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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/4098?offset=1100</link>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4551/au-kbc-lab</guid>
  <pubDate>Sun, 15 Sep 2013 09:33:59 -0500</pubDate>
  <link></link>
  <title><![CDATA[AU-KBC Lab]]></title>
  <description><![CDATA[
<p>Conducting Clinical Trial Management Course combined with the Apollo Hospitals. Major Research in bioinformatics as Drug Discovery, Functional Genomics, Comparative genomics, Data Mining </p>

<p>More @ http://www.au-kbc.org/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/38302/senior-bioinformatics-scientist-at-elucidata</guid>
  <pubDate>Tue, 27 Nov 2018 04:05:57 -0600</pubDate>
  <link></link>
  <title><![CDATA[Senior Bioinformatics Scientist at Elucidata]]></title>
  <description><![CDATA[
<p>Key Responsibilities <br />- Process and analyse metabolomic, transcriptional, genomics, proteomics <br />and any other kind of biological data. <br />- Interpret the data in the context of relevant biological literature to generate <br />actionable insights. <br />- Communicate the findings from data and literature to biologists and use the <br />biological insights to derive next steps/analyses. <br />- Communicate work through blogs, meet-ups, research papers, posters, etc. <br />- Identify, troubleshoot, and implement improvements to existing pipelines <br />and algorithms. <br />- Identify and implement new tools and pipelines to use for different types of <br />biological data. <br />- Work in a multi-disciplinary team with biologists, data scientists and data <br />analysts. <br />- Help with any other requirements (from database design to generating <br />prototypes for the product team).</p>

<p>Requirements <br />- 3-5 years of relevant bioinformatics experience such as public data mining, <br />processing, analysing and visualising omics data, etc. <br />- Ph.D., Masters or Bachelors in Bioinformatics, Biotechnology, <br />Computational Biology, or related field. <br />- Understanding of molecular biology and biochemistry. <br />- Comfort and experience with biological research and data. <br />- Proficient in a programming language used for bioinformatics such as R or <br />python. <br />- Excellent communication skills. <br />- Ability to summarise and simplify complex analyses for a non-technical <br />audience. <br />- Strong analytical skills, curiosity and a knack to solve difficult problems. <br />- Work well in multi-disciplinary teams with people of vastly different <br />backgrounds. <br />- Demonstrated success in collaboration and independent work.</p>

<p>More at https://angel.co/elucidata/jobs/460104-senior-bioinformatics-scientist</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/6458/bigre-lab</guid>
  <pubDate>Sun, 17 Nov 2013 10:35:49 -0600</pubDate>
  <link></link>
  <title><![CDATA[BIGRE Lab]]></title>
  <description><![CDATA[
<p>The Laboratoire de Bioinformatique des Génomes et des Réseaux (Genome and Network Bioinformatics) is specialized in the conception, implementation, evaluation and application of bioinformatics approaches for the analysis of genome, transcriptome, proteome and metabolism.<br />Our main activities include</p>

<p>Analysis of regulatory sequences (RSAT project)<br />Classification and analysis of mobile genetic elements (ACLAME project).<br />Analysis of molecular interaction networks (NeAT project)<br />Inference of metabolic pathways from genomic and post-genomic data <br />(metabolic pathfinding, see also metabolic pathfinding in NeAT)<br />Critical assesment of protein interactions (CAPRI)</p>

<p>Lab Page http://www.bigre.ulb.ac.be/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/39025/binc-exam-merged-with-dbt-bet-jrf-exam</guid>
	<pubDate>Thu, 21 Feb 2019 09:37:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/39025/binc-exam-merged-with-dbt-bet-jrf-exam</link>
	<title><![CDATA[BINC Exam merged with DBT- BET JRF Exam]]></title>
	<description><![CDATA[<p>Another breaking news received has been received from the Department of biotechnology &ndash; DBT. As per a notification released by DBT, Bioinformatics National Certification (BINC) Exam conducted once per year by DBT has been now merged with DBT- BET JRF Exam.</p><p>Also, Bioinformatics Industrial Training Program (BIITP) is merged with the HRD Biotechnology Industrial Training Programme (BITP).</p><p>While this comes as a surprise for a lot of participants. We believe this is a good attempt to unify and create a national benchmark for talent. And we appreciate this endeavor from Department of biotechnology.</p><p>However, such last-minute announcements can create confusion. Thus candidates are advised to go through the complete notification DBT-BET JRF 2019 via the link below.If you have any kind of doubts, you must contact DBT JRF or Biotecnika for any kind of help &amp; assistance.</p><p><br />Attention:-Bioinformatics Programs (BINC and BIITP)</p><p>1. Bioinformatics National Certification (BINC) has been merged with DBT-Junior<br />Research Fellow (BET Exam)</p><p>2. Bioinformatics Industrial Training Program (BIITP) is merged with HRDBiotechnology Industrial Training Programme (BITP).</p><p>Students of Bioinformatics, who are interested to apply for Fellowship or Industrial<br />Training may keep track of the advertisement of DBT-JRF (BET Exam) and BITP<br />of DBT.</p><p>&nbsp;More at&nbsp;http://www.bcil.nic.in/files/Attention_Bioinformatics_Programs_(BINC_and_BIITP).pdf</p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/2349/bioinformatics-understanding-of-living-systems-through-information-science</guid>
	<pubDate>Wed, 14 Aug 2013 11:50:17 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/2349/bioinformatics-understanding-of-living-systems-through-information-science</link>
	<title><![CDATA[Bioinformatics -- Understanding of living systems through  information science]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/6Ovd_GOM9-g" frameborder="0" allowfullscreen></iframe>Recently, the progress of the Human Genome Project, aiming to decode all human DNA sequences, has highlighted a research field called bioinformatics. In this new field, computers and techniques from information science are not just used as tools to advance life science research; they're expected to have a major impact on how we think about the life sciences.

