<?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/26306?offset=1550</link>
	<atom:link href="https://bioinformaticsonline.com/related/26306?offset=1550" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5947/jrf-national-jalma-institute-of-leprosy-and-other-mycobacterial-diseases</guid>
  <pubDate>Mon, 28 Oct 2013 10:42:48 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF @ NATIONAL JALMA INSTITUTE OF LEPROSY AND OTHER MYCOBACTERIAL DISEASES]]></title>
  <description><![CDATA[
<p>NATIONAL JALMA INSTITUTE OF LEPROSY AND OTHER MYCOBACTERIAL DISEASES</p>

<p>(INDIAN COUNCIL OF MEDICAL RESEARCH)</p>

<p>P.O BOX 101,<br />Dr. M. Miyazaki Marg,<br />Tajganj, Agra - 282001</p>

<p>Applications are invited for a walk-in interview to be held in the Seminar Hall of the on 15th November, 2013, 9:30 am for temporary positions of JRF, Lab Technician and Field attendant in a ICMR funded project entitled "Elucidating the strain differentiation and transmission dynamics of M. leprae through simple sequence repeats ISSR-PCR marker"</p>

<p>1. JRF (one Post)</p>

<p>    Essential qualification: Candidates with M.Sc/IVI.Tech or equivalent degree in any life science related subjects with UGC-CSIR/ICMR/DBT-Net qualified</p>

<p>    Desirable qualification: Experience in Molecular Biology/Computational Biology will be preferred.</p>

<p>    Age. Maximum 28 years as on 11.11.2013. Age relaxation as per GOI rules.</p>

<p>    Emoluments: Rs. 6,000 + 20% HRA per Month</p>

<p>2. Lab Technician (One Post)</p>

<p>    Essential Qualification: 12th with DMLT/B.SCA4.SC in Life sciences</p>

<p>    Desirable qualification: Experience in Molecular Biology/Computational Biology will be preferred.</p>

<p>    Age: Maximum 30 years as on 11.11.2013. Age relaxation as per GOI rules.</p>

<p>    Emoluments: Rs13,760/ Per Month</p>

<p>3. Field Attendant (One Post)</p>

<p>Essential Qualification: 10th Pass</p>

<p>Desirable Qualification: Experience in field work</p>

<p>Age: Maximum 28 years as on 11.11.2013. Age relaxation as per GOI rules.</p>

<p>Emoluments: Rsl2,040l Per Month</p>

<p>Terms: posts are purely temporary. Appointment will be initially made for a period of one (01) year and may be extended further based on the performance of the candidate up to completion of the project.</p>

<p>Application &amp; Selection procedure: candidates have to appear in the walk-in-interview in person along with an application/CV on plain paper giving details of at educational qualificationq experience and submit photocopies of relevant documents at the time of interview. Selection will be based on the performance of the candidate in the interview' Candidates will not be sent any interview call letter separately. No TA/DA will be paid to the candidate for appearing in the interview. selection is not possible without appearing in the interview. All candidates must report by 9:00am on the date of interview. Advance copy of CV may be sent to m.sarathipartha@gmail.com</p>

<p>Advertisement: http://www.jalma-icmr.org.in/P_S_M_advertisment.pdf</p>
]]></description>
</item>

