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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30976?offset=890</link>
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	<description><![CDATA[]]></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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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43690/ucsc-sars-cov-2-genome-browser</guid>
	<pubDate>Thu, 06 Jan 2022 06:48:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43690/ucsc-sars-cov-2-genome-browser</link>
	<title><![CDATA[UCSC SARS-CoV-2 Genome Browser]]></title>
	<description><![CDATA[<p><span>The UCSC SARS-CoV-2 Genome Browser (</span><a href="https://genome.ucsc.edu/covid19.html">https://genome.ucsc.edu/covid19.html</a><span>) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT&ndash;PCR and sequencing primers and CRISPR guides. We invite all investigators to contribute to this resource to accelerate research and development activities globally.</span></p><p>Address of the bookmark: <a href="https://www.nature.com/articles/s41588-020-0700-8" rel="nofollow">https://www.nature.com/articles/s41588-020-0700-8</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10841/ra-at-iisr-kozhikode</guid>
  <pubDate>Thu, 15 May 2014 10:08:09 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA at IISR Kozhikode]]></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>Walk- in- Test cum Interview (based on test) for the selection of Research Associate</p>

<p>under the scheme “Distributed Information Sub Centre –DISC” &amp; Research Assistant under scheme “Phytophthora, Fusarium and Ralstonia diseases of Horticultural and Field Crops” will be held at this Institute as per details indicated below.</p>

<p>WALK -IN- TEST CUM INTERVIEW</p>

<p>Name of the post : Research Associate</p>

<p>Date of Interview : 21-05-2014 at 10.00 AM</p>

<p>No. of posts : One</p>

<p>Qualifications : a)Essential</p>

<p>Ph.D Degree in Bioinformatics OR :  Masters degree in Bioinformatics with a minimum of<br />60% marks or equivalent OGPA with at least two years research experience as evidenced from fellowship/ associateship/training/published papers etc.</p>

<p>b)Desirable: Experience in NGS data analysis.</p>

<p>Emoluments : Rs. 23,000/- per month + HRA (Masters Degree Holders)</p>

<p>Rs. 24,000/- per month + HRA (Ph.D Degree Holders)</p>

<p>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)</p>

<p>Duration of Project : Till 31-03-2017.</p>

<p>Title of Assigment : Research Assistant (on contract basis)</p>

<p>No. of vacancy : One</p>

<p>Qualification : Essential : Post Graduation in Bioinformatics and  Minimum one year experience in NGS data analysis</p>

<p>Desirable : Experience in Perl/Python/R</p>

<p>Remuneration : Rs. 20,000/- per month (consolidated)</p>

<p>Scope of work :</p>

<p>1. Analysis of different file formats and their conversions.</p>

<p>2. Assessing the quality of data and filtering of raw reads.<br />3. Assembling the raw reads-de novo as well as reference  mapping.<br />4. Compression of aligned reads using Jam tools<br />5. RNA-seq. Analysis<br />6. Differential expression testing involving Normalization,  Statistical testing, heat map generation &amp; hierarchical  clustering<br />7. Annotating the assembled genome and geneet testing  and their validation<br />8. Metabolic pathway analysis<br />9. Comparative genomics<br />10. Setting up of genome browsers.</p>

<p>Period of Assigment : Initially for six months.</p>

<p>Date &amp; Venue of Interview : 21-05-2014 at IISR, Kozhikode at 10.00 AM</p>

<p>More at http://www.spices.res.in/pdf/disc-advtmnt.pdf</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43859/mumco-is-a-simple-bash-script-that-uses-whole-genome-alignment-information-provided-by-mummer-v4-to-detect-variants</guid>
	<pubDate>Wed, 27 Apr 2022 04:34:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43859/mumco-is-a-simple-bash-script-that-uses-whole-genome-alignment-information-provided-by-mummer-v4-to-detect-variants</link>
	<title><![CDATA[MUM&amp;Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v4) to detect variants.]]></title>
	<description><![CDATA[<p dir="auto">MUM&amp;Co is able to detect:<br>Deletions, insertions, tandem duplications and tandem contractions (&gt;=50bp &amp; &lt;=150kb)<br>Inversions (&gt;=1kb) and translocations (&gt;=10kb)</p><p>Address of the bookmark: <a href="https://github.com/SAMtoBAM/MUMandCo" rel="nofollow">https://github.com/SAMtoBAM/MUMandCo</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/11000/professorassociate-professor-assistant-professor-at-chettinad-academy-of-research-and-education</guid>
  <pubDate>Sat, 24 May 2014 00:00:15 -0500</pubDate>
  <link></link>
  <title><![CDATA[Professor/Associate Professor/ Assistant Professor at Chettinad Academy of Research and Education]]></title>
  <description><![CDATA[
<p>OPEN FACULTY POSITION</p>

