<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44707?offset=140</link>
	<atom:link href="https://bioinformaticsonline.com/related/44707?offset=140" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</guid>
	<pubDate>Mon, 17 Aug 2020 05:21:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</link>
	<title><![CDATA[SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis]]></title>
	<description><![CDATA[<p><span>SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, &hellip;).</span><br><span>The bioinformatics treatment is based on Vsearch [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/27781170">Rognes 2016</a><span>] which showed to be both accurate and fast [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/26664811">Wescott 2015</a><span>].The statistical analysis is based on DESeq2 R package [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/20979621">Anders and Huber 2010</a><span>] which robustly identifies the differential abundant features as suggested in [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/">McMurdie and Holmes 2014</a><span>] and [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/">Jonsson2016</a><span>]. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/25516281">Love 2014</a><span>].</span><br><span>SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN is available&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_presentation.pdf">here</a><span>&nbsp;and a poster&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_poster.pdf">here</a><span>.&nbsp;</span></p>
<p><span>More at&nbsp;<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4</a></span></p><p>Address of the bookmark: <a href="https://github.com/aghozlane/shaman" rel="nofollow">https://github.com/aghozlane/shaman</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43447/rna-seq-workflow-gene-level-exploratory-analysis-and-differential-expression</guid>
	<pubDate>Sat, 09 Oct 2021 07:59:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43447/rna-seq-workflow-gene-level-exploratory-analysis-and-differential-expression</link>
	<title><![CDATA[RNA-seq workflow: gene-level exploratory analysis and differential expression]]></title>
	<description><![CDATA[<p><span>Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count datasets for downstream analysis. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.</span></p><p>Address of the bookmark: <a href="http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html" rel="nofollow">http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44716/exploring-rna-sequence-analysis-tools-for-every-bioinformatician</guid>
	<pubDate>Fri, 13 Dec 2024 04:03:04 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44716/exploring-rna-sequence-analysis-tools-for-every-bioinformatician</link>
	<title><![CDATA[Exploring RNA Sequence Analysis: Tools for Every Bioinformatician]]></title>
	<description><![CDATA[<p>RNA sequence analysis has become an essential part of modern biological research. From RNA-seq pipelines to specialized tools for specific RNA types, here's a comprehensive guide to tools you can use to make sense of RNA data.</p><h4><strong>1. RNA-Seq Analysis Pipelines</strong></h4><p>RNA-seq is one of the most popular techniques for studying RNA. These tools streamline processing raw sequence data:</p><ul>
<li><strong>FASTQC</strong>: For quality control of raw RNA-seq reads.</li>
<li><strong>Trimmomatic</strong>: For trimming and filtering RNA-seq reads.</li>
<li><strong>HISAT2/STAR</strong>: High-performance aligners for RNA-seq reads.</li>
<li><strong>FeatureCounts</strong>: For quantifying gene expression.</li>
<li><strong>DESeq2/EdgeR</strong>: For differential expression analysis.</li>
</ul><h4><strong>2. Transcriptome Assembly and Annotation</strong></h4><p>For analyzing transcriptomes from non-model organisms or assembling novel transcripts:</p><ul>
<li><strong>Trinity</strong>: For de novo transcriptome assembly.</li>
<li><strong>StringTie</strong>: For transcript assembly and quantification from RNA-seq alignments.</li>
<li><strong>TransDecoder</strong>: To predict coding regions within assembled transcripts.</li>
<li><strong>TAU</strong>: Tools for annotating non-coding and coding RNAs.</li>
</ul><h4><strong>3. Exploring Non-Coding RNA (ncRNA)</strong></h4><p>Non-coding RNAs play critical regulatory roles. Dedicated tools for studying them include:</p><ul>
<li><strong>Infernal</strong>: For identifying ncRNA sequences based on covariance models.</li>
<li><strong>Rfam</strong>: Database and tools for ncRNA families.</li>
<li><strong>miRDeep</strong>: For identifying microRNAs in RNA-seq datasets.</li>
</ul><h4><strong>4. RNA Structure and Motif Analysis</strong></h4><p>Structural biology of RNA helps in understanding its function:</p><ul>
<li><strong>RNAfold (ViennaRNA)</strong>: Predicts secondary structures from RNA sequences.</li>
