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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/17176?offset=1000</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/fun/view/44845/a-bioinformatician%E2%80%99s-lament</guid>
	<pubDate>Thu, 29 May 2025 01:33:31 -0500</pubDate>
	<link>https://bioinformaticsonline.com/fun/view/44845/a-bioinformatician%E2%80%99s-lament</link>
	<title><![CDATA[A Bioinformatician’s Lament]]></title>
	<description><![CDATA[<div><div dir="auto"><p><em>"I have a presentation tomorrow,"</em>&nbsp;they say,</p><p>With hopeful eyes, like it&rsquo;s all child's play.<br />As if results bloom overnight, full-grown&mdash;<br />Not wrangled from chaos, and error-prone.</p><p><strong>Oh brave soul, sit, let&rsquo;s walk through the tale,</strong><br />Of pipelines broken and servers that fail.<br />The journey starts: &ldquo;The data? It&rsquo;s there&mdash;<br />Just fetch it from S3, easy, I swear.&rdquo;</p><p>Now I summon&nbsp;<code>awscli</code>&nbsp;with dread,<br />Reset my keys, credentials fed.<br />Configure regions, IAM roles too&mdash;<br />All this, and still no peek at the view.</p><p>Next up, the tool: &ldquo;It&rsquo;s open source!&rdquo;<br />On GitHub, rotting, no sign of remorse.<br />Python 2.7, some GCC trick&mdash;<br />The install alone might make you sick.</p><p>Finally, progress! The pipeline runs&hellip;<br />Till RAM collapses and error stuns.<br />Oh, and the metadata? A crime,<br />Merged cells, font soup, out of time.</p><p>Sample IDs&mdash;what a cryptic game:<br /><code>Sample_1</code>,&nbsp;<code>S1</code>,&nbsp;<code>sample-1</code>... the same?<br />Controls mislabeled, cases flipped,<br />No wonder my sanity's starting to slip.</p><p>Then QC plots, PCA joy&mdash;<br />Wait, that&rsquo;s a tumor labeled as a boy?<br />Clusters cross, and axes lie,<br />And I still don&rsquo;t know&nbsp;<em>which</em>&nbsp;sample&rsquo;s "guy."</p><p>But the clock ticks on, and it&rsquo;s half-past doom,<br />They want the final UMAP soon.<br />With pastel colors, labeled clear&mdash;<br />"Can we move that legend to&nbsp;<em>right here</em>?"</p><p>Tweak by tweak, I adjust each frame,<br />Resize Panel B, annotate a name.<br />Export the plot&mdash;it starts to gleam&hellip;<br />Then my laptop crashes. I scream.</p><p>This is the grind, the long-haul game,<br />Where science hides behind code and flame.<br />No &ldquo;Export to Nature&rdquo; button to press,<br />Just toil and logic and hope for success.</p><p>So next time you whisper that fated line&mdash;<br />&ldquo;I have a talk, can you make it shine?&rdquo;<br />Know: bioinformatics is craft, not a click,<br />It&rsquo;s science with scars, not just a quick fix.</p><p><strong>To all who debug at 3AM light,</strong><br />Who ghostwrite figures through sleepless night&mdash;<br />You are the backbone, silent and true,<br />First-author-worthy, if only they knew.<br /><br /></p><hr><p><em><br />"कल मेरी प्रेज़ेंटेशन है,"</em>&nbsp;वो कहते हैं,</p></div></div><div><div dir="auto"><p>आशा भरी आँखों से, जैसे सब सहज है।<br />जैसे परिणाम रातोंरात प्रकट हो जाएं&mdash;<br />ना कि डेटा की भूलभुलैया से उखाड़े जाएं।</p><p><strong>आओ बैठो, एक किस्सा सुनाता हूँ,</strong><br />जहाँ पाइपलाइन टूटती है, और सर्वर भी थक जाते हैं।<br />कहानी शुरू होती है: &ldquo;डेटा तो है&mdash;<br />बस S3 बकेट में, एकदम पास में कहीं।&rdquo;</p><p>अब&nbsp;<code>awscli</code>&nbsp;बुलाता हूँ डरते हुए,<br />कुंजी सेट करूँ, क्रेडेंशियल जोड़ूं, रीजन भरूँ।<br />इतनी मशक्कत, फिर भी डेटा नहीं मिला,<br />बस सेटअप में ही पूरा दिन चला।</p><p>फिर आता है टूल: &ldquo;ओपन-सोर्स है!&rdquo;<br />GitHub पर है, 2019 से सूखा पड़ा है।<br />Python 2.7 चाहिए, एक पुराना कम्पाइलर,<br />और साथ में थोड़ी सी दुआ की ताकत।</p><p>आख़िरकार टूल चला, खुशी सी हुई,<br />लेकिन रन करते ही, मेमोरी ने हार मानी।<br />और मेटाडेटा? एक एक्सेल की आफ़त,<br />मर्ज़ किए हुए सेल, बस और क्या चाहिए काफ़ियत?</p><p>सैंपल आईडी? बस भगवान ही जाने&mdash;<br /><code>Sample_1</code>,&nbsp;<code>sample-1</code>,&nbsp;<code>S1</code>, और&nbsp;<code>control1</code>&mdash;<br />ये सब एक ही सैंपल हैं क्या?<br />पता तब चलता है जब पूछो दो-तीन बार।</p><p>काउंट मैट्रिक्स तैयार, अब R या Python की बारी,<br />QC करो, PCA प्लॉट&mdash;पर कुछ गड़बड़ भारी।<br />ट्यूमर और नॉर्मल का अदला-बदली खेल,<br />बार-बार, वही पुरानी झमेल।</p><p>आख़िर में आया मॉडलिंग का समय,<br />स्टैट्स, प्लॉट्स, डिफरेंशियल एक्सप्रेशन का श्रम।<br />लेकिन घड़ी में 5 बज चुके हैं जनाब,<br />और 8 बजे तक UMAP चाहिए, साफ़-सुथरा जबाब।</p><p>तो मैं कोड लिखता हूँ रात भर बैठ कर,<br />कलर पैलेट, जीन लेबल, लीजेंड बाहर रख कर।<br />फ़ॉन्ट, पैनल, एक्सिस सब सुधार,<br />एक्सपोर्ट करता हूँ... और लैपटॉप कहता है&mdash;"अब नहीं यार!"</p><p>इसीलिए बायोइन्फॉर्मेटिक्स में लगता है समय,<br />ये &ldquo;बस सीरत चलाओ&rdquo; या &ldquo;वोल्कैनो प्लॉट बनाओ&rdquo; नहीं है।