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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/36239?offset=830</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/20440/linux-operating-system-aimed-at-scientists</guid>
	<pubDate>Mon, 19 Jan 2015 08:30:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/20440/linux-operating-system-aimed-at-scientists</link>
	<title><![CDATA[Linux operating system aimed at scientists]]></title>
	<description><![CDATA[<p>The Bio-Linux operating system is based on Ubuntu 14.04 LTS (Trusty Tahr), and the previous version was using Ubuntu 12.04 LTS. The developers only use LTS releases and that means that upgrades for this distro don't come along all that often.<br /> <br /> This Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just skimming the surface of what the OS can do. Users have access to even more apps from the official repositories.</p><h3>Bio-Linux is using an Ubuntu LTS version as its base</h3><p>The fact that it uses Ubuntu LTS versions for the base is a good thing because it means its users won't have to worry about the support. Ubuntu 14.04 LTS is supported until 2019, so people who are using Bio-Linux shouldn't have a problem.<br /> <br /> "An updated Bio-Linux 8 version is now on the website in ISO and OVA versions. As usual, there is no need to download this version if you are an existing user. All updates to existing packages will be applied to your system through the update manager and new packages are all available via apt-get or Synaptic," reads the <a href="http://nebclists.nerc.ac.uk/pipermail/bio-linux-announce/2015-January/000020.html" target="_blank">announcement</a>.<br /> <br /> The changelog also states that a problem that was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the beginners tutorial specific to Bio-Linux 8 has been improved.<br /> <br /> Check out the official announcement for a complete list of changes and updates. You can <a href="http://linux.softpedia.com/get/System/Operating-Systems/Linux-Distributions/Bio-Linux-45495.shtml" target="_blank"><strong>download Bio-Linux 8.0.5</strong></a> right now from Softpedia and give it a spin. It has the Unity desktop and now it runs very well in virtual environments.</p><p>Reference @ http://news.softpedia.com/news/Bioinformatics-Distro-Bio-Linux-8-0-5-Now-Available-for-Download-469867.shtml</p>]]></description>
	<dc:creator>Pranjali Yadav</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36723/hapsembler-an-assembler-for-highly-polymorphic-genomes</guid>
	<pubDate>Tue, 22 May 2018 04:09:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36723/hapsembler-an-assembler-for-highly-polymorphic-genomes</link>
	<title><![CDATA[Hapsembler: An Assembler for Highly Polymorphic Genomes]]></title>
	<description><![CDATA[Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. 

http://compbio.cs.toronto.edu/hapsembler/<p>Address of the bookmark: <a href="http://compbio.cs.toronto.edu/hapsembler/" rel="nofollow">http://compbio.cs.toronto.edu/hapsembler/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/20585/dna-transcription-advanced</guid>
	<pubDate>Thu, 29 Jan 2015 05:31:42 -0600</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/20585/dna-transcription-advanced</link>
	<title><![CDATA[DNA Transcription (Advanced)]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/SMtWvDbfHLo" frameborder="0" allowfullscreen></iframe><p>Transcription is the process by which the information in DNA is copied into messenger RNA (mRNA) for protein production. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: The Central Dogma of Molecular Biology: "DNA makes RNA makes protein" Here the process begins. Transcription factors assemble at a specific promoter region along the DNA. The length of DNA following the promoter is a gene and it contains the recipe for a protein. A mediator protein complex arrives carrying the enzyme RNA polymerase. It manoeuvres the RNA polymerase into place... inserting it with the help of other factors between the strands of the DNA double helix. The assembled collection of all these factors is referred to as the transcription initiation complex... and now it is ready to be activated. The initiation complex requires contact with activator proteins, which bind to specific sequences of DNA known as enhancer regions. These regions may be thousands of base pairs distant from the start of the gene. Contact between the activator proteins and the initiation-complex releases the copying mechanism. The RNA polymerase unzips a small portion of the DNA helix exposing the bases on each strand. Only one of the strands is copied. It acts as a template for the synthesis of an RNA molecule which is assembled one sub-unit at a time by matching the DNA letter code on the template strand. The sub-units can be seen here entering the enzyme through its intake hole and they are joined together to form the long messenger RNA chain snaking out of the top.</p>]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r</guid>
	<pubDate>Mon, 09 Jul 2018 05:20:50 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r</link>
	<title><![CDATA[ASAR: Advanced metagenomic Sequence Analysis in R]]></title>
	<description><![CDATA[<p><span>An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.</span></p>
<p><span><span>To read the manual, please click the link&nbsp;</span><a href="https://askarbek-orakov.github.io/ASAR/">https://askarbek-orakov.github.io/ASAR/</a></span></p><p>Address of the bookmark: <a href="https://github.com/Askarbek-orakov/ASAR" rel="nofollow">https://github.com/Askarbek-orakov/ASAR</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20958/ra-bioinformatics-at-ciba</guid>
  <pubDate>Mon, 02 Feb 2015 22:52:50 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at CIBA]]></title>
  <description><![CDATA[
<p>The following posts are to be filled purely on temporary basis under CIBA Component of “Centre for Agricultural Bioinformatics (CABin)” project at this Institute.</p>

<p>Research Associate – one post</p>

<p>Date &amp; Time of Interview 18th Feb 2015 at 10.00 a.m.</p>

<p>Essential Qualification Ph.d / M.Sc./ M.Phil (Bioinformatics) With 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience in the relevant subject.</p>

<p>Desirable qualification: Experience in Java/ C++/ PHP/ PERL/ Python etc. based application development using Linux, Apache and MySQL/Oracle.</p>

<p>Emoluments Rs.24000/- p.m. + 30% HRA for Ph.D holders / Rs.23000/- p.m. + 30% HRA for Master Degree holders A consolidated pay Rs.25000/- per month.</p>