<li><strong>RNAstructure</strong>: Tools for RNA secondary structure prediction and analysis.</li>
<li><strong>MEME Suite</strong>: For identifying motifs in RNA sequences.</li>
<li><strong>IntaRNA</strong>: For RNA-RNA interaction prediction.</li>
</ul><h4><strong>5. RNA Editing and Modifications</strong></h4><p>Epitranscriptomics is a growing field focusing on RNA modifications:</p><ul>
<li><strong>REDItools</strong>: For RNA editing analysis.</li>
<li><strong>m6Aboost</strong>: For identifying m6A modifications in RNA.</li>
</ul><h4><strong>6. Long-Read RNA Sequencing Analysis</strong></h4><p>Long-read technologies like Nanopore and PacBio are transforming RNA research:</p><ul>
<li><strong>FLAIR</strong>: For isoform-level analysis of long-read RNA-seq data.</li>
<li><strong>NanoMod</strong>: For detecting modifications in RNA from Nanopore sequencing.</li>
</ul><h4><strong>7. RNA-Protein Interactions</strong></h4><p>To study RNA-protein interactions and complexes:</p><ul>
<li><strong>RBPmap</strong>: For identifying RNA-binding protein motifs.</li>
<li><strong>PARalyzer</strong>: For analyzing PAR-CLIP data.</li>
</ul><h4><strong>8. Functional Enrichment Analysis</strong></h4><p>Understanding biological functions and pathways from RNA-seq data:</p><ul>
<li><strong>getENRICH</strong>: A tool designed for pathway enrichment analysis of non-model organisms (hypergeometric P-value calculation with FDR correction).</li>
<li><strong>ClusterProfiler</strong>: For GO and KEGG pathway enrichment analysis.</li>
</ul><h4><strong>9. Visualization and Data Sharing</strong></h4><p>Presenting and sharing RNA sequence analysis results effectively:</p><ul>
<li><strong>IGV</strong>: Genome browser for visualizing RNA-seq alignments.</li>
<li><strong>Circos</strong>: Circular visualization of RNA-seq data.</li>
<li><strong>DashBio</strong>: A Python library for creating bioinformatics visualizations.</li>
</ul><h4><strong>Conclusion</strong></h4><p>The bioinformatics landscape for RNA sequence analysis is vast, with tools catering to specific needs. Whether you&rsquo;re studying coding RNAs, non-coding RNAs, or exploring RNA-protein interactions, the right tools can transform your data into biological insights.</p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/7933/senior-programmer-biotech-park</guid>
  <pubDate>Mon, 20 Jan 2014 04:50:36 -0600</pubDate>
  <link></link>
  <title><![CDATA[SENIOR PROGRAMMER @ Biotech Park]]></title>
  <description><![CDATA[
<p>Advt. No. (1)/BP/2014<br />A walk-in-interview will be held in the Biotech Park Office at Sector G, Jankipuram, Kursi Road, Lucknow (U.P.) January 31, 2014 at 11.00 A.M. for the following posts of DBT sponsored project tenable at Biotech Park. Interested candidates fulfilling the requisite qualifications, experience and age as given below, on the date of interview, may appear before the Selection Committee. The candidate will have to join immediately. Appointment will be made initially for six months extendable on satisfactory performance till the duration of the project.<br />INTERVIEW ON January 31, 2014 at 11.00 A.M.<br /> <br />SENIOR PROGRAMMER (ONE POST)<br />Educational Qualification<br />M.Sc./B. Tech Bioinformatics with minimum 60% marks with two years of relevant experience	<br />Job Requirement	<br />Development of databases in multi user environment and application softwares, updating and maintenance of website, Drug designing and QSAR study etc.<br />Desirable<br />Knowledge of Bioinformatics tools, Windows, Linux, C++, JAVA / JAVA Script, Visual Basic, CGI, DBMS/RDBMS and HTML. Experience in various domains of bioinformatics such as structure based drug designing, Newtonian dynamics and QSAR studies.<br />Age<br />Below 35 years (as on the date of interview)<br />Emoluments<br />Rs. 12,000/- per month fixed.<br />Note: All the candidates should report for interview on or before 10.30 A.M<br />General Conditions<br />The aforesaid positions are purely temporary and do not give the incumbent any right whatsoever for appointment on regular basis.<br />The applicant will have to submit typed and duly signed application on plain paper on the day of interview stating:<br />    (a) Advertisement No.<br />    (b) Position applied for<br />    (c) Name of Applicant (in Block letters)<br />    (d) Father’s Name<br />    (e) Date of Birth<br />    (f) Sex<br />    (g) Age as on the date of interview (dd / mm / yy )<br />    (h) Address (Permanent &amp; correspondence)<br />    (i) Educational Qualifications (High School onwards) with examination passed, year, % marks, subjects<br />    (j) Employment experience, if any i.e. Name of employer, nature of employment, date of joining and leaving.<br />Applications must be accompanied by a latest passport size photograph and attested copies of certificates<br />Original certificates/degree and testimonials should be produced by the candidate for verification at the time of interview.</p>