<br />ये है सिस्टम एडमिन का काम, डेटा की सफ़ाई,<br />QC, डिबगिंग, और सांइस की सच्ची लड़ाई।</p><p><strong>तो कुछ सीखें इस व्यथा से आप भी आज:</strong><br />24 घंटे पहले चमत्कार मत माँगिए।<br />अच्छे फ़िगर साफ़ डेटा से बनते हैं।<br />बायोइन्फॉर्मेटिक्स जादू नहीं, विज्ञान है।<br />समय से बात कीजिए, प्रक्रिया का सम्मान कीजिए।</p><p><strong>और उन सभी बायोइन्फॉर्मेटिशियनों को सलाम,</strong><br />जो दूसरों की प्रेज़ेंटेशन के लिए रातों में जागते हैं&mdash;<br />तुम हो फ़िगर्स के भूत लेखक,<br />तुम हो बिना नाम के सह-लेखक।<br />तुम पहले लेखक बनने के हक़दार हो&mdash;<br />और एक लंबी नींद के भी।</p><p>Note: Written with the help of AI/LLM Tools !</p></div></div>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/1219/research-with-help-of-bioinformatics-helpful</guid>
	<pubDate>Fri, 02 Aug 2013 11:20:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/1219/research-with-help-of-bioinformatics-helpful</link>
	<title><![CDATA[Research with help of bioinformatics helpful]]></title>
	<description><![CDATA[<p>Endocrinologist G.R. Sridhar says</p><blockquote><p>Research with the help of bioinformatics with a trans-disciplinary approach is yielding good results.</p><p>http://www.thehindu.com/features/education/research/research-with-help-of-bioinformatics-helpful/article2295629.ece</p></blockquote>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44910/courses-to-get-you-started-with-bioinformatics</guid>
	<pubDate>Tue, 30 Sep 2025 13:07:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44910/courses-to-get-you-started-with-bioinformatics</link>
	<title><![CDATA[Courses to Get You Started with Bioinformatics]]></title>
	<description><![CDATA[<p>Bioinformatics is now at the heart of modern biology and medicine. From decoding genomes and predicting antimicrobial resistance, to developing personalized medicine and advancing evolutionary research, computational skills are no longer optional &mdash; they are essential.</p><p>Yet, for many students, biologists, and even computer scientists, the question is: <em>&ldquo;Where do I begin?&rdquo;</em> With so many platforms, books, and tutorials available, it&rsquo;s easy to feel overwhelmed.</p><p>To make it easier, I&rsquo;ve compiled <strong>10 excellent resources</strong> &mdash; ranging from beginner-friendly introductions to advanced computational genomics courses. Many of these are freely available, created by pioneers in the field, and widely used in classrooms and research labs worldwide.</p><p>Whether you are a complete beginner or looking to strengthen your foundations, these courses will help you build the skills needed to analyze biological data, design workflows, and think computationally about complex biological systems.<br /><br /></p><h3>1. <a href="https://rafalab.dfci.harvard.edu/pages/harvardx.html?utm_source=chatgpt.com" target="_new">HarvardX Data Analysis for Genomics by Rafael Irizarry<span></span></a></h3><p>From the almighty Rafa, this set of online courses (via edX/HarvardX) is a classic starting point for genomic data science and bioinformatics.</p><h3>2. <a href="https://github.com/quinlan-lab/applied-computational-genomics" target="_new">Applied Computational Genomics &ndash; Aaron Quinlan<span></span></a></h3><p>Aaron Quinlan (creator of <strong>bedtools</strong> and many other tools) has made his course materials open. A practical, tool-driven genomics introduction.</p><h3>3. <a target="_new">Bioinformatics Algorithms (Coursera + Companion Book)<span></span></a></h3><p>Find the highly visual video classes on Coursera, backed by the popular <em>Bioinformatics Algorithms</em> book.</p><h3>4. <a href="https://vis.usal.es/rodrigo/documentos/papers/biostar-handbook.pdf?utm_source=chatgpt.com" target="_new">The Biostar Handbook<span></span></a></h3><p>Not a course per se, but a hands-on manual by Istvan (founder of <strong>Biostars.org</strong>) that&rsquo;s even used in classes at Penn State.</p><h3>5. <a href="https://liulab-dfci.github.io/bioinfo-combio/?utm_source=chatgpt.com" target="_new">Introduction to Bioinformatics and Computational Biology (by Shirley Liu)<span></span></a></h3><p>A comprehensive introduction from Shirley Liu&rsquo;s lab (Harvard DFCI). Covers both theory and computational practice.</p><h3>6. <a target="_new">Data Carpentry: Genomics Workshops<span></span></a></h3><p>Community-driven training workshops that focus on practical, reproducible research. I was honored to serve as curriculum committee chair here.</p><h3>7. <a href="https://github.com/schatzlab/appliedgenomics2018" target="_new">Computational Genomics: Applied Comparative Genomics<span></span></a></h3><p>From the Schatz Lab &mdash; applied comparative genomics with real-world data.