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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32633?offset=1140</link>
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	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4873/vveks-lab</guid>
  <pubDate>Thu, 26 Sep 2013 11:11:39 -0500</pubDate>
  <link></link>
  <title><![CDATA[Vvek's Lab]]></title>
  <description><![CDATA[
<p>Broad Area of Research: RNA biology (microRNA, lncRNA), Stem cells, Functional genomics, Epigenomics and Cancer</p>

<p>RNAs, especially non-coding RNAs (such as microRNA, long ncRNAs) are recently identified to be very abundant in mammalian organisms and play some key roles in gene expression regulation, gene silencing, and also implicated in disease progression, stem cell pluripotency etc. Current research activities of our lab include analysis of expression pattern of ncRNAs by microarray and next-gen sequencing data and understanding the role of miRNAs or other regulatory RNAs in various diseases, especially cancer and validation by reporter assays (renilla/luciferase) and other experimental tools.</p>

<p>More @ http://vvekslab.in/index.html</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/39469/introduction-to-bioinformatics</guid>
	<pubDate>Wed, 05 Jun 2019 14:58:11 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/39469/introduction-to-bioinformatics</link>
	<title><![CDATA[Introduction to Bioinformatics]]></title>
	<description><![CDATA[<p><img src="https://edu.t-bio.info/wp-content/uploads/2017/07/Introduction-Course-Title-11.jpg" alt="Introduction to Bioinformatics Course" width="600" height="315.6" style="vertical-align: top; border: 0px; border: 0px;"></p><p>Introduction to bioinformatics is a course for biologists and clinicians that would like to learn more about the way bioinformatics is used in healthcare, biotech and pharmaceuitcal industry as well as basic research. The course covers many of the topics transformed by the emergence of big data and computational technologies. To learn more about the course, visit:&nbsp;<a href="https://edu.t-bio.info/course/introduction-bioinformatics/">https://edu.t-bio.info/course/introduction-bioinformatics/</a></p>]]></description>
	<dc:creator>eliabrodsky</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/5462/showreel-2008-cortical-studios</guid>
	<pubDate>Sat, 12 Oct 2013 18:33:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/5462/showreel-2008-cortical-studios</link>
	<title><![CDATA[Showreel 2008 - Cortical Studios]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/qrReqMKe7Xg" frameborder="0" allowfullscreen></iframe>We are a bioinformatics company that combines 3D animation, multimedia and scientific knowledge to meet your communication needs. With our academic background in the fields of biotechnology and molecular cellbiology and our computer expertise we provide cutting edge 3D animation productions for even the most complex projects. We translate complex scientific information into comprehensible artistic imagery in order to improve communication in the life sciences. Please feel free to contact us with any questions regarding the possibilities for your unique project.

Cortical Studios
Keizersgracht 8
1015 CN
Amsterdam
The Netherlands
info@corticalstudios.nl
www.corticalstudios.nl]]></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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7813/research-associate-indian-institute-of-spices-research</guid>
  <pubDate>Wed, 08 Jan 2014 10:10:03 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Associate @ INDIAN INSTITUTE OF SPICES RESEARCH]]></title>
  <description><![CDATA[
<p>INDIAN INSTITUTE OF SPICES RESEARCH<br />(Indian Council of Agricultural Research)<br />Marikunnu P.O., Kozhikode – 673 012, Kerala</p>

<p>Phone No. 0495 2731 410</p>

<p>WALK -IN- TEST CUM INTERVIEW<br />Walk- in- Test cum Interview (based on test) for the selection of Research Associate (Bioinformatics) &amp; Bioinformatic Trainees under the scheme ‘Distributed Information Sub Centre- DISC’ will be held at this Institute as per details indicated below.</p>

<p>Research Associate<br />Date of Interview : 21 -01-2014 at 10.00 A.M<br />Qualifications :<br />a) Essential: Doctorate degree in Bioinformatics or Biotechnology/Life Sciences/Biochemistry with expertise in  Bioinformatics as evidenced by publications.<br />OR Three years research experience after  MVSc/MPharm/ME/MTech with Bioinformatics Specialization.<br />b Desirable: Experience in handling NGS data  Programming skills in Python/Bioperl<br />Emoluments : Rs:22000/- per month + HRA  (higher pay upto Rs.24000/- can be paid depending on the qualifications and experience.<br />Upper age limit : 40 years for Men &amp; 45 years for Women as on date of Interview (Upper Age limits are relaxable for SC, ST and OBC candidates as per Govt. of India norms (at present 5 years for SC/ST and 3 years for OBC)<br />Duration of Project : Till the closure of the project.</p>