<p>Tenure: Initially upto six months and extendable based on performance.<br />The upper age limit can be relaxed up to 5 years in the case of applicant belonging to SC/ST/Woman/Physically handicapped and 3 years for OBCs.<br />No TA/DA will be paid for attending the interview.<br />More at http://www.biotechpark.org.in/index1.htm</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8384/post-doc-in-genomics-of-fungi</guid>
  <pubDate>Tue, 18 Feb 2014 13:47:08 -0600</pubDate>
  <link></link>
  <title><![CDATA[Post-doc in Genomics of Fungi]]></title>
  <description><![CDATA[
<p>Post-doc in Genomics of Fungi</p>

<p>Fungi are of central importance for the global carbon cycle because of<br />their role in the degredation of complex organic matter such as plant<br />material. Fungi also represent one of the last frontiers of<br />biodiversity, as their taxonomic diversity and metabolic potential<br />remain poorly understood. This is particularly true for those fungi that<br />are abundant in freshwaters.</p>

<p>\"MycoLink\" (Linking aquatic mycodiversity to ecosystem function) is an interdisciplinary project integrating the expertise of 4 Leibniz Institutes: IGB, ZALF, DSMZ, the Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), the Leibniz Centre for Agricultural Landscape Research (ZALF), and the Leibniz-Institute of Zoo- and Wildlife Research in Berlin (IZW). We are seeking to recruit outstanding young scientists to establish an innovative research program, and currently invite applications for:</p>

<p>PostDoc will focus on global biodiversity and evolutionary genomics of freshwater fungi, using second- and third-generation sequencing and bioinformatics to analyse natural populations and experimental cultures. For further information, contact Michael T. Monaghan (monaghan@igb-berlin.de) (http://monaghanlab.org).</p>

<p>PostDoc will focus on the ecological and functional role of aquatic fungi by combining state-of-the-art biochemical analyses with modeling in experimental and natural ecosystems. For further information, contact Hans-Peter Grossart &amp; Katrin Premke (hgrossart@igb-berlin.de; premke@igb-berlin.de)</p>

<p>Applicants must hold a PhD in a relevant field. Positions are available for up to three years. Salary is according to the German TvD. Positions will be based at IGB Berlin, IGB Neuglobsow, and at the Berlin Centre for Genomics in Biodiversity Research. The institutes of the Leibniz Association strive to increase the proportion of female scientists. Therefore, female candidates are specifically encouraged to apply. Disabled applicants with identical technical and personal qualification will be preferentially selected.</p>

<p>Please submit a curriculum vitae (including publication list), a brief statement of motivation and research interests, and the names and contact information of two referees. Please send all documents as a single pdf file to monaghan@igb-berlin.de. </p>