<p>Chettinad Academy of Research and Education (CARE) invites applications from eligible and translational research-oriented candidates to the posts of Professor/Associate Professor/ Assistant Professor  Computational Biology, Bioinformatics, and Pharmaceutical Chemistry.</p>

<p>Emoluments: As per UGC norms (Adequate Compensation for Postdoctoral/Teaching experience)</p>

<p>Candidates fulfilling the eligibility criteria as per the UGC norms can send their full CV with copies of certificates and reference letters to the following address by post or by e-mail on or before 31st May 2014</p>

<p>The Registrar,<br />Chettinad Academy of Research and Education,<br />Chettinad Health City<br />Kelambakkam, Chennai 603 103<br />Tamil Nadu<br />T +91 (0)44 4741 1000<br />F +91 (0)44 4741 1011<br />Email: jobs @chettinadhealthcity.com</p>

<p>Advertisement: http://182.73.176.163/chc/ads2014.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44322/genome-context-viewer-gcv</guid>
	<pubDate>Sun, 21 May 2023 19:33:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44322/genome-context-viewer-gcv</link>
	<title><![CDATA[Genome Context Viewer (GCV)]]></title>
	<description><![CDATA[<p><span>The Genome Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. Specifically, it uses functional annotations as a unit of search and comparison. By adopting a common set of annotations, data-store operators can deploy federated instances of GCV, allowing users to compare genomes from different providers in a single interface.</span></p><p>Address of the bookmark: <a href="https://github.com/legumeinfo/gcv" rel="nofollow">https://github.com/legumeinfo/gcv</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/11107/the-minerva-research-group-for-bioinformatics</guid>
  <pubDate>Tue, 27 May 2014 15:48:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[The Minerva Research Group for Bioinformatics]]></title>
  <description><![CDATA[
<p>The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.</p>

<p>http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27</p>

<p>Kelso Group<br />Department of Evolutionary Genetics<br />Max Planck Institute for Evolutionary Anthropology<br />Deutscher Platz 6<br />04103 Leipzig<br />Germany<br />Phone: +49 341 3550 500</p>