<item>
  <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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/7032/computer-experts-in-biotechnology-laboratory</guid>
	<pubDate>Wed, 04 Dec 2013 02:11:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/file/view/7032/computer-experts-in-biotechnology-laboratory</link>
	<title><![CDATA[Computer experts in biotechnology laboratory]]></title>
	<description><![CDATA[<p>Only bioinformatician can understand that <strong>multiplication</strong> and <strong>division</strong> are different but same thing :)</p><p><span>Disclaimer:</span>&nbsp;This cartoon is solely designed to create humour and fun, not to offend any computer experts.</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/7032" length="35726" type="image/gif" />
</item>
<item>
	<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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44930/bioinformatics-the-bridge-between-curiosity-and-discovery</guid>
	<pubDate>Mon, 24 Nov 2025 05:16:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44930/bioinformatics-the-bridge-between-curiosity-and-discovery</link>
	<title><![CDATA[Bioinformatics: The Bridge Between Curiosity and Discovery]]></title>
	<description><![CDATA[<p>In the sprawling universe of modern science, bioinformatics stands as one of the most transformative and empowering fields of our time. It is where biology meets computation, where data becomes meaning, and where curiosity becomes discovery. If you&rsquo;ve stepped into this world&mdash;or are considering it&mdash;here&rsquo;s your reminder: you&rsquo;re part of a revolution.</p><p><strong>Why Bioinformatics Matters More Than Ever</strong></p><p>Every day, our world generates massive amounts of biological data&mdash;from genome sequences to microbiome profiles to real-time pathogen surveillance. Hidden within these datasets are the answers to some of the greatest challenges humanity faces: emerging diseases, antimicrobial resistance, environmental stress, genetic disorders, sustainable agriculture, and more.</p><p>Bioinformatics isn&rsquo;t just a skill.<br />It&rsquo;s the language of the future of biology.</p><p>By mastering it, you give yourself the power to:</p><p>Decode genomes and understand life at its most fundamental level</p><p>Identify patterns no microscope could ever reveal</p><p>Predict disease outbreaks before they occur</p><p>Accelerate drug discovery with computational precision</p><p>Contribute to open-source tools that empower scientists worldwide</p><p>You don&rsquo;t just follow science&mdash;you drive it.</p><p><strong>Every Expert Was Once a Beginner</strong></p><p>Many newcomers feel intimidated. Command-line interfaces. R scripts. Python packages. Next-generation sequencing data. Complex machine learning models.</p><p>But here&rsquo;s the truth: every bioinformatician started exactly where you are now&mdash;curious, unsure, but excited.</p><p>No one writes perfect code on day one.</p><p>No one understands genomics pipelines immediately.</p><p>What makes you a bioinformatician is not perfection, but perseverance.</p><p>When your script throws a cryptic error&hellip;<br />When your data refuses to format&hellip;<br />When your pipeline runs for 6 hours only to crash&hellip;</p><p>Remember: this is part of the journey.<br />Every error teaches you. Every retry strengthens you. Every breakthrough energizes you.</p><p>Bioinformatics Is Not Just a Career&mdash;It&rsquo;s a Mindset</p><p>It&rsquo;s the mindset of:</p><p>Problem-solving.</p><p>Continuous learning.</p><p>Turning chaos into clarity.</p><p>Seeing what others can&rsquo;t.</p><p>Bioinformaticians are detectives of biological complexity. You sit at the intersection of innovation, using tools that can shape public health, medicine, agriculture, and ecology. Few fields give you such direct impact on the world.</p><p><strong>Your Contribution Matters</strong></p><p>As you work on your script, pipeline, genome, or model, remember:</p><p>Somewhere, your analysis might contribute to:</p><p>A new therapy</p><p>A faster diagnostic test</p><p>A better understanding of a pathogen</p><p>A more resilient crop</p><p>An open-source dataset that helps thousands</p><p>A discovery that rewrites textbooks</p><p>Your code may be small, but its ripple effect is powerful.</p><p>The Future Is Bioinformatics&mdash;And You Are Part of It</p><p>The world is shifting. Wet labs are integrating AI. Hospitals rely on genomic insights. Farmers use gene-level predictions. Governments monitor disease in real time. Students launch pipelines that become global tools.</p><p>This is a golden era&mdash;and you are not late.<br />You are exactly where you need to be.</p><p>Keep Pushing. Keep Learning. Keep Discovering.</p><p>Bioinformatics is a journey filled with challenges, but also with unmatched rewards.</p><p>So the next time you feel stuck, frustrated, or overwhelmed, remember:<br />You&rsquo;re building the science of tomorrow.</p><p>Be proud. Stay curious. Keep going.<br />Your work matters more than you think.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/853/ragan-lab</guid>
  <pubDate>Sun, 14 Jul 2013 12:03:43 -0500</pubDate>
  <link></link>
  <title><![CDATA[Ragan Lab]]></title>
  <description><![CDATA[
<p>Computational systems biology</p>

