filters: rq &gt;= 0.7</div><div>Pbalign.task_options.concordant: false</div><div>Genomic_consensus.task_options.min_coverage: 5</div><div>falcon_ns.task_options.HGAP_SeedCoverage_str: 30</div><div>falcon_ns.task_options.HGAP_AggressiveAsm_bool: false</div><div>Genomic_consensus.task_options.algorithm: best</div><div>falcon_ns.task_options.HGAP_SeedLengthCutoff_str: -1</div><div>Genomic_consensus.task_options.diploid: false</div><div>&nbsp;</div><div>MeDuSa</div><div>-random 100</div><div>&nbsp;</div><div>Prokka</div><div>--usegenus</div><div>--force</div><div>--addgenes</div><div>--rfam</div><div>--rawproduct</div><div>&nbsp;</div><div>cmsearch (taxonomy, 16S)</div><div>--rfam</div><div>--noali</div><div>&nbsp;</div><div>blastn (taxonomy, 16S)</div><div>-evalue 1E-10</div><div>&nbsp;</div><div>blastn (MLST)</div><div>-ungapped</div></div><div><div>-dust no</div><div>-evalue 1E-20</div><div>-word_size 32</div><div>-culling_limit 2</div><div>-perc_identity 95</div><div>&nbsp;</div><div>blastp (VF)</div><div>-culling_limit 2</div><div>&nbsp;</div><div>RGI (ABR)</div><div>--input_type contig</div><div>&nbsp;</div><div>bowtie2 (mapping)</div><div>--sensitive</div><div>&nbsp;</div><div>minimap2 (mapping)</div><div>-a</div><div>-x map-ont</div><div>&nbsp;</div><div>samtools mpileup (SNP&nbsp;detection)</div><div>-uRI</div><div>&nbsp;</div><div>bcftools call (SNP detection)</div><div>--variants-only</div><div>--skip-variants indels</div><div>--output-type v</div><div>--ploidy 1</div><div>-c</div><div>&nbsp;</div><div>SNPsift filter (SNP detection)</div><div>"( QUAL &gt;= 30 ) &amp; (( na FILTER ) | (FILTER = 'PASS')) &amp;</div><div>( DP &gt;= 20 ) &amp; ( MQ &gt;= 20 )"</div><div>&nbsp;</div><div>SNPeff ann (SNP detection)</div><div>-nodownload</div><div>-no-intron</div><div>-no-downstream</div><div>-no SPLICE_SITE_REGION</div><div>-upDownStreamLen 250</div><div>&nbsp;</div><div>bcftools consensus</div><div>(phylogenetic tree)</div><div>--haplotype 1</div><div>&nbsp;</div><div>fasttreemp</div><div>-nt</div><div>-boot 100</div><div>&nbsp;</div><div>roary</div><div>-e</div><div>-n</div><div>-cd 100</div><div>-g 100000</div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/4162/4273%CF%80-bioinformatics-education-on-low-cost-arm-hardware</guid>
	<pubDate>Mon, 02 Sep 2013 07:02:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/4162/4273%CF%80-bioinformatics-education-on-low-cost-arm-hardware</link>
	<title><![CDATA[4273π: Bioinformatics education on low cost ARM hardware]]></title>
	<description><![CDATA[<p>Are you teaching bioinformatics at universities and found it complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. Hmm don't worry there is one new OS for the rescue. 4273<em>&pi;</em>, an operating system image for Raspberry Pi based on Raspbian Linux. It provides an attractive, general-purpose computing environment, within which the course 4273&pi; Bioinformatics for Biologists is embedded.<br /><br />Though far slower than current desktop and laptop computers, the Raspberry Pi is notably faster than the Cray 1 supercomputer, a marvel of computer speed in its day. The Raspberry Pi approach includes all the benefits of the laptop approach, above, but at lower cost. In addition, the Raspberry Pi is a new and exciting computer system, which in itself can add interest to the course.<br /><br />As the Raspbian operating system, Raspberry Pi firmware and hardware and 4273&pi; Bioinformatics for Biologists teaching material develop, further releases of 4273&pi; will be made available. It is anticipated that there will be a minimum of two releases per year during the next four years.</p><p>4273<em>&pi;</em> is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.</p><p>Descriptive paper @ http://www.biomedcentral.com/1471-2105/14/243</p><p>Image source: BMC Bioinformatics</p><p><img src="http://www.biomedcentral.com/content/download/figures/1471-2105-14-243-1.png" alt="image" style="border: 0px; border: 0px;"></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/42664/common-bioinformatics-interview-questions</guid>
	<pubDate>Sat, 23 Jan 2021 06:07:50 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/42664/common-bioinformatics-interview-questions</link>
	<title><![CDATA[Common Bioinformatics Interview Questions !]]></title>
	<description><![CDATA[<p>The possibility of an interview for a bioinformatics position in the life sciences may be very disquieting, but the same concerns emerge time and again in my experience. So, it is exceedingly worthwhile to plan for future bioinformatics interview questions. Doing this will really give you the advantage in obtaining the position.</p><p>The following 5 questions are those that I have heard many times during the job-search process. There is no reason for not planning responses in such situations.</p><p><strong>1. Tell Us About Yourself</strong><br />This is a very typical opener in interviews. It's a perfect question to ask, and getting something planned will really help you concentrate and ease in the conversation. However, you need to make sure that your response is applicable to the job you're interviewing.<br />It's probably better to keep your answer professional. Try to include these in the answer as well: where did your love of science and bioinformatics come from? How the heck did you end up in this field? Why programming and scripting ?</p><p><strong>2. What is your plan for your bioinformatics career? / How do you look at yourself in five years? / How are your personal objectives to accomplish these goals / What are the plan for your research fundings ?</strong></p><p>Your CV/resume has already impressed the selection panel if you have been invited for an interview. The questions from the bioinformatics interview team provide an incentive for you to market yourself and illustrate the work in question with the most appropriate knowledge.</p><p><strong>3. What do you understand about the job description/What would your suggested research path be if you were a successful candidate?</strong><br />Summarize the specifics of the advertised bioinformatics position in your own words. Follow on with some suggestions of how you want to extend your research and create your own projects within the community.</p><p><strong>4. Will you work as a group or do you want to work on your own?</strong><br />This requirement can vary from jobs to job, so when addressing, be alert. A company/research PI may need a bioinformatician that is able to work on a single project autonomously, or they may need a person who can help direct and organize a team. In your response, refer to the job description.</p><p><strong>5. What particular methods have you used to date with your experiments?</strong><br />You might have experience with all the laboratory techniques described in the job description, but stress the ones you highly experienced with. Highlight your professional abilities and stress that you are extremely capable of mastering new techniques with others ...</p><p>At the end of the day, remember that you're questioning the jury as well as they're interviewing you. You will ought to think of any questions you would like the interview panel to pose. This indicates that you have done your homework and serious about the position.</p><p>All the best for your future job interview.</p>]]></description>
	<dc:creator>Jit</dc:creator>
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