<p>Job: <br />http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome</guid>
	<pubDate>Thu, 08 Aug 2024 23:31:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome</link>
	<title><![CDATA[Tools to access the quality of your assembled genome !]]></title>
	<description><![CDATA[<ul dir="auto">
<li><a href="https://github.com/linsalrob/fasta_validator">FASTA VALIDATOR</a>&nbsp;+&nbsp;<a href="https://github.com/shenwei356/seqkit">SEQKIT RMDUP</a>: FASTA validation</li>
<li><a href="https://genometools.org/tools/gt_gff3validator.html">GENOMETOOLS GT GFF3VALIDATOR</a>: GFF3 validation</li>
<li><a href="https://github.com/PlantandFoodResearch/assemblathon2-analysis/blob/a93cba25d847434f7eadc04e63b58c567c46a56d/assemblathon_stats.pl">ASSEMBLATHON STATS</a>: Assembly statistics</li>
<li><a href="https://genometools.org/tools/gt_stat.html">GENOMETOOLS GT STAT</a>: Annotation statistics</li>
<li><a href="https://github.com/ncbi/fcs">NCBI FCS ADAPTOR</a>: Adaptor contamination pass/fail</li>
<li><a href="https://github.com/ncbi/fcs">NCBI FCS GX</a>: Foreign organism contamination pass/fail</li>
<li><a href="https://gitlab.com/ezlab/busco">BUSCO</a>: Gene-space completeness estimation</li>
<li><a href="https://github.com/tolkit/telomeric-identifier">TIDK</a>: Telomere repeat identification</li>
<li><a href="https://github.com/oushujun/LTR_retriever/blob/master/LAI">LAI</a>: Continuity of repetitive sequences</li>
<li><a href="https://github.com/DerrickWood/kraken2">KRAKEN2</a>: Taxonomy classification</li>
<li><a href="https://github.com/igvteam/juicebox.js">HIC CONTACT MAP</a>: Alignment and visualisation of HiC data</li>
<li><a href="https://github.com/mummer4/mummer">MUMMER</a>&nbsp;&rarr;&nbsp;<a href="http://circos.ca/documentation/">CIRCOS</a>&nbsp;+&nbsp;<a href="https://plotly.com/">DOTPLOT</a>&nbsp;&amp;&nbsp;<a href="https://github.com/lh3/minimap2">MINIMAP2</a>&nbsp;&rarr;&nbsp;<a href="https://github.com/schneebergerlab/plotsr">PLOTSR</a>: Synteny analysis</li>
<li><a href="https://github.com/marbl/merqury">MERQURY</a>: K-mer completeness, consensus quality and phasing assessment</li>
</ul>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11582/monitor-running-jobs-on-linux-server</guid>
	<pubDate>Fri, 06 Jun 2014 16:18:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11582/monitor-running-jobs-on-linux-server</link>
	<title><![CDATA[Monitor running jobs on Linux server]]></title>
	<description><![CDATA[<p>You as a bioinformatican run lots of program on your servers. Sometime the shared server is also used by your colleague. If server is busy you sometime need to check the running programs and want to monitor the running programs as well. The "top" command will come in handy when you need to find out if things are still running, how long they&rsquo;ve been running, or how much memory is being used.<br /><br />&lsquo;top&rsquo; is very simple to run: type<br /><br />%% top<br /><br />You&rsquo;ll get a screen that looks like this, and is updated regularly:<br /><br /><img src="http://bioinformaticsonline.com/mod/photo/top.png" width="659" height="582" alt="image" style="border: 0px;"><br />Simple, right? Heh.<br /><br />First! Note that you can use &lsquo;q&rsquo; or &lsquo;CTRL-C&rsquo; to exit from &lsquo;top&rsquo;.<br /><br />Now let&rsquo;s read and understand at each line independently.<br /><br />The first line:<br /><br />top - 23:00:48 up 39 days,&nbsp; 2 user,&nbsp; load average: 0.00, 0.00, 0.00<br /><br />The first line tells you the current time, how long the machine has been up, how many users are logged in, and the short/medium/long-term compute load on the machine. If you run something for a long time, you&rsquo;ll see these numbers go up. Right now, the machine is basically just sitting there, so these are all close to 0.<br /><br />The second line:</p><p>Tasks:&nbsp; 239 total,&nbsp;&nbsp; 1 running,&nbsp; 238 sleeping,&nbsp;&nbsp; 0 stopped,&nbsp;&nbsp; 0 zombie<br /><br />This line tells you how many processes are running. If you are using laptops machines it&rsquo;s not so interesting because you really are the only one using this machine.<br /><br />Cpu(s):&nbsp; 0.0%us,&nbsp; 0.0%sy,&nbsp; 0.0%ni,100.0%id,&nbsp; 0.0%wa,&nbsp; 0.0%hi,&nbsp; 0.0%si,&nbsp; 0.0%st<br /><br />This line contains the CPU load. The first two numbers are how busy the system is doing computation (&ldquo;us&rdquo; stands for &ldquo;user&rdquo;) and how busy the system is doing system-y things like accessing disks or network (&ldquo;sy&rdquo; stands for &ldquo;system&rdquo;). We&rsquo;ll talk more about this later.