<p>Age Limit Maximum 40 years for men and 45 years for women as on date of interview. Age limits are relaxable for SC / ST / OBC candidates as per rules. Maximum 40 years for men and 45 years for women as on date of interview. Age limits are relaxable for SC / ST / OBC candidates as per rules.</p>

<p>Eligible Candidates may appear for the Walk-in-interview with original Certificate of Ph.D. / Master’s / relevant degree, passport size photograph and bio-data enclosing attested copies of educational qualification &amp; experience certificates. TA / DA will not be paid for attending the interview.</p>

<p>Advertisement: www.ciba.res.in/attachments/jobs/CABin-3006.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus</guid>
	<pubDate>Wed, 24 Oct 2018 23:35:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus</link>
	<title><![CDATA[BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus]]></title>
	<description><![CDATA[<p><span>BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads.&nbsp;</span></p><p>Address of the bookmark: <a href="http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/" rel="nofollow">http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20957/jrf-in-bioinformatics-tezpur-university</guid>
  <pubDate>Mon, 02 Feb 2015 22:50:14 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF in Bioinformatics @ Tezpur University]]></title>
  <description><![CDATA[
<p>Applications are invited for one temporary position of Junior Research Fellow (JRF) in the DBT Twinning Project entitled ‘In-Silico design and evaluation of sequences for γD crystalline protein’ under the Principal Investigator Dr. Anupam Nath Jha, Assistant Professor, Department of Molecular Biology and Biotechnology, Tezpur University.</p>

<p>Educational Qualification: Candidate must possess a M.Sc. in Bioinformatics/ Biotechnology/ Computer Science/ Physics/ Chemistry or B.Tech. or M.Tech. in Bioinformatics/ Biotechnology/ Computer Science from a recognized University/ Institute with minimum 60% marks or equivalent CGPA for general category and for SC/ST/OBC relaxation will be given as per Govt. of India rules.</p>

<p>Fellowship: Rs 16,000/- (Rupees sixteen thousand) only + 10% HRA per month for NET/GATE/BET/BINC qualified candidates. Rs. 12,000/- (Rupees twelve thousand) only + 10% HRA per month for other candidates.</p>

<p>Duration: Initially for a period of six (06) months which may be extended depending upon status of the project or until further order, whichever is earlier.</p>

<p>Age: Candidate should not be more than 28 years of age on the date of interview. Upper age limit may be relaxed up to 5 years in the case of candidate belonging to SC/ ST /OBC /Women / Physically Challenged.</p>

<p>Interested candidates may send their application on plain paper by post along with his/her educational qualifications, recent passport/stamp size photograph and contact phone number to Dr. Anupam Nath Jha, Principal Investigator, Department of Molecular Biology and Biotechnology, Tezpur University, Napaam – 784028 or mail it to anjha@tezu.ernet.in within 20 days of publication of this advertisement.</p>

<p>Only shortlisted candidates will be informed by e-mail or phone for an interview. N.B. No TA/DA will be paid for attending the interview. For further details contact: Dr. Anupam Nath Jha, Assistant Professor, Principal Investigator Department of Molecular Biology &amp; Biotechnology Tezpur University, Napaam, Tezpur-784028 (Assam)</p>

<p>Advertisement: www.tezu.ernet.in/ProjectWalkin/Advt-ANJ-5323-A.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38316/simba-a-genome-assembly-project-management-system</guid>
	<pubDate>Thu, 29 Nov 2018 08:52:25 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38316/simba-a-genome-assembly-project-management-system</link>
	<title><![CDATA[SIMBA: a Genome Assembly Project Management System]]></title>
	<description><![CDATA[<p><span>SIMBA</span><span>, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.</span></p><p>Address of the bookmark: <a href="http://ufmg-simba.sourceforge.net/" rel="nofollow">http://ufmg-simba.sourceforge.net/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21453/ra-research-associate-bioinformaticscomputational-biologist</guid>
  <pubDate>Thu, 26 Feb 2015 03:44:24 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA / Research Associate Bioinformatics/Computational Biologist]]></title>
  <description><![CDATA[
<p>The following posts are urgently required to be filled for the Department of Biotechnology, Government of India funded project entitled "Computational Core for Plant Metabolomics" administrated by Prof Indira Ghosh, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067 </p>

<p>RA / Research Associate (Bioinformatics/Computational Biologist) <br />Salary: Rs. 23000/- + HRA <br />Vacancy: 1 <br />Essential Qualifications: PhD, preferably in plant biotechnology/biochemistry/Bioinformatics with experience in analyzing high throughput omics-based data. Desired Skills: Prior experience in handling and guiding bioinformatics, metabolomics data, managing the project portal, preparing and filing reports etc. Will be expected to communicate with user groups and coordinate with LIMS group in Hyderabad and the Cheminformatics group in Delhi.</p>

<p>Address:	Prof Indira Ghosh, room #12 Project Investigator, (Core Metabolomics) School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067.</p>

<p>Apply Details	<br />Last Date: March 3rd 2015 <br />Web/Notification URL	http://www.jnu.ac.in/Career/currentjobs. htm</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38668/gvolante-completeness-assessment-of-genometranscriptome-sequences</guid>
	<pubDate>Sun, 13 Jan 2019 07:03:25 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38668/gvolante-completeness-assessment-of-genometranscriptome-sequences</link>
	<title><![CDATA[gVolante: Completeness Assessment of Genome/Transcriptome Sequences]]></title>
	<description><![CDATA[<p><span>A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section</span></p><p>Address of the bookmark: <a href="https://gvolante.riken.jp/analysis.html" rel="nofollow">https://gvolante.riken.jp/analysis.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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