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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/9213?offset=1090</link>
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	<description><![CDATA[]]></description>
	
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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/opportunity/view/10124/jrf-at-bose-institute-kolkata</guid>
  <pubDate>Mon, 21 Apr 2014 19:41:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF at Bose Institute, Kolkata]]></title>
  <description><![CDATA[
<p>ADVT. No. S/BIC/01/2014-15</p>

<p>Bose Institute, Kolkata, invites applications from Indian Citizens for ONE (01) temporary position of Junior Research Fellow in the DBT sponsored project entitled, “Centre of Excellance (CoE) in Bioinformatics at Bose Institute”, running under Prof. Pinakpani Chakrabarti, Project Co-ordinatior, Bioinformatics Centre. The project is tenable upto 31.03.2017, but duration of the fellowship is one year only. The JRF will work with one of the faculty members of the center based on his / her motivation in any specific area on Bioinformatics.</p>

<p>Essential Qualification: 1st class M.Sc. / M.Tech degree in any stream of Chemical/ Biological Sciences with CSIR-UGC-NET-JRF / ICMR-JRF / DBT-JRF or CSIR-UGCNET- LS / GATE qualification.</p>

<p>Desirable qualification:</p>

<p>(i) Specialized knowledge in Organic / Physical chemistry.<br />(ii) Any exposure to research involving the small molecules (like drug) and / or protein structure determination or prediction.<br />(iii) Basic knowledge in computer programming, e.g. using FORTRAN, C, shell, perl etc.<br />(iv) Hands-on-experience on any of the following software : CHARMM/AMBER/NAMD/GROMACS,Gaussian/Gamess, Haddock/Autodock, Schrodinger etc. (or any other software serving similar purposes in molecular modeling)</p>

<p>Fellowship :</p>

<p>(i) Rs. 16,000/- p.m., plus admissible HRA &amp; Medical Benefit for M.Sc. with CSIRUGC NET-JRF/ICMR-JRF/DBT-JRF or M.Tech. with CSIR-UGC NETJRF/<br />ICMR-JRF/DBT-JRF/CSIR-UGC NET-LS/GATE<br />(ii) Rs. 12,000/- p.m., plus admissible HRA &amp; Medical Benefit for M.Sc. with CSIRUGC NET-LS/GATE</p>

<p>Age : Below 28 years as on the day on which the application is made (relaxable in case of SC/ST/OBC/WOMEN candidates only as per rule).</p>

<p>Interested and eligible candidates should apply on plain paper duly signed by them clearly mentioning the area of interest in research, possession of any desirable qualification (s) as mentioned above and quoting Advertisement No. on the envelop as well as application with complete Bio-data giving e-mail ID, Phone No. and details of qualification i.e. examination passed, year, division, percentage of marks, from Secondary onwards with attested copies of testimonials, addressed to the Registrar, Bose Institute, P-1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 on or before April 25, 2014.</p>

<p>The shortlisted candidates will be called for an interview. Applicants are advised to check our website for future updates.</p>

<p>Advertisement: www.boseinst.ernet.in/ADVT/14/p_2.pdf</p>
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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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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10262/research-fellow-phd-candidate-in-computational-biology-%E2%80%93-2-positions</guid>
  <pubDate>Fri, 25 Apr 2014 20:19:58 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research fellow (PhD candidate) in computational biology – 2 positions]]></title>
  <description><![CDATA[
<p>At the Department of Informatics two 4-year positions as research fellow are available in the field of computational biology connected to the Computational Biology Unit. The positions are linked to the project “Integrated genomics - linking transcriptional and translational regulation over developmental time” supported by the Bergen Research Foundation</p>

<p>The fate of a cell is ultimately the product of the regulation of its genes. Gene regulation is a coordinated process acting at multiple levels of which transcription and translation are the most prominent. The Valen group is dedicated to the fundamental question of how transcription and translation is integrated to obtain the desired protein abundance. The recent development of high-throughput next generation sequencing techniques to monitor both active translation and transcription has made it possible to study this connection at the genome scale.</p>

<p>This project aims to elucidate the links between regulation of translation and transcription. The applicant will analyze next generation sequencing data and model gene regulation on a genome-wide level to identify the features that affect the translational output of transcripts. The work will be done in close collaboration with experimental scientists who will test the predictions of the computational models.</p>

<p>Additional information on the position can be obtained by contacting Eivind Valen (eivind.valen@ii.uib.no).</p>

<p>The research fellow must take part in the University’s approved PhD program leading to the degree within a time limit of 3 years. Application for admission to the PhD program, including a project plan outline for the training module, will be worked out in collaboration with the research group in question.</p>

<p>In total, the fellowship period is 4 years, 25 % of this will be allocated to teaching and/or administrative duties. The fellowship period may be reduced if the successful applicant has held previous employment as a research fellow or similar.</p>

<p>http://www.jobbnorge.no/en/available-jobs/job/102235/research-fellow-phd-candidate-in-computational-biology-2-positions</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/43044/kanthida-lab</guid>
  <pubDate>Wed, 28 Apr 2021 02:27:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[Kanthida Lab !]]></title>
  <description><![CDATA[
<p>Research Interest: </p>

<p>Bioinformatics </p>

<p>High-throughput and high-dimensional data analysis</p>

<p>Microbiome data analysis (Main focus)</p>

<p>Next-generation and third-generation sequencing data analysis for genomics</p>