<br /><br />Mem:&nbsp;&nbsp; 49457320k total,&nbsp;&nbsp;&nbsp; 3492174k used,&nbsp; 14535596k free,&nbsp;&nbsp;&nbsp; 1435148k buffers<br /><br />This should be easy to understand &ndash; how much memory you&rsquo;re using! <br /><br />Swap:&nbsp;&nbsp; 539356k total,&nbsp;&nbsp; 28332k used,&nbsp;&nbsp; 836562k free,&nbsp;&nbsp;&nbsp; 29862014k cached<br /><br />Swap is just on-disk memory that can be used to &ldquo;swap&rdquo; out programs from main memory. Again, we&rsquo;ll talk about this later.:<br /><br />PID USER&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PR&nbsp; NI&nbsp; VIRT&nbsp; RES&nbsp; SHR S %CPU %MEM&nbsp;&nbsp;&nbsp; TIME+&nbsp; COMMAND<br />&nbsp; 1 root&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 39 &nbsp; 19&nbsp; 0&nbsp; 0&nbsp; 0 S&nbsp; 0.0&nbsp; 0.0&nbsp;&nbsp; 246:57.22 kipmi0<br />&nbsp; 2 root&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; RT&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp; 0 S&nbsp; 0.0&nbsp; 0.0&nbsp;&nbsp; 0:00.00 migration/0<br /><br />And... finally! What&rsquo;s actually running! The two most important numbers are the %CPU and %MEM towards the right, as well as the COMMAND. This tells you how compute- and memory-intensive your program is. Right now, nothing&rsquo;s running so the numbers aren&rsquo;t very interesting, but just wait until we run something...</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44770/nvidia-and-arc-institute-unveil-evo-2-a-breakthrough-ai-for-dna-design</guid>
	<pubDate>Fri, 21 Feb 2025 10:39:47 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44770/nvidia-and-arc-institute-unveil-evo-2-a-breakthrough-ai-for-dna-design</link>
	<title><![CDATA[NVIDIA and Arc Institute Unveil Evo 2: A Breakthrough AI for DNA Design]]></title>
	<description><![CDATA[<p>NVIDIA and the Arc Institute have introduced <strong style="font-size: 12.8px;">Evo 2</strong>, a groundbreaking AI model designed to <strong style="font-size: 12.8px;">understand, predict, and generate DNA sequences</strong>. This marks a major advancement in computational biology, offering scientists an unprecedented tool to decode the genetic blueprint of life and even design entirely new biological systems.</p><h3><strong>The Power of Evo 2: AI Meets DNA</strong></h3><p>Evo 2 is <strong>the largest AI model for biology ever created</strong>, trained on an astonishing <strong>9.3 trillion DNA "letters"</strong> (nucleotides) carefully selected from genomes spanning the entire tree of life. This massive dataset ensures that Evo 2 can recognize patterns and relationships in genetic sequences at an unparalleled scale.</p><p>For the first time, scientists can <strong>design DNA with AI</strong>, moving beyond simple sequence analysis to active DNA generation. Evo 2 enables researchers to <strong>predict, modify, and even create entire genetic sequences</strong>, opening new possibilities in medicine, agriculture, and synthetic biology.</p><h3><strong>Decoding the Dark Genome</strong></h3><p>One of the biggest challenges in genetics is understanding the <strong>non-coding regions</strong> of DNA&mdash;vast stretches of the genome that do not code for proteins but play crucial roles in regulating gene expression. These regions control when and how genes are activated, influencing everything from development to disease.</p><p>Evo 2 is designed to <strong>decode these non-coding elements</strong>, helping researchers uncover their functions and use this knowledge to develop gene-based therapies, synthetic life forms, and precision agriculture solutions.</p><h3><strong>From Reading DNA to Writing It</strong></h3><p>To put Evo 2&rsquo;s impact into perspective:</p><ul>
<li><strong>Previous AI models could "read" DNA</strong> like a book, analyzing genetic sequences and identifying patterns.</li>
<li><strong>Evo 2 can "write" entirely new DNA</strong>, designing functional genes, chromosomes, and even full genomes from scratch.</li>
</ul><p>This means scientists can now <strong>engineer biological systems with AI</strong>, designing new proteins, metabolic pathways, and genetic circuits to address real-world challenges.</p><h3><strong>A Step Toward Generative Biology</strong></h3><p>The Arc Institute describes Evo 2 as a major step toward <strong>"generative biology"</strong>&mdash;a revolutionary approach where AI is used to create <strong>novel biological structures</strong> rather than just analyzing existing ones. This could lead to breakthroughs such as:</p><ul>
<li><strong>New medicines</strong>: AI-generated enzymes and proteins tailored for targeted therapies.</li>
<li><strong>Disease-resistant crops</strong>: Genetically optimized plants for higher yield and climate resilience.</li>
<li><strong>Synthetic organisms</strong>: Custom-designed microbes for bioremediation, biofuel production, and industrial applications.</li>
</ul><h3><strong>An Open-Source Revolution</strong></h3><p>Unlike many proprietary AI models, <strong>Evo 2 is open source</strong>, making its capabilities accessible to researchers worldwide. This democratization of AI-driven biology means that scientists from different disciplines can <strong>collaborate, experiment, and innovate</strong>, accelerating discoveries in genetic engineering and synthetic biology.</p><p>With Evo 2, the boundaries of what&rsquo;s possible in <strong>DNA design, genetic engineering, and biological innovation</strong> are being redrawn. The future of life sciences is no longer just about understanding life&rsquo;s code&mdash;it&rsquo;s about writing it.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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