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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30249?offset=1020</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era</guid>
	<pubDate>Sun, 22 Dec 2013 17:31:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/7387/bioinformatics-software-for-biologists-in-the-genomics-era</link>
	<title><![CDATA[Bioinformatics software for biologists in the genomics era]]></title>
	<description><![CDATA[<p>The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.</p><p>Address of the bookmark: <a href="http://bioinformatics.oxfordjournals.org/content/23/14/1713.full" rel="nofollow">http://bioinformatics.oxfordjournals.org/content/23/14/1713.full</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44483/baclife-an-automated-genome-mining-tool-for-identification-of-lifestyle-associated-genes</guid>
	<pubDate>Fri, 15 Mar 2024 04:59:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44483/baclife-an-automated-genome-mining-tool-for-identification-of-lifestyle-associated-genes</link>
	<title><![CDATA[bacLIFE: an automated genome mining tool for identification of lifestyle associated genes]]></title>
	<description><![CDATA[<p style="margin-top: 0px; margin-bottom: 16px; color: #1f2328; font-size: 16px; font-style: normal; font-weight: 400; text-align: start; background-color: #ffffff;" dir="auto">bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated<span>&nbsp;</span><strong style="font-weight: var(--base-text-weight-semibold, 600);">lifestyle-associated genes (LAGs)</strong>, and biosynthetic gene clusters associated with each lifestyle detected. This whole process is divided into different modules:</p>
<ul style="margin-top: 0px; margin-bottom: 16px; color: #1f2328; font-size: 16px; font-style: normal; font-weight: 400; text-align: start; background-color: #ffffff;" dir="auto">
<li><strong style="font-weight: var(--base-text-weight-semibold, 600);">Clustering module</strong><span>&nbsp;</span>Predicts, clusters and annotates the genes of every input genome</li>
<li style="margin-top: 0.25em;"><strong style="font-weight: var(--base-text-weight-semibold, 600);">Lifestyle prediction</strong><span>&nbsp;</span>Employs a machine learning model to forecast bacterial lifestyle or other specified metadata</li>
<li style="margin-top: 0.25em;"><strong style="font-weight: var(--base-text-weight-semibold, 600);">Analitical module (Shiny app)</strong><span>&nbsp;</span>Results from the previous modules are embedded in a user-friendly interface for comprehensive and interactive comparative genomics.</li>
</ul>
<p style="margin-top: 0px; margin-bottom: 16px; color: #1f2328; font-size: 16px; font-style: normal; font-weight: 400; text-align: start; background-color: #ffffff;" dir="auto">You can find the complete wiki here [<a href="https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki">https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki</a>]</p><p>Address of the bookmark: <a href="https://github.com/Carrion-lab/bacLIFE" rel="nofollow">https://github.com/Carrion-lab/bacLIFE</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7753/jrf-pondicherry-university</guid>
  <pubDate>Fri, 03 Jan 2014 16:48:56 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF @ PONDICHERRY UNIVERSITY]]></title>
  <description><![CDATA[
<p>PONDICHERRY UNIVERSITY</p>

<p>CENTRE FOR BIOINFORMATICS</p>

<p>PUDUCHERRY</p>

<p>Applications are invited for one Project Assistant to work in the UGC sponsored Research Award "Molecular Docking and Dynamics studies to understand the interacting mechanism of oncogenic 101 protein with its cellular proteins".</p>

<p>The duration for the fellowship is 12months only with consolidated pay ofRs. 5,000 per month.</p>

<p>Application on plain paper with following details: Name, Address, Data of Birth, Father's Name, Nationality, Educational Qualification (SSLC onwards-enclose attested copies of certificate) and Researcb Experience may be addressed to Dr. R. Krishna, Principle Investigator (PI), UGC Research Award, Centre for Bioinformatics, Pondicherry University, Pondicherry - 605 014.</p>

<p>Application should reach in January 261h , 2013.</p>

<p>Essential Qualification: M.Sc. in Bioinformatics/Biophysics with good academic record.</p>

<p>Qualification for Project Fellow:</p>

<p>M.Sc in Bioinformatics/Biophysics.</p>

<p>The person to be considered for appointment as Project Fellow must have second class master degree with a minimum of 55% marks in the subject concerned or a related subject.</p>

<p>The candidate to be appointed as Project Fellows should be below thc age of40 years at the time of appointment.</p>

<p>Desirable Qualification for this Project: Research Experience in Small/Macromolecule Crystallography and Structural Bioinformatics.</p>