<p>General Terms and conditions<br />1. The above positions are purely on temporary basis and is co-terminus with the closure of the project. There is no provision of re-employment after termination of project.<br />The selected candidate will not have any right for claiming pay scale or absorption<br />against any regular post being vacant on a later date at this Institute.<br />2 . No TA/DA will be paid for attending the Interview.<br />3. Canvassing in any form will lead to cancellation of candidate.<br />4. The decision of Director, IISR would be final and binding in all aspects.<br />5. Candidates will not be permitted to enter the Examination Hall after 10.00 A.M.<br />6. Candidates who secure the minimum marks prescribed by the Institute in written test  only will be eligible for calling for the interview. The number of candidates to be  called for the interview will be decided by the Director of the Institute.<br />7 Those who do not possess original Degree/PG certificate or Provisional certificate will not be allowed to attend the Test/Interview.</p>

<p>Note: All relevant certificates (in original) and bio data, No objection certificate in case he/she is employed elsewhere and experience certificate in original (if any) need to be produced at the time of interview.<br />Advertisement: http://spicebioinfo.res.in/downloads/DISC-Website.pdf</p>
]]></description>
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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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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4947/experimental-scientific-officer-bioinformatics</guid>
  <pubDate>Fri, 27 Sep 2013 11:09:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[Experimental Scientific Officer (Bioinformatics)]]></title>
  <description><![CDATA[
<p>Closing Date:  8 October 2013</p>

<p>Salary:   £27,854 - £29,541, with progression to £36,298</p>

<p>You will perform cutting edge computational biology within the Faculty of Medical Sciences, with a particular focus on the Northern Institute for Cancer Research (NICR), and contribute to the delivery of Faculty wide programmes of training, analytical services and skill transfer between Faculty Institutes.</p>

<p>You will have a relevant first degree or equivalent qualifications and/or experience in a relevant scientific/technical role, together with previous specialist experience at a senior level in bioinformatics. A PhD is desirable.</p>

<p>This position is part of the Bioinformatics Support Unit but physically located for the majority of the time in the NICR buildings.</p>

<p>Tenable for three years.</p>

<p>Informal enquiries to unit head Dr Simon Cockell: 0191 222 7253; simon.cockell@ncl.ac.uk</p>

<p>For more information visit @ https://www15.i-grasp.com/fe/tpl_newcastle02.asp?s=4A515F4E5A565B1A&amp;jobid=50667,2552984041&amp;key=70203469&amp;c=725434237887&amp;pagestamp=sepghtjhowdqpsxuyn</p>

<p>You can also find several other jobs @http://bsu.ncl.ac.uk/support/recruitment/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41202/biocontainers</guid>
	<pubDate>Thu, 20 Feb 2020 05:29:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41202/biocontainers</link>
	<title><![CDATA[BioContainers]]></title>
	<description><![CDATA[<p><span>BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics packages (e.g conda) and containers (e.g docker, singularity). BioContainers is based on the popular frameworks&nbsp;</span><a href="https://conda.io/">Conda</a><span>,&nbsp;</span><a href="https://www.docker.com/">Docker</a><span>&nbsp;and&nbsp;</span><a href="https://www.sylabs.io/docs/">Singularity</a><span>.</span></p><p>Address of the bookmark: <a href="https://biocontainers.pro/#/" rel="nofollow">https://biocontainers.pro/#/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/5220/paolo-ruggerone-lab</guid>
  <pubDate>Tue, 01 Oct 2013 14:15:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[Paolo Ruggerone Lab]]></title>
  <description><![CDATA[
<p>Efflux pumps (RND family)</p>

<p>Functioning of efflux systems in Gram-negative bacteria<br />Determinants of the compound-efflux system interactions<br />Action of inhibitors on efflux systems<br />Structural and dynamical features of the efflux systems</p>

<p>TatA<br />Assembly of the TatA system<br />Study of the dynamical features of the charge zipper</p>

<p>Methods<br />Setup of a kinetic Monte Carlo (KMC) scheme to study the flux of antibiotics through porins and efflux systems<br />Setup of protocol to integrate MD results in a ligand-based approach</p>

<p>Viral inhibitors<br />Interactions of selected compounds with RNA-dependent RNA polymerases (RdRps) of HCV and BVDV<br />Assessment of the role of mutations in RdRps<br />Antimicrobial peptides</p>

<p>Interactions of antimicrobial peptides with membranes: structure and dynamics<br />Interactions between antimicrobial peptides in the presence of different membranes<br />Protein-protein interactions<br />Effects of mutations</p>

<p>Lab Page<br />http://www.dsf.unica.it/~paolo/Site/Home.html</p>
]]></description>
</item>
<item>
	<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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