<p>Review of the applications will start on 21 February 2014 and continue until the positions are filled. Interviews for shortlisted applicants will take place in March.</p>

<p>Biodiversity, Ecology, and Genomics of Aquatic Fungi<br />Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany</p>

<p>Deadline for applications : unknown.</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8122/internships-indian-institute-of-science</guid>
  <pubDate>Sun, 02 Feb 2014 03:05:58 -0600</pubDate>
  <link></link>
  <title><![CDATA[Internships @ Indian Institute of Science]]></title>
  <description><![CDATA[
<p>Internships available for Bachelors and Masters students</p>

<p>Each node will host student interns interested in pursuing a research career in mathematical or computational biology at institutions located in its region.</p>

<p>Eligibility: Bachelors (3rd or 4th year) and Masters students</p>

<p>Average duration: 3 months (could be more in certain cases). These internships can be availed at any time during 2014 subject to consent from the faculty mentor.</p>

<p>Fellowship amount: Rs. 10,000 per month. In addition, outstation interns can receive up to Rs. 5000 per month for accommodation and Rs. 3000 for travel from and to their home place.</p>

<p>Application procedure: Apply online at http://nnmcb.appzone.co.in/</p>

<p>Deadline: February 10, 2014</p>

<p>Contact Information:</p>

<p>National Network for Mathematical and Computational Biology</p>

<p>Department of Mathematics</p>

<p>Indian Institute of Science</p>

<p>Bangalore 560 012</p>

<p>Tel: 080-2293 2893</p>

<p>Email: nnmcb@math.iisc.ernet.in</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/8265/list-of-generic-simulation-softwaretoolsresource-with-brief-description-and-homepage</guid>
	<pubDate>Mon, 10 Feb 2014 05:57:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/8265/list-of-generic-simulation-softwaretoolsresource-with-brief-description-and-homepage</link>
	<title><![CDATA[List of generic simulation software/tools/resource with brief description and homepage !!!]]></title>
	<description><![CDATA[<p>List of generic simulation software/tools/resource with brief description and homepage</p><p><img src="http://www.evolution-of-life.com/fileadmin/images/carousel/genetic.PNG" alt="image" style="border: 0px;"></p><p>ALF <br />A Simulation Framework for Genome Evolution <br />http://www.cbrg.ethz.ch/alf<br /><br />Bayesian Serial SimCoal <br />Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. <br />http://www.stanford.edu/group/hadlylab/ssc/index.html<br /><br />BEERS <br />BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data <br />http://cbil.upenn.edu/beers/<br /><br />BOTTLENECK <br />Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies <br />http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html<br /><br />BottleSim <br />BottleSim is a computer simulation program for simulating the process of population bottlenecks <br />http://chkuo.name/software/bottlesim.html<br /><br />CASS <br />Protein Sequence Simulation <br />http://www.wyomingbioinformatics.org/liberlesgroup/cass/<br /><br />CDPOP <br />CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior. <br />http://cel.dbs.umt.edu/cdpop<br /><br />CoalFace <br />CoalFace is a simulation of the coalescent process with the visual display of gene genealogies. <br />http://web.up.ac.za/default.asp?ipkcategoryid=3283<br /><br />CoaSim <br />CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. <br />http://users-birc.au.dk/mailund/coasim/index.html<br /><br />cosi <br />The cosi package is written in C and is available as a tar file. <br />http://www.broadinstitute.org/~sfs/cosi/<br /><br />CS-PSeq-Gen <br />A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny <br />http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen.html<br /><br />DAWG <br />An application designed to simulate the evolution of recombinant DNA sequences in continuous time <br />http://scit.us/projects/dawg<br /><br />Easypop <br />EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions <br />http://www.unil.ch/dee/page36926_fr.html<br /><br />EggLib <br />EggLib is a C++/Python library and program package for evolutionary genetics and genomics. <br />http://egglib.sourceforge.net/<br /><br />EvolSimulator <br />A simulation test bed for hypotheses of genome evolution <br />http://acb.qfab.org/acb/evolsim/<br /><br />EvolveAGene <br />A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions <br />http://bellinghamresearchinstitute.com/software/index.html<br /><br />fastsimcoal <br />A continuous-&not;‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios <br />http://cmpg.unibe.ch/software/fastsimcoal/<br /><br />FastSLINK <br />Simulation of Marker and Phenotype Data in Pedigrees <br />http://watson.hgen.pitt.edu/<br /><br />FFPopSim <br />C++/Python library for population genetics. <br />http://webdav.tuebingen.mpg.de/ffpopsim/<br /><br />FLUX SIMULATOR <br />The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. <br />http://flux.sammeth.net/simulator.html<br /><br />ForSim <br />ForSim: A Forward Evolutionary Computer Simulation <br />http://www.anthro.psu.edu/weiss_lab/research.shtml<br /><br />ForwSim <br />The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. <br />http://badri-populationgeneticsimulators.blogspot.com/<br /><br />FPG <br />Forward Population Genetic simulation <br />http://genfaculty.rutgers.edu/hey/software#fpg<br /><br />FREGENE <br />FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. <br />http://www.ebi.ac.uk/projects/bargen/download/fregen/documentation_html.html<br /><br />GAMETES <br />Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. <br />http://sourceforge.net/projects/gametes/?source=navbar<br /><br />GASP <br />Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. <br />http://research.nhgri.nih.gov/gasp/<br /><br />GemSIM <br />Next generation sequencing read simulator <br />http://sourceforge.net/projects/gemsim/<br /><br />GeneArtisan <br />Simulation of Markers in Case-Control Study Designs <br />http://www.rannala.org/?page_id=241<br /><br />GENOME <br />A rapid coalescent-based whole genome simulator <br />http://www.sph.umich.edu/csg/liang/genome/<br /><br />GenomePop2 <br />GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. <br />http://webs.uvigo.es/acraaj/genomepop2.htm<br /><br />GenomeSimla <br />GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested <br />http://chgr.mc.vanderbilt.edu/genomesimla/<br /><br />GENS2 <br />Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. <br />https://sourceforge.net/projects/gensim/<br /><br />GWAsimulator <br />A rapid whole genome simulation program <br />http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator<br /><br />HAP-SAMPLE <br />An association simulator for candidate regions or genome scans <br />http://www.hapsample.org/<br /><br />HAPGEN <br />A simulator for the simulation of case control datasets at SNP markers <br />https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html<br /><br />HapSim <br />A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients <br />http://cran.r-project.org/web/packages/hapsim/index.html<br /><br />HAPSIMU <br />A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model <br />http://l.web.umkc.edu/liujian/<br /><br />IBDsim <br />IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. <br />http://raphael.leblois.free.fr/<br /><br />indel-Seq-Gen <br />A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies <br />http://bioinfolab.unl.edu/~cstrope/isg/<br /><br />Indelible <br />A powerful and flexible simulator of biological evolution <br />http://abacus.gene.ucl.ac.uk/software/indelible/<br /><br />invertFREGENE <br />InvertFREGENE is a forward-in-time simulator of inversions in population genetic data <br />http://www.ebi.ac.uk/projects/bargen/<br /><br />kernalPop <br />A spatially explicit population genetic simulation engine <br />http://cran.r-project.org/src/contrib/archive/kernelpop/<br /><br />MaCS <br />Markovian Coalescent Simulator <br />http://www-hsc.usc.edu/~garykche/<br /><br />Mason <br />A package for the simulation of nucleotide data. <br />http://www.seqan.de/projects/mason/<br /><br />mbs <br />modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection <br />http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html<br /><br />Mendel's Accountant <br />Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine <br />http://mendelsaccount.sourceforge.net/<br /><br />MetaSim <br />A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets <br />http://ab.inf.uni-tuebingen.de/software/metasim/<br /><br />mlcoalsim <br />Multilocus Coalescent Simulations <br />http://code.google.com/p/mlcoalsim-v1/<br /><br />ms <br />The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. <br />http://home.uchicago.edu/~rhudson1/source/mksamples.html<br /><br />msHOT <br />The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. <br />http://home.uchicago.edu/~rhudson1/<br /><br />msms <br />A coalescent Simlation tool with selection. <br />http://www.mabs.at/ewing/msms/index.shtml<br /><br />MySSP <br />A program for the simulation of DNA sequence evolution across a phylogenetic tree <br />http://www.rosenberglab.net/software.php<br /><br />Nemo <br />A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework. <br />http://nemo2.sourceforge.net/<br /><br />NetRecodon <br />Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography <br />http://code.google.com/p/netrecodon/<br /><br />PEDAGOG <br />Software for simulating eco-evolutionary population dynamics <br />https://bcrc.bio.umass.edu/pedigreesoftware/node/5<br /><br />phenosim <br />A tool to add phenotypes to simulated genotypes <br />http://evoplant.uni-hohenheim.de/doku.php?id=software:software<br /><br />PhyloSim <br />An R package for the Monte Carlo simulation of sequence evolution <br />http://bit.ly/rlsim-git<br /><br />pIRS <br />Profile-based Illumina pair-end reads simulator <br />https://code.google.com/p/pirs/<br /><br />ProteinEvolver <br />Simulation of protein evolution along phylogenies under structure-based substitution models <br />http://code.google.com/p/proteinevolver/<br /><br />QMSim <br />QTL and Marker Simulator <br />http://www.aps.uoguelph.ca/~msargol/qmsim/<br /><br />quantiNEMO <br />An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population <br />http://www2.unil.ch/popgen/softwares/quantinemo/<br /><br />RECOAL <br />Simulates new haplotype data from a reference population of haplotypes. <br />ftp://popgen.usc.edu/<br /><br />Recodon <br />Coalescent simulation of coding DNA sequences with recombination, migration and demography <br />http://code.google.com/p/recodon/<br /><br />rlsim <br />A package for simulating RNA-seq library preparation with parameter estimation <br />http://bit.ly/rlsim-git<br /><br />Rmetasim <br />Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R <br />http://linum.cofc.edu/software.html#metasim<br /><br />RNA Seq Simulator <br />RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. <br />http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator<br /><br />Rose <br />Random model of sequence evolution <br />http://bibiserv.techfak.uni-bielefeld.de/rose/<br /><br />SelSim <br />SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection <br />http://www.well.ox.ac.uk/~spencer/selsim/<br /><br />Seq-Gen <br />An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. <br />http://tree.bio.ed.ac.uk/software/seqgen/<br /><br />SEQPower <br />Statistical power analysis for sequence-based association studies <br />http://bioinformatics.org/spower/<br /><br />SeqSIMLA <br />SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. <br />http://seqsimla.sourceforge.net/<br /><br />Serial NetEvolve <br />A flexible utility for generating serially-sampled sequences along a tree or recombinant network <br />http://biorg.cis.fiu.edu/sne/<br /><br />SFS_CODE <br />SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. <br />http://sfscode.sourceforge.net/sfs_code/index/index.html<br /><br />SIBSIM <br />Quantitative phenotype simulation in extended pedigrees <br />http://sourceforge.net/projects/sibsim/<br /><br />SIMCOAL2 <br />A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models <br />http://cmpg.unibe.ch/software/simcoal2/<br /><br />SimCopy <br />An R package simulating the evolution of copy number profiles along a tree. <br />http://bit.ly/simcopy<br /><br />SIMLA <br />SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. <br />http://www.chg.duke.edu/research/simla.html<br /><br />SimPed <br />A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures <br />http://www.hgsc.bcm.tmc.edu/content/simped<br /><br />Simprot <br />A program to simulate protein evolution by substitution, insertion and deletion <br />http://www.uhnresearch.ca/labs/tillier/software.htm#3<br /><br />SimRare <br />Rare variant simulation and analysis tool <br />http://code.google.com/p/simrare/<br /><br />simuGWAS <br />A forward-time simulator that simulates realistic samples for genome-wide association studies. <br />http://simupop.sourceforge.net/cookbook/simucomplexdisease<br /><br />simuPOP <br />simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. <br />http://simupop.sourceforge.net/<br /><br />SISSI <br />A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. <br />http://www.cibiv.at/software/sissi/<br /><br />SNPsim <br />Coalescent simulation of hotspot recombination <br />http://code.google.com/p/phylosoftware/<br /><br />SPIP <br />SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user <br />http://swfsc.noaa.gov/textblock.aspx?division=fed&amp;id=3434<br /><br />Splatche <br />Spatial and Temporal Coalescences in Heterogeneous Environment <br />http://www.splatche.com/<br /><br />srv <br />Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. <br />http://simupop.sourceforge.net/cookbook/simurarevariants<br /><br />SUP <br />SLINK/FastSLINK utility program <br />http://mlemire.freeshell.org/software.html<br /><br />TreesimJ <br />A flexible, forward-time population genetic simulator <br />http://code.google.com/p/treesimj/<br /><br />Vortex <br />VORTEX is an individual-based simulation model for population viability analysis (PVA). <br />http://www.vortex9.org/vortex.html<br /><br />References:</p><p>Image www.evolution-of-life.com</p><p>www.cancer.gov</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8520/rcb-gurgaon-bioinformatics-rapa-openings</guid>
  <pubDate>Thu, 27 Feb 2014 08:42:15 -0600</pubDate>
  <link></link>
  <title><![CDATA[RCB Gurgaon Bioinformatics RA/PA Openings]]></title>
  <description><![CDATA[
<p>Advt. No.1/2014</p>