<p>Gene expression data analysis</p>

<p>Machine learning for biological data</p>

<p>Biomarkers identification </p>

<p>Database and web-application for biological data</p>

<p>More at <br />https://sites.google.com/mail.kmutt.ac.th/kanthida-k/home?authuser=0</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/10415/bioinformatician-stuck-in-wet-lab</guid>
	<pubDate>Tue, 06 May 2014 12:46:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/10415/bioinformatician-stuck-in-wet-lab</link>
	<title><![CDATA[Bioinformatician stuck in wet-lab]]></title>
	<description><![CDATA[<p>This guide is aimed at pet bioinformaticians, and is meant to guide them towards better career development.</p>
<p><strong>1. Make friends with local bioinformatics groups</strong><br> <strong>2. Talk to your computing group</strong><br> <strong>3. Obtain clear expectations</strong><br> <strong>4. Rewrite your job description</strong><br> <strong>5. Papers</strong><br> <strong>6. Attend bioinformatics meetings</strong><br> <strong>7. Try first, ask later</strong></p><p>Address of the bookmark: <a href="http://biomickwatson.wordpress.com/2013/04/23/a-guide-for-the-lonely-bioinformatician/" rel="nofollow">http://biomickwatson.wordpress.com/2013/04/23/a-guide-for-the-lonely-bioinformatician/</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43323/biostarhandbook</guid>
	<pubDate>Fri, 27 Aug 2021 01:31:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43323/biostarhandbook</link>
	<title><![CDATA[biostarhandbook]]></title>
	<description><![CDATA[<p>Nice book collection for bioinformatician ... highly recommended.</p><p>Address of the bookmark: <a href="https://www.biostarhandbook.com/" rel="nofollow">https://www.biostarhandbook.com/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10881/special-project-scientist-%E2%80%93-sorghum-genomics</guid>
  <pubDate>Tue, 20 May 2014 00:34:39 -0500</pubDate>
  <link></link>
  <title><![CDATA[Special Project Scientist – Sorghum Genomics]]></title>
  <description><![CDATA[
<p>ICRISAT is seeking applications from Indian Nationals for a Special Project Scientist to work on a sorghum genomics activities related to sequencing/re-sequencing projects utilizing New Generation Sequencing platforms.</p>

<p>The Job detail</p>

<p>    Advancing the SNP-discovery and polymorphism assessment work across several germplasm panels representing global genetic diversity<br />    Population genetic and genomic analyses, testing the hypothesis related to adaptation in multiple geographic regions<br />    Develop SNP assays from large scale GBS and other re-sequencing data for several target traits utilizing available phenotyping data<br />    Combined analyses of genotypic and phenotypic data for discovery of marker-trait associations, and conducting GWAS<br />    Processing, analyzing, and archiving large-scale genomic data sets, assessing data quality, conducting analyses, interpreting findings, and communicating findings to others including preparation of reports, presentations, posters and journal articles<br />    Providing support to MSc and PhD students on topic related to its major core of research<br />    Any other work assigned by the supervisor</p>

<p>The Person:</p>

<p>    PhD in bioinformatics, genetics, computational biology preferably with 1 to 2 years of experience;<br />    familiar with standard bioinformatics tools and scripting languages and emerging and evolving software platforms relevant to bioinformatics and computational biology;<br />    ability to create new analytical pipelines; experience with handling large data sets;<br />    ability to program in at least two of the following: C++, PERL, Python, R, Java.<br />    will use next-generation sequencing technologies to generate marker data for genetic mapping and transcriptome data for expression QTL mapping, and will be responsible for data generation as well as data analysis.</p>

<p>Period and Remuneration: The assignment is for a period of two years, and can be extended for another year depending on performance. ICRISAT pays a very attractive all inclusive lump sum assignment fee payable in Indian Rupees.</p>

<p>How to Apply: Please send your application by email to icrisatjobs@cgiar.org, stating the job title (Special project Scientist-Sorghum Genomics) clearly in the subject column, addressed to the Director, Human Resources and Operations, ICRISAT, Patancheru, Andhra Pradesh 502 324, India, latest by 10 June 2014. The application should include an up-to-date Curriculum Vitae, a short statement of competencies and experience for the position, and the names and addresses (including phone/e-mail) of three referees. Only short-listed candidates will be contacted.</p>

<p>More at: http://www.icrisat.org/careers/Special-Project-Scientist-Sorghum-Genomics.htm</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/44400/pevzner-lab</guid>
  <pubDate>Thu, 02 Nov 2023 05:39:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[Pevzner Lab !]]></title>
  <description><![CDATA[
<p>The laboratory works on genome sequencing, immunoproteogenomics, antibiotics sequencing, and comparative genomics - computational technologies that enabled new applications and allowed scientists to attack biological problems that remained beyond the reach of previous techniques.</p>

<p>https://bioalgorithms.ucsd.edu/research4.html</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/10739/science-for-life-laboratory-scilifelab-sweden</guid>
  <pubDate>Sat, 10 May 2014 06:22:30 -0500</pubDate>
  <link></link>
  <title><![CDATA[Science for Life Laboratory (SciLifeLab)-Sweden]]></title>
  <description><![CDATA[
<p>Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource and a collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University.</p>

<p>Webpage : https://www.scilifelab.se/about-us/<br />Opportunity: https://www.scilifelab.se/about-us/career/</p>
]]></description>
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