Q. The main feature of bioinformatics is, it utilizes computers to analyze life. One is example is the genome. In all organisms, DNA contains genetic information, and this is called the genome. But the amount of information involved is huge, so recently, it's been read using next-generation sequencers, and analyzed by computers. In bioinformatics research, what we do is utilize those genome information to investigate the principles of life.

As an organism evolves, its genome sequence changes through sudden mutations. Additionally, at the genome level, mutations called rearrangements, such as inversions, transpositions, and duplications, occur. 

The genome comparison system developed by the Sakakibara Lab calculates homologous sequences called anchors, which are conserved between species. If the genome is considered as a long text, then anchors can be thought of as words.

Q. We're coming to understand the genomes of various organisms - not just humans, but monkeys, chimpanzees, bacteria, and so on. The first method used to analyze a genome is comparing it with the genomes of other organisms, to see where it's the same and where it's different. In that way, the content of the genome is decoded bit by bit, using computers. By contrast, in our method, we've developed software called Murasaki, which we also use to analyze large genomes, by comparing them with those of other organisms.

The Sakakibara Lab uses a next-generation sequencer at Keio University, along with a cluster machine with hundreds of CPUs. In this way, the Lab is analyzing genome mutations that cause cancer, and the genome of the natto production strain Bacillus subtilis.

Until now, genome analysis could only be done in national-scale projects. But now, next-generation sequencer development has made genome analysis possible in an ordinary lab. In a world-first achievement, the Sakakibara Lab has decoded the natto bacillus genome, through analysis using Keio's next-generation sequencer.

Q. In the future, biology and the life sciences may become almost entirely information science and computer science. And in healthcare, that may enable us, for example, to predict whether individuals are susceptible to cancer, or to certain lifestyle-related diseases, by understanding their personal genome data. So, I think it's amply possible that we can make use of such information effectively, to help people live longer and be free from disease, by thinking about their lifestyle habits.
 
Bioinformatics is only two decades old. In this field, many areas are still unknown. Professor Sakakibara, having been involved since the beginning, will continue tackling new, challenging research projects.]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40235/bioinformatics-web-development-course</guid>
	<pubDate>Wed, 06 Nov 2019 20:42:48 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40235/bioinformatics-web-development-course</link>
	<title><![CDATA[Bioinformatics web development course]]></title>
	<description><![CDATA[<p>This web development course, targeted at Biology and Bioinformatics students, aims at teaching from scratch all the skills needed to setup a fully working Linux web server and to develop and deploy web applications for Bioinformatics.</p>
<p>No previous programming knowledge is assumed. By following this tutorial you will learn the fundamental concepts of programming by using scripting languages: variables, types, arrays, cycles, conditional statements, functions, objects, regular expressions, files reading and manipulation et-cetera.</p><p>Address of the bookmark: <a href="http://www.cellbiol.com/bioinformatics_web_development/introduction/" rel="nofollow">http://www.cellbiol.com/bioinformatics_web_development/introduction/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4547/bioinformatics-infrastructure-facility</guid>
  <pubDate>Sun, 15 Sep 2013 09:22:25 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Infrastructure Facility]]></title>
  <description><![CDATA[
<p>The Bioinformatics Infrastructure Facility has started working in the year 2007 at Presidency College, Kolkata. It is one of the premier institutes of India and boasts of a rich heritage and great alumni. The Infrastructure Facility has a dedicated team headed by Sayak Ganguli and ably supported by Priayanka Dhar. The coordinator of the facility is Abhijit Datta of the Post Graduate Department of Botany. The lab mainly focusses on the analysis of the RNA Induced Silencing Complex. Recent highlights include the presentation of a paper at the RNAi World Congress.</p>

<p>More @ http://bioinfo-presiuniv.edu.in/index.php</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/40945/the-clark-lab</guid>
  <pubDate>Fri, 07 Feb 2020 13:57:24 -0600</pubDate>
  <link></link>
  <title><![CDATA[The Clark Lab]]></title>
  <description><![CDATA[
<p>Study the process of Adaptive Evolution, during which species adopt novel traits to overcome challenges. We retrace the evolutionary histories of genomic elements to determine the changes underlying adaptation and to discover previously unknown genetic networks. These discoveries have already led to advances in human health, species conservation, and molecular biology. </p>