<p>Recruitment for Research Associate and Project Assistant positions</p>

<p>Regional Centre for Biotechnology (RCB) is an autonomous academic institution established by the Department of Biotechnology, Govt. of India with regional and global partnerships synergizing with the programmes of UNESCO as a Category II Centre. The primary focus of RCB is to provide world class education, training and conduct innovative research at the interface of multiple disciplines to create high quality human resource in disciplinary and interdisciplinary areas of biotechnology in a globally competitive research milieu. </p>

<p>Research Associate (02 Position)</p>

<p>Consolidated emoluments Rs.22000/- + 30% H.R.A. p.m.</p>

<p>Essential: Ph.D. in Natural Sciences, minimum 60% marks in all qualifying exams and below 35 years of age.</p>

<p>Desirable: Prior experience at the PhD level in Biochemistry, Bioinformatics and Proteomics with a strong motivation for a career in research is highly desirable.</p>

<p>Strong PhD level training with proteins chemistry, protein purification and statistical analysis of proteomics or genomics dataset will be preferred. Either/ both qualifications should be substantiated by published papers.</p>

<p>Inter-Institutional Program for  Maternal, Neonatal and Infant  Sciences: A translational approach to studying preterm birth. </p>

<p>Principal Investigator: Dr. Dinakar M. Salunke </p>

<p>Applicants may apply along with the requisite documents (attested copies) pertaining to proof of date of birth, academic/professional qualifications, experience (if any), in the prescribed format available on our websites: www.rcb.res.in and www.rcb.ac.in. Applications should be sent to the Registrar, Regional Centre for Biotechnology, 180 Udyog Vihar Phase 1, Gurgaon-122016, Haryana, India, through Registered Post on or before Feb 28, 2014. A soft copy of the application should be sent by email to registrar@rcb.res.in. Incomplete applications or applications received after Feb 28, 2014 will not be entertained. </p>