</p><h3>8. <a href="https://biodatascience.github.io/compbio/?utm_source=chatgpt.com" target="_new">Introduction to Computational Biology (Mike Love, creator of DESeq2)<span></span></a></h3><p>This course bridges statistics, biology, and computation &mdash; a solid primer for anyone entering computational biology.</p><h3>9. <a target="_new">MIT Computational Biology (6.047 / 6.878 / HST.507) by Manolis Kellis<span></span></a></h3><p>Covers genomes, networks, evolution, and health. A deep-dive from MIT&rsquo;s OpenCourseWare archive.</p><h3>10. <a href="https://github.com/applied-bioinformatics/iab2" target="_new">An Introduction to Applied Bioinformatics<span></span></a></h3><p>An interactive textbook with Python code, designed for practical applied bioinformatics learning.</p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/45116/recommended-reading-list</guid>
	<pubDate>Sat, 18 Apr 2026 19:25:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/45116/recommended-reading-list</link>
	<title><![CDATA[Recommended reading list]]></title>
	<description><![CDATA[<p>Some of the following titles might be available as ebooks&bull;</p><p>Population genetics: A concise guide. John Gillespie.The Johns Hopkins University Press (1997)&bull;</p><p>Population genetics. J. S. Gale. Wiley (1980)&bull;</p><p>Evolutionary genetics. John Maynard-Smith. Oxford University Press (1998)&bull;</p><p>The growth of biological thought. Ernst Mayr. Harvard University Press (1985)&bull;</p><p>Guns, germs and steel. Jared Diamond. W. W. Norton (2007)&bull;</p><p>Evolutionary theory: Mathematical and conceptual foundations. Sean Rice. Oxford University Press (2004)</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/2560/great-place-to-study-bioinformatics-in-europe</guid>
	<pubDate>Sun, 18 Aug 2013 18:41:34 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/2560/great-place-to-study-bioinformatics-in-europe</link>
	<title><![CDATA[Great Place to Study Bioinformatics in Europe]]></title>
	<description><![CDATA[<p>Study bioinformatics is like being jack of all trade so it is important you choose where it will be good backup of computer science, and natural science infrastructure and faculty. Especially having a good teachers in computer science is indispensible.&nbsp;</p><p><strong>Few places in Europe where good (and @some places no tution fees) master bioinformatics courses and recommended are</strong>:</p><p><strong>KU Leuven, Belgium</strong></p><p><a href="http://onderwijsaanbod.kuleuven.be/opleidingen/e/CQ_50269018.htm">http://onderwijsaanbod.kuleuven.be/opleidingen/e/CQ_50269018.htm</a></p><p><strong>ETH, Zurich</strong></p><p><a href="http://www.cbb.ethz.ch/">http://www.cbb.ethz.ch/</a></p><p><strong>University of Copenhagen, Denmark</strong></p><p><a href="http://studies.ku.dk/masters/bioinformatics/">http://studies.ku.dk/masters/bioinformatics/</a></p><p><strong>University of Helsinki, Finland</strong></p><p><a href="http://www.cs.helsinki.fi/en/mbi/">http://www.cs.helsinki.fi/en/mbi/</a></p><p><strong>Stockholm University, Sweden</strong></p><p><a href="http://www.sbc.su.se/masters/">http://www.sbc.su.se/masters/</a></p><p><strong>Universities in Netherlands</strong></p><p><a href="http://www.nbic.nl/education/msc-programmes/">http://www.nbic.nl/education/msc-programmes/</a></p><p><strong>TUM , Munich Germany</strong></p><p><a href="http://www.mastersportal.eu/studies/865/bioinformatics.html">http://www.mastersportal.eu/studies/865/bioinformatics.html</a></p><p><strong>University of Bergen, Norway</strong></p><p><a href="http://www.uib.no/en/studieprogram/MAMN-INF/BI/plan">http://www.uib.no/en/studieprogram/MAMN-INF/BI/plan</a></p><p><strong>Goethe-University in Frankfurt am Main</strong></p><p><a href="http://www.uni-frankfurt.de/58444439/mabi">http://www.uni-frankfurt.de/58444439/mabi</a></p><p><strong>Other links</strong>:</p><p><a href="http://www.masterstudies.com/Masters-Degree/Bioinformatics/Europe/">http://www.masterstudies.com/Masters-Degree/Bioinformatics/Europe/</a></p><p><a href="https://studyinsweden.se/programmes/?query=bioinformatics&amp;period=ht-2016&amp;level=ma&amp;subject=natural-science&amp;university=#search">https://studyinsweden.se/programmes/?query=bioinformatics&amp;period=ht-2016&amp;level=ma&amp;subject=natural-science&amp;university=#search</a></p><p>&nbsp;</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1491/2013-nextgen-genomics-bioinformatics-technologies-ngbt-conference-new-delhi-india</guid>
  <pubDate>Thu, 08 Aug 2013 16:21:16 -0500</pubDate>
  <link></link>
  <title><![CDATA[2013 NextGen Genomics &amp; Bioinformatics Technologies (NGBT) Conference, New Delhi, INDIA]]></title>
  <description><![CDATA[
<p>2013 NextGen Genomics &amp; Bioinformatics Technologies (NGBT) Conference</p>