<p>Research Area: <br />breast cancer; pancreatic cancer; prostate cancer; gastrointestinal disorders; urohaemolytic disorders; staphylococcal diseases</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/7989/cancers-cure-is-on-the-way</guid>
	<pubDate>Wed, 22 Jan 2014 12:00:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/7989/cancers-cure-is-on-the-way</link>
	<title><![CDATA[Cancers cure is on the way !!!]]></title>
	<description><![CDATA[<p>The study on blind mole rat (Spalax) was carried out by researchers from the University of Haifa, Israel, and published in the peer-reviewed scientific journal BMC Biology.</p><p>The blind mole rat (Spalax) is an intriguing creature worthy of study. This was animal research examining the resistance subterranean blind mole rats (Spalax) have to cancers. Blind mole rats are one of a unique group of animals that spend their lives underground, are tolerant of very low oxygen levels (down to only 3% concentration &ndash; levels that would kill a human), have a long lifespan of more than 20 years, which is exceptional for a small rodent, and show no clear signs of ageing or age-related diseases.</p><p>This research has demonstrated the unique abilities of the blind mole rat to resist cancer, even when directly given potent cancer-causing chemicals. In this study researchers gave blind mole rats potent cancer-causing chemicals either through injections or applied directly to the skin, but the animals didn't develop cancer.<br /><br />Remarkably, connective tissue cells (fibroblasts) taken from the blind mole rat even prevented the growth of human cancer cells when they were grown together in the laboratory.<br /><br />In the laboratory, the researchers also demonstrated how connective tissue cells called fibroblasts taken from the animal seem to play an important role in this cancer resistance. These cells prevented the growth of human cancer cells when the two types of cells were grown together in the laboratory.<br /><br />The researchers concluded that, "This report provides pioneering evidence that Spalax [the blind mole rat] is not only resistant to spontaneous cancer, but also to experimentally induced cancer, and shows the unique ability of Spalax fibroblasts to inhibit growth and kill cancer cells, but not normal cells, either through direct fibroblast-cancer cell interaction or via soluble factors."</p><p>Nonetheless, there remains optimism that understanding the anti-cancer mechanisms of mole rats may one day help inform further cancer treatments for humans, but a lot more research &ndash; and probably a significant amount of time &ndash; is needed before this can be considered.</p><p><img src="http://i.telegraph.co.uk/multimedia/archive/02599/naked-mole-rat_2599114b.jpg" alt="image" width="620" height="387" style="border: 0px; border: 0px;"></p><p>Reference:</p><p>Image: telegraph.co.uk</p><p>http://www.biomedcentral.com/1741-7007/11/91</p><p>Manov, Irena, et al. "Pronounced cancer resistance in a subterranean rodent, the blind mole-rat, Spalax: in vivo and in vitro evidence." BMC biology 11.1 (2013): 91.</p><p>http://www.nhs.uk/news/2014/01January/Pages/Claims-of-a-universal-cure-for-cancer-misleading.aspx</p><p>http://www.express.co.uk/news/health/454188/EXCLUSIVE-Cure-for-ALL-cancers-is-on-the-way-as-scientists-discover-major-breakthrough</p><p>http://www.dailymail.co.uk/health/article-2540321/Could-mole-rats-hold-key-cure-cancer-Scientists-hail-potentially-life-changing-breakthrough.html</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7362/junior-research-fellow-jrf-project-fellow-kalasalingam-university</guid>
  <pubDate>Thu, 19 Dec 2013 13:23:39 -0600</pubDate>
  <link></link>
  <title><![CDATA[Junior Research Fellow (JRF) / Project Fellow @ Kalasalingam University]]></title>
  <description><![CDATA[
<p>Applications are invited from interested candidates for the post of one Junior Research Fellow / Project Fellow on a purely temporary basis in a time bound research project (3 years) sponsored by Science and Engineering Research Board, Government of India, New Delhi.</p>

<p>Name of the fellowship: Junior Research Fellow (JRF) / Project Fellow</p>

<p>Title of the project: Genome-wide Mapping of Murine Specific Dengue T-cell Epitopes: Computational Prediction, Identification and use as Candidate Vaccines</p>

<p>Duration: 3 years</p>

<p>Fellowship: Rs. 18,000 for first 2 years and Rs. 20,000 for 3rdyear (for M.Tech. candidates)</p>

<p>Rs. 16,000 for first 2 years and Rs. 18,000 for 3rdyear (for M.Sc. candidates with NET qualification)</p>

<p>Rs. 8,000 for first 2 years and Rs. 10,000 for 3rdyear (for M.Sc. candidates without NET qualification)</p>

<p>Qualifications: M.Tech. in Biotechnology / M.Sc. in any branch of Life Sciences</p>

<p>Desirable Experience: Minimum of two years research experience in any of the following areas: Immunology / Microbiology / Gene Manipulation / Bioinformatics</p>

<p>Interested and eligible candidates may apply with their resume along with relevant documents and a passport size photograph to the Principal Investigator by post (or e-mail) on or before December 31, 2013. Only short listed candidates will be called for written test and/or interview. Selected candidate may register for PhD in Kalasalingam University. No TA/DA will be paid for attending interview.</p>

<p>Dr. K. Sundar<br />Principal Investigator (SERB Project)<br />Department of Biotechnology<br />Kalasalingam University<br />Krishnankoil – 626126, Tamil Nadu<br />sundarkr@klu.ac.in</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/38838/computer-scientistbioinformatician-at-ieo-in-milan-italy</guid>
  <pubDate>Thu, 31 Jan 2019 09:10:12 -0600</pubDate>
  <link></link>
  <title><![CDATA[Computer scientist/bioinformatician at IEO in Milan, Italy]]></title>
  <description><![CDATA[
<p>We are looking for a computer scientist or a bioinformatician with a strong computation background to join the bioinformatics unit of the IEO in Milan. Web development, scripting, experience with spring boot, hpc, docker are appreciated. The candidate will evolve in a research environment (next generation sequencing among others). The selected candidate will consolidate our team for the development and maintenance of the bioinformatics resources, and will have the opportunity to support the research groups in setting new tools and pipelines.</p>

<p>Place of employment and work</p>

<p>The candidate will be located at the Department of Experimental Oncology of the European Institute of Oncology in Milan (Italy), one of Europe’s leading research institutes in biomedical research, where he/she will also interact with one of the largest computational biology communities in Italy</p>

<p>Requirements:</p>

<p>The candidate should have a good knowledge of the UNIX system and good programming skills (bash, R, python, java). Background in bioinformatics would be appreciated but is not mandatory. Additional experience with containers (docker, singularity),  grid computing, web frameworks, continuous integrations will be appreciated.</p>

<p>For further info or to arrange an informal interview, please write to arnaud.ceol@ieo.it</p>
]]></description>
</item>

</channel>
</rss>