<p>More at http://clark.genetics.utah.edu/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/2573/most-commonly-used-awk-by-bioinformatician</guid>
	<pubDate>Mon, 19 Aug 2013 01:12:38 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/2573/most-commonly-used-awk-by-bioinformatician</link>
	<title><![CDATA[Most Commonly used Awk by Bioinformatician]]></title>
	<description><![CDATA[<p style="text-align: center;">&nbsp;</p><p>Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases.</p><p>Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single call to awk. For a simple script, most of the timelag is in loading these apps into memory, and it's much faster to do it all with one. This is ideal for something like an openbox pipe menu where you want to generate something on the fly. You can use awk to make a neat one-liner for some quick job in the terminal, or build an awk section into a shell script. You can find a lot of online tutorials, but here I will only show a few examples which cover most of bioinformatician daily uses of awk.</p><p>choose rows where column 3 is larger than column 5:</p><p>awk '$3&gt;$5' input.txt &gt; output.txt</p><p>extract column 2,4,5:</p><p>awk '{print $2,$4,$5}' input.txt &gt; output.txt</p><p>awk 'BEGIN{OFS="\t"}{print $2,$4,$5}' input.txt</p><p>show rows between 20th and 80th:</p><p>awk 'NR&gt;=20&amp;&amp;NR&lt;=80' input.txt &gt; output.txt</p><p>calculate the average of column 2:</p><p>awk '{x+=$2}END{print x/NR}' input.txt</p><p>regex (egrep):</p><p>awk '/^test[0-9]+/' input.txt</p><p>calculate the sum of column 2 and 3 and put it at the end of a row or replace the first column:</p><p>awk '{print $0,$2+$3}' input.txt</p><p>awk '{$1=$2+$3;print}' input.txt</p><p>join two files on column 1:</p><p>awk 'BEGIN{while((getline&lt;"file1.txt")&gt;0)l[$1]=$0}$1 in l{print $0"\t"l[$1]}' file2.txt &gt; output.txt</p><p>count number of occurrence of column 2 (uniq -c):</p><p>awk '{l[$2]++}END{for (x in l) print x,l[x]}' input.txt</p><p>apply "uniq" on column 2, only printing the first occurrence (uniq):</p><p>awk '!($2 in l){print;l[$2]=1}' input.txt</p><p>count different words (wc):</p><p>awk '{for(i=1;i!=NF;++i)c[$i]++}END{for (x in c) print x,c[x]}' input.txt</p><p>deal with simple CSV:</p><p>awk -F, '{print $1,$2}'</p><p>substitution (sed is simpler in this case):</p><p>awk '{sub(/test/, "no", $0);print}' input.txt</p><p>&nbsp;</p><p>OK now here's where to read this stuff properly explained. roll</p><p>Two thorough tutorials:</p><p>http://www.gnu.org/software/gawk/manual/gawk.html</p><p>http://www.grymoire.com/Unix/Awk.html</p><p>A famous list of useful one-liners - though they're short, many are quite tricky:</p><p>http://www.pement.org/awk/awk1line.txt</p><p>And some nice explanations of those one-liners. After reading this you'll have a pretty good grasp!</p><p>http://www.catonmat.net/blog/awk-one-li &hellip; -part-one/</p><p>http://www.catonmat.net/blog/ten-awk-ti &hellip; -pitfalls/</p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4106/phd-at-national-institute-for-research-in-reproductive-health</guid>
  <pubDate>Fri, 30 Aug 2013 04:50:35 -0500</pubDate>
  <link></link>
  <title><![CDATA[PhD at National Institute for Research in Reproductive Health]]></title>
  <description><![CDATA[
<p>National Institute for Research in Reproductive Health</p>

<p>(Indian Council of Medical Research )<br />Jehangir Merwanji Street, Parel, Mumbai 400 012</p>

<p>Advertisement No. 1/NIRRH/Ph.D. 2013<br />Admission to Ph.D. Programme – 2013</p>

<p>National Institute for Research in Reproductive Health, Mumbai, a premier institute of the Indian Council of Medical Research, conducts basic, clinical and operational research in different areas of reproductive health. The thrust areas of research include: Fertility Regulation, Infertility and Reproductive Disorders, Reproductive Tract Infections, Maternal and Child Health, Osteoporosis, Genetic Disorders, Stem Cell Biology, Structural Biology, Bioinformatics and Reproductive Toxicology. Institute is affiliated to the University of Mumbai for the award of Ph.D. degree in Applied Biology, Biochemistry, Life Sciences and Biotechnology. The institute invites applications from young and bright students for enrollment in Ph.D. programme.</p>

<p>More at http://www.nirrh.res.in/announcements/phd_program_2013.htm</p>
]]></description>
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