<p>SciGenom Research Foundation (SGRF) and Institute of Genomics and Integrative Biology (IGIB) are pleased to host the Next-Generation Sequencing and Bioinformatics for Genomics &amp; Healthcare conference.</p>

<p>In the ten years since the first human reference genome was completed for US$3 billion the sequencing technologies have radically changed leading to great reduction in sequencing cost. Today a human genome can be sequenced for under US$ 5000 in less than two weeks. It is expected that by the end of 2015 the cost of sequencing a human genome will drop to below thousand dollars. The next generation sequencing technologies over the past five years have enabled a large number of genomic studies that impact human health and disease. Also, this has made possible the growth of microbial, animal and plant genomics studies. While the data production has increased at a rapid pace challenges remain in analyzing and understanding the data. The conference will cover the next generation sequencing (NGS) technologies, bioinformatics for NGS and applications of NGS in many areas including personalized medicine.</p>

<p>For more info : http://www.scigenomconferences.com/2013/default.php</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1720/postdoctoral-associate-bioinformatics-at-duke-university-medical-center</guid>
  <pubDate>Sat, 10 Aug 2013 18:38:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral Associate - Bioinformatics  at Duke University Medical Center]]></title>
  <description><![CDATA[
<p>The Department of Biostatistics and Bioinformatics at Duke University Medical Center is seeking a Postdoctoral Associate for a one year appointment to work on several high-dimensional research projects. The specific goals of the project are to identify genes or molecular markers that are predictive of clinical outcomes in renal and prostate cancer.</p>