<p>For more details, refer the web site: www.pondiuni.edu.in/sites/default/files/BIC-311213.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/88/regular-expression-cheat-sheet</guid>
	<pubDate>Tue, 09 Jul 2013 17:38:42 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/88/regular-expression-cheat-sheet</link>
	<title><![CDATA[Regular Expression Cheat Sheet]]></title>
	<description><![CDATA[<p><span>The Regular Expression are the sole of Perl language, and for bioinformatician it is just a magical stick to resolve gingatic string data. We did not find any good and user friendly regular expression cheat sheet, hence write our own cheat sheet.&nbsp;</span><span>The Regular Expressions Cheat Sheet, a quick reference guide for regular expressions, including symbols, ranges, grouping, assertions and some sample patterns to get you started.</span></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/88" length="14944" type="application/pdf" />
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7998/faculty-positions-at-iiit-allahabad</guid>
  <pubDate>Thu, 23 Jan 2014 06:19:34 -0600</pubDate>
  <link></link>
  <title><![CDATA[FACULTY POSITIONS AT IIIT-ALLAHABAD]]></title>
  <description><![CDATA[
<p>OPENINGS OF FACULTY POSITIONS AT IIIT-ALLAHABAD</p>

<p>(Under Tenure-Track Model)</p>

<p>Open Advt. No IIITA/DIC/16012014</p>

<p>IIIT-Allahabad has several Openings for the Faculty positions at the Assistant Professor level.</p>

<p>It is a regular tenure-track faculty positions for 3-5 years in teaching and research. A regular faculty is expected to engage heavily in research and teaching. The eligibility criteria for regular faculty positions are similar as in IITs. For an Assistant Professor position, a candidate must have a PhD (in IT/Computer Science &amp;/or Engineering/Electrical, Electronics &amp;/or Communication Engineering/etc; for interdisciplinary areas the PhD may be in an appropriate field), plus three years experience. However, for PhDs from a well known University/Institute (e.g. IITs/IISc/TIFR/ISI in India or well known research universities across the world), and a good research/academic record, the 3 years experience requirement may be waived.</p>

<p>The pay scale for faculty is same as in IITs. Other benefits include initiation research grant, travel support, book grant, professional society membership, etc., and personal benefits such as medical/LTC, on campus subsidized family housing with excellent modern infrastructural facilities.</p>

<p>Areas of Interest</p>

<p>IIIT-Allahabad aims to build strong research groups in important and emerging areas in CS/IT/ECE as well as in emerging interdisciplinary areas, and applications are invited in all these areas. Some of the areas of special interest, besides strengthening the existing research areas, are : Software Engineering, Theoretical Computer Science, Cyber Physical Systems, Robotics, Network science, Digital Media, Computational neuroscience, Machine learning, Healthcare informatics, Computational Biology, Communications networks (both at hardware and protocol levels), Circuits (including VLSI, analog, low power, etc), Energy systems and technologies, Biomedical electronics and systems, Computer Architecture, signal/image processing, Embedded and control systems.</p>

<p>Application Process</p>

<p>Interested candidates can apply by sending their detailed CV with list of publications clearly mentioning Journal names and citation index with three references through email entitled “Faculty positions at IIIT Allahabad” to faculty.applications@iiita.ac.in. Do not send your applications in any other email addresses. Applications will be considered regularly, hence there is no deadline for applying.</p>

<p>Important Clarifications on Eligibility</p>

<p>A PhD in CS/IT (or other disciplines, as announced) is the minimum expected requirement for an Assistant Professor.</p>

<p>Advertisement: http://iiita.ac.in/pub/Faculty-Position-IIITA1.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/3917/the-story-of-you-encode-and-the-human-genome</guid>
	<pubDate>Sat, 24 Aug 2013 18:49:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/3917/the-story-of-you-encode-and-the-human-genome</link>
	<title><![CDATA[The Story of You: ENCODE and the human genome]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/TwXXgEz9o4w" frameborder="0" allowfullscreen></iframe><p>Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE</p>]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4960/genome-epigenome-new-understanding-of-the-pathogens-in-your-food</guid>
	<pubDate>Fri, 27 Sep 2013 11:30:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4960/genome-epigenome-new-understanding-of-the-pathogens-in-your-food</link>
	<title><![CDATA[Genome + Epigenome = New Understanding of the Pathogens in Your Food]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/hGtHs_C1BFA" frameborder="0" allowfullscreen></iframe>UC Davis's Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close genomes and analyze methylation; Weimer reports that his team has already discovered new epigenetic modifications in Salmonella and Listeria with the technology. www.pacb.com/microbe]]></description>
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8198/scientist-positions-at-rajiv-gandhi-centre-for-biotechnology</guid>
  <pubDate>Thu, 06 Feb 2014 23:18:49 -0600</pubDate>
  <link></link>
  <title><![CDATA[Scientist Positions at Rajiv Gandhi Centre for Biotechnology]]></title>
  <description><![CDATA[
<p>Rajiv Gandhi Centre for Biotechnology</p>