<p>More at https://www.rcb.res.in/Advt-1._for_websites_PTB-revised.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/8504/update-genome-workbench-2715-released</guid>
	<pubDate>Wed, 26 Feb 2014 16:12:17 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/8504/update-genome-workbench-2715-released</link>
	<title><![CDATA[Update Genome Workbench 2.7.15 released]]></title>
	<description><![CDATA[<p>NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.</p><p><img src="http://www.ncbi.nlm.nih.gov/core/assets/gbench/images/firstscreen_still.gif" alt="Introductory screen shot" style="border: 0px; border: 0px;"></p><p>Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.</p><p>Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.</p><p>NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.</p><p>&nbsp;New Features in Genome Workbench 2.7.15 <br /><br /></p><ul>
<li>Multiple Alignment View: implemented adaptive feature display when zooming in</li>
<li>Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.</li>
<li>Binary packages for Linux OpenSUSE 13.1 are now available</li>
</ul><p><br />Bug Fixes and Improvements in Genome Workbench 2.7.15 <br /><br /></p><ul>
<li>Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities</li>
<li>Multiple Pane View: fixed crash on loading BLAST results</li>
<li>Graphical Sequence View: fixed crash on zooming in and out, related to SNP track</li>
<li>Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error</li>
<li>Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name</li>
<li>Text View / Flat File: fixed Mac OS rendering issues</li>
<li>Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands</li>
<li>File Import: optimization improvement to speed up load of files containing multiple project items</li>
<li>File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers</li>
<li>Mac OS: improved tooltips for toolbar buttons</li>
<li>Phylogenetic Tree Builder Tool: improved diagnostics of errors</li>
<li>Multiple Alignment View: optimizations to avoid main GUI freezes</li>
<li>Open Dialog: removed duplicate elements in table of genomes (load Genome)</li>
<li>PDF export: fixed issue with XREF table errors</li>
<li>Tree View: fixed issues with showing Force Layout progress on Mac OS</li>
<li>Tree View: PDF export fixed issues for showing labels of collapsed nodes</li>
<li>Tree View: added an option to stop layout</li>
<li>Tree View: broadcasting mechanism fixed not to accumulate selected nodes</li>
</ul><p>Reference:</p><p>NCBI news</p><p>http://www.ncbi.nlm.nih.gov/tools/gbench/</p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/8857/junior-research-fellow-at-iari</guid>
  <pubDate>Mon, 10 Mar 2014 13:10:56 -0500</pubDate>
  <link></link>
  <title><![CDATA[Junior Research Fellow at IARI]]></title>
  <description><![CDATA[
<p>DIVISION OF NEMATOLOGY<br />INDIAN AGRICULTURAL RESEARCH INSTITUTE<br />NEW DELHI 110012</p>

<p>Applications are invited for the posts of one Junior Research Fellow in the DBT funded project entitled “Plant parasitic nematode genome informatics - insilico resource development”. The project is for a period of three years.</p>

<p>Essential qualifications for JRF: First class M. Sc. / M. Tech in Bioinformatics. Knowledge of programming language, pearl, Statistics and database – HTML, CSS, Java script.</p>

<p>Desirable qualifications: Experience in handling next generation sequencing data</p>

<p>Age limit: 35 years maximum (5 year relaxation for SC/ST and women candidates) Emoluments: 16,000 + 30% HRA.</p>

<p>The post is purely temporary in nature and is co-terminus with the project. The appointment would be initially for one year and may be extended further upon satisfactory performance.</p>

<p>Those who are interested in pursuing Ph.D with strong research aptitude are preferred.</p>

<p>Interested candidates may attend the Walk in interview on 25th March 2014 along with the duly filled application forms (format in the following page) with all the relevant documents.</p>

<p>Venue: Division of Nematology, Indian Agricultural Research Institute, New Delhi 110012 (Room No. 306, 3rd floor, LBS building)</p>

<p>Reporting Time: Interested candidates should report strictly between 10.00 to 10.30 AM.</p>

<p>Interview time: 10.30 AM</p>

<p>Short-listed candidates will be called for interview at New Delhi. However, no TA and DA will be paid for attending the interview.</p>

<p>Advertisement:</p>

<p>https://www.iari.res.in/files/JRF_Nema-07032014-20140307-170017.pdf</p>
]]></description>
</item>

</channel>
</rss>