<p>Candidates must have: a PhD degree in statistics, biostatistics or bioinformatics, extensive experience in analyzing high-dimensional data (microarray, SNP, CNVs) and of validation approaches. In addition, experience in penalized regression methods, data base manipulation; and strong programming skills in order to conduct Monte Carlo studies and applications (R). Candidate must have excellent communication skills (verbal, written and presentation), a strong proficiency in Linux system.</p>

<p>This position is available immediately and will be filled as soon as possible. Appointment could be extended beyond the first year based on additional funding.</p>

<p>For more information about the Department of Biostatistics and Bioinformatics, please visit our website: http://www.biostat.duke.edu.</p>

<p>For more info: http://biostat.duke.edu/sites/biostat.duke.edu/files/Halabi%20-%20Postdoc%20Job%20Posting%202013%20updated.pdf</p>

<p>Duke University is an Equal Opportunity/Affirmative Action Employer.</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4211/socbin-bioinformatics-2014</guid>
  <pubDate>Tue, 03 Sep 2013 18:50:20 -0500</pubDate>
  <link></link>
  <title><![CDATA[SocBiN Bioinformatics 2014]]></title>
  <description><![CDATA[
<p>14th annual conference in Bioinformatics</p>

<p>Date : June 10-13</p>

<p>Organizers: The Society for Bioinformatics in Northern European countries (SocBiN) and the Norwegian Bioinformatics Platform / ELIXIR.NO </p>

<p>Venue: Department of Informatics, University of Oslo, Norway</p>

<p>Topics:<br />Tools and technologies for integrative bioinformatics<br />Metagenomics<br />Comparative genomics and phylogeny<br />Post-ENCODE bioinformatics<br />Gene regulation<br />Cancer genomes<br />Marine genomics</p>
]]></description>
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  <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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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/7812/bioinformatics-infrastructure-speed-up-indian-agriculture</guid>
	<pubDate>Tue, 07 Jan 2014 12:44:44 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/7812/bioinformatics-infrastructure-speed-up-indian-agriculture</link>
	<title><![CDATA[Bioinformatics infrastructure speed up Indian agriculture]]></title>
	<description><![CDATA[<p>"<span>Realizing the paradigm shift it can bring about, the government is focusing on increased bioinformatics intervention in agri-sciences. Currently under process, the national grid on bioinformatics is expected make much better sense out of huge genomic" - </span></p><p><span></span><a href="http://www.biospectrumindia.com/biospecindia/features/203849/supercomputing-indian-agriculture-fast-track-mode/page/1">http://www.biospectrumindia.com/biospecindia/features/203849/supercomputing-indian-agriculture-fast-track-mode/page/1</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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