<p>An Autonomous National Institute under Government of India,<br />Ministry of Science &amp; Technology<br />Department of Biotechnology</p>

<p>No: RGCB/ Advt./2014/1   <br />January 24, 2014</p>

<p>Scientist Positions</p>

<p>Group Leader in Computational Biology/Bioinformatics<br />A highly motivated and innovative individual who will pursue basic research, solve biological problems with emphasis on computational and quantitative experimental methods and build active bridges to translational research. The scientist will also provide computational biology support to analyze complex data sets generated by RGCB scientists and collaborators.</p>

<p>Location: Thiruvananthapuram (Trivandrum)</p>

<p>The above positions will be at the E-II, F or equivalent levels. For senior applicants with an outstanding track record, an option of a contract career path for research excellence at Scientist G or H equivalent level can also be discussed. All positions will initially be for 5 years. Essential and desired qualifications as well as other relevant details for all the above positions are posted on the RGCB website (http://www.rgcb.res.in). The last date for receiving applications is March 14, 2014.   </p>

<p>Sd/-<br />Director</p>

<p>Rajiv Gandhi Centre for Biotechnology<br />Thycaud, P.O., Poojappura,<br />Thiruvananthapuram, Kerala, India-695 014<br />Ph.: 91-471-2529400 (30 Lines), 2347975, 2348104, 2348753, 2345899<br />Fax: 91-471-2348096, 2346333</p>

<p>More at http://rgcb.res.in/jobs.html</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/18653/genetic-code-amino-acid</guid>
	<pubDate>Sun, 26 Oct 2014 07:45:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/18653/genetic-code-amino-acid</link>
	<title><![CDATA[Genetic code - Amino Acid]]></title>
	<description><![CDATA[<p>The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon.</p><p>The image summarise all in one.</p><p>More at http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html</p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/18653" length="226605" type="image/jpeg" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/8382/c-dac-launch-supercomputing-facility-param-bio-blaze</guid>
	<pubDate>Tue, 18 Feb 2014 11:55:14 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/8382/c-dac-launch-supercomputing-facility-param-bio-blaze</link>
	<title><![CDATA[C-DAC launch supercomputing facility "Param Bio Blaze" !!!]]></title>
	<description><![CDATA[<p>The bioinformatics centre at Centre for Development of Advanced Computing (C-DAC) completed 10 years, this month. Established in 2004, the centre has been widely used by numerous researchers across the globe and has an ultimate aim of making personalised drugs depending on the composition of a human body.<br /><br />When biological data is processed using computer science, statistics, mathematics and engineering, it constitutes bioinformatics. The technological advancements are bringing new dimensions to the understanding of molecular basis of living organisms. There is immense data generated due to computing, but storage and analysis of this data is becoming a challenge, therefore there is an urgent need of supercomputers.</p><p>The&nbsp;C-DAC will launch Param Bio Blaze, a supercomputing facility, to address the challenges in bioinformatics on Tuesday at a three-day symposium, titled: 'Accelerating biology: Computing life'. The supercomputing facility will be inaugurated on Tuesday by Ramakrishna Ramaswamy, vice-chancellor, Central University of Hyderabad at the Yashada. The new C-DAC's facility will have a capacity of 10 teraflop and will be able to analyse human cells and its functions.</p><p><img src="http://www.datacenterjournal.com/wp-content/uploads/2012/06/supercomputer.jpg" alt="image" width="1024" height="632" style="border: 0px; border: 0px;"></p><p><br />Param Bio Blaze will help have a larger storage space and better computing facility for the bioinformatics sector. The facility will help capture the movement of molecules and also interaction between two molecules and the effects.<br /><br />Applications of Param BioBlaze<br /><br />- Collaboration with National Centre for Cell Science for research on Malaria and understanding how the disease spreads<br /><br />- Collaborative work with Tata Memorial hospital on breast cancer and find out the difference between normal tissues and tissues from breast cancer patients<br /><br />- Designing anti-cancer molecules, a collaborative research with the University of Pune</p><p>Reference:</p><p>Times of India</p><p>Image:datacenterjournal.com</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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