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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32485?offset=770</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40272/seq-a-high-performance-pythonic-language-for-bioinformatics</guid>
	<pubDate>Sat, 23 Nov 2019 08:58:12 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40272/seq-a-high-performance-pythonic-language-for-bioinformatics</link>
	<title><![CDATA[Seq: A high-performance, Pythonic language for bioinformatics]]></title>
	<description><![CDATA[<p>&nbsp;</p>
<p>Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C/C++.</p>
<p>Learn more by following the&nbsp;<a href="https://github.com/seq-lang/seq/blob/master/docs/sphinx/tutorial.rst">tutorial</a>&nbsp;or from the&nbsp;<a href="https://github.com/seq-lang/seq/blob/master/docs/sphinx/cookbook.rst">cookbook</a>.</p><p>Address of the bookmark: <a href="https://seq-lang.org" rel="nofollow">https://seq-lang.org</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4552/imtech-lab</guid>
  <pubDate>Sun, 15 Sep 2013 09:41:04 -0500</pubDate>
  <link></link>
  <title><![CDATA[IMTECH Lab]]></title>
  <description><![CDATA[
<p>Computer Aided Protein Structure Prediction; Identification of Vaccine<br />Candidates (T-Epitope prediction); Analysis of Nucleotide/Protein Sequences; Development of Web Server/</p>

<p>Software; Creation of Public Domain Resources in Biology<br />Present Status::</p>

<p>Developing prediction methods for gene, beta-turn, secondary structure and MHC-binding sites.<br />Area of Interest ::</p>

<p>Comparison of force field simulations. Analysis of DNA-protein interactions using molecular mechanics methods.Drug Target Identification using in silico biology.</p>

<p>More @ http://www.imtech.res.in/bic/index.php?option=com_content&amp;view=article&amp;id=65</p>

<p>PIs: http://www.imtech.res.in/bic/index.php?option=com_content&amp;view=article&amp;id=69</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/view/2023</guid>
	<pubDate>Mon, 12 Aug 2013 09:36:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/view/2023</link>
	<title><![CDATA[What is the objective of BINC examination?]]></title>
	<description><![CDATA[<p>I personally did not understand the objective behind BINC examination. Is government only try to show off that they are doing something to promote Indian bioinformatics sector?</p><p>Moreover, It looks like BINC indirectly putting&nbsp;an extra burden to bioinformatician, mentally and financially.</p>]]></description>
	<dc:creator>Neel</dc:creator>
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<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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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/2425/phd-fellowship-computational-biologybioinformatics-cork-ireland-cork-ireland</guid>
  <pubDate>Thu, 15 Aug 2013 14:09:00 -0500</pubDate>
  <link></link>
  <title><![CDATA[Ph.D. Fellowship (Computational Biology/Bioinformatics) : Cork, Ireland : Cork, Ireland]]></title>
  <description><![CDATA[
<p>Ph.D. Fellowship (18,000 euro/pa, plus tuition fees at the EU students rate) is available for four years to work on development of Bioinformatics resources for the analysis and visualization of ribosome profiling data. Ribosome profiling (ribo-seq) is a technology that allows mapping positions of the ribosomes on the whole transcriptome level with a nucleotide precision. The technology allows obtaining high resolution digital snapshots of gene expression in cells. The position is available starting on the 1st of October, 2013.</p>

<p>Candidate:<br />The candidate is expected to have B.S. or M.S. degree in the disciplines such as Computer Science, Statistics, Applied Mathematics, Physics or Electrical Engineering. The candidates with the backgrounds in Life Science disciplines such as Bioinformatics, Computational or Quantitative Biology will also be considered.</p>

<p>Location:<br />The position is available at LAPTI (http://lapti.ucc.ie) that is located in the Western Gate Building (http://www.stwarchitects.com/project-information.php?c=1&amp;p=09993) at University College Cork. Western Gate Building Research Complex hosts several UCC departments and provides ideal environment for interdisciplinary research. Cork (sometimes referenced as “Venice of Ireland”) is the second most populous city in the Republic. It has friendly cosmopolitan atmosphere and vibrant culture. A number of American industrial giants such as Apple , EMC and Pfizer have chosen Cork as a home for their European headquarters.</p>

<p>Application process:<br />The details of the application process are given at http://lapti.ucc.ie/jobs.html. To ensure prompt processing of your application use the subject line: ‘Ph.D. computational’. All applications received prior to August the 1st are guaranteed equal consideration. However, applications at the later dates will also be considered until the position is filled.</p>
]]></description>
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<item>
	<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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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/2336/3rd-annual-next-generation-sequencing-asia-congress-2013-at-singapore-singapore</guid>
  <pubDate>Wed, 14 Aug 2013 09:55:04 -0500</pubDate>
  <link></link>
  <title><![CDATA[3rd Annual Next Generation Sequencing Asia Congress 2013 at Singapore, Singapore]]></title>
  <description><![CDATA[
<p>The 3rd Annual Next Generation Sequencing Asia Congress is to be held on the 22nd and 23rd of October 2013 in Singapore. Over the 2 days, the conference will provide an overview of the current options of next-generation sequencing platforms, technologies, applications and the newest computational tools for the analysis of next-generation sequencing data and analytical genomics as well as overcoming data management problems. The event will attract over 200 senior-level decision makers working in areas such as next generation sequencing, analytical genomics, computational biology, oncology, RNA profiling, molecular genomics, biomarkers, bioinformatics &amp; data management and clinical &amp; diagnostics development.</p>

<p>Dated : 22 Nov 2013 -23 Nov 2013</p>

<p>http://www.ngsasia-congress.com/</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/fun/view/2383/golden-rules-of-bioinformatics</guid>
	<pubDate>Wed, 14 Aug 2013 21:11:33 -0500</pubDate>
	<link>https://bioinformaticsonline.com/fun/view/2383/golden-rules-of-bioinformatics</link>
	<title><![CDATA[Golden Rules of Bioinformatics]]></title>
	<description><![CDATA[<ol>
<li>All constant are variable.</li>
<li>Copy and paste is a genetic error.</li>
<li>First solve the problem, then write the code.</li>
<li>No matter what goes wrong, it will probably look right.</li>
<li>Any simple problem can be insoluble if enough metting are held to discuss it. :P</li>
<li>Stastics is a systematic method of comming to the wrong conclusion with confidence.</li>
<li>Bug is a undocumented feature in programming languages.</li>
<li>Good biological programmer goes on summer holiday with raincoat. [because see 1]</li>
<li>Thanks god Google know python is not a python and multiplication and division are the same thing.</li>
<li>Don' be clever, complex biology will trick you.</li>
</ol>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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