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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/28915?offset=710</link>
	<atom:link href="https://bioinformaticsonline.com/related/28915?offset=710" rel="self" type="application/rss+xml" />
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22147/research-associate-bioinformatics-job-position-in-nipgr</guid>
  <pubDate>Sun, 19 Apr 2015 14:55:19 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics job position in NIPGR]]></title>
  <description><![CDATA[
<p>NIPGR Recruitment 2015 – Apply for Research Associate Posts</p>

<p>NIPGR is commonly known as National Institute of Plant Genome Research. Recently, it’s great opportunity for those candidates who are interested to do job in NIPGR. National Institute of Plant Genome Research (NIPGR) had found to build a bridge between the branches of natural sciences and due this connection it is steeping on the heaps of success. Its objectives to preserve, research, production and the advancement in the trait are very clear and also being appreciated by the nation and had been contributing for the further enrichment of the institute. NIPGR had announced the recruitment to further make improvements and amendments by the young potential in their panel. The recruitment is being announced for the post is mentioned below. We are giving a complete information to applicants for find their eligibility as per desired post under NIPGR Recruitment 2015 project but if the candidates are not satisfied with this information then they can download an official advertisement of NIPGR recruitment 2015 from the link defined ahead under the head of reference.</p>

<p>NIPGR Recruitment 2015 for the 1 post of Research Associate: National Institute of Plant Genome Research (NIPGR) had instigated the progression of the recruitment and this process is linked thoroughly so as the 1 post of Research Associate. Applicants are associated and linked with the education to be PHD degree in the life science, biotechnology, bioinformatics or molecular biology. Applicants are associated with the dispatch of the application along with the required certificates so as on the date of 24th Feb 2015.</p>

<p>The recruitment notification and application @ http://www.nipgr.res.in/careers/vacancies_latest.php#</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources</guid>
	<pubDate>Tue, 28 Jun 2022 04:08:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources</link>
	<title><![CDATA[List of comparative genomics resources !]]></title>
	<description><![CDATA[<div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1096638041"><span>3D-GENOMICS -- A Database to Compare Structural and Functional Annotations of Proteins between Sequenced Genomes</span></a></div><p>Compare structural and functional annotations of proteins between sequenced genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1100640374"><span>ARED Organism -- expansion of ARED reveals AU-rich element cluster variations between human and mouse</span></a></div><p>View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1234973128"><span>ATGC -- Alignable Tight Genomic Clusters Database</span></a></div><p>Find information about orthologous genes in prokaryotes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174596104"><span>AnimalQTLdb -- a livestock QTL database tool set for positional QTL information mining and beyond</span></a></div><p>Search for publicly available QTL data on livestocks and animal species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20110518150135"><span>BGDB -- Bovine Genome Database</span></a></div><p>Find information about bovine genomics data.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1229012662"><span>COMPARE -- a multi-organism system for cross-species data comparison and transfer of information</span></a></div><p>A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1218141952"><span>CONDOR -- COnserved Non-coDing Orthologous Regions</span></a></div><p>A database resource of developmentally associated conserved non-coding elements.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1099057221"><span>CORG -- A database for COmparative Regulatory Genomics</span></a></div><p>Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1203608896"><span>COXPRESdb -- a database of coexpressed gene networks in mammals</span></a></div><p>Find coexpressed gene lists and networks in human and mouse.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1097763045"><span>CVTree -- A Phylogenetic Tree Reconstruction Tool Based on Whole Genomes</span></a></div><p>Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1232729680"><span>CleanEST -- the cleansed EST libraries database</span></a></div><p>A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1256926144"><span>CoCoa -- COefficient of COAncestry software</span></a></div><p>Find information about the ancestral relationship between genes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1227549154"><span>CoGemiR -- a comparative genomics microRNA database</span></a></div><p>Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1117678221"><span>Comparative Genometrics (CG) -- a database dedicated to biometric comparisons of whole genomes</span></a></div><p>Conduct comparative biometric analysis of chromosomes of different organisms.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1151007916"><span>DoTS -- Database Of Transcribed Sequences</span></a></div><p>Search for Indices of gene and transcripts in human and mouse.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174510065"><span>DroSpeGe -- rapid access database for new Drosophila species genomes</span></a></div><p>Search and compare 12 new and old Drosophila genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1098208414"><span>ECR Browser -- A Tool for Visualizing and Accessing Data from Comparisons of Multiple Vertebrate Genomes</span></a></div><p>Access to whole genome alignments of human, mouse, rat and fish sequences.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209738459"><span>EPGD -- Eukaryotic Paralog Group Database</span></a></div><p>Find eukaryotic paralog/paralogon information.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1232726869"><span>EVOG -- evolutionary visualizer for overlapping genes</span></a></div><p>Analyze the evolutionary process of overlapping genes when comparing different species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1227633714"><span>GNAT -- Inter-species gene mention normalization (ISGN)</span></a></div><p>The first publicly available system reported to handle inter-species gene mention normalization.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1229438992"><span>GenColors -- annotation and comparative genomics of prokaryotes made easy</span></a></div><p>A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1151086258"><span>GeneNest gene indices</span></a></div><p>Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174489378"><span>GenomeTrafac -- a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs</span></a></div><p>Use comparative genomics approach to characterize gene models and identify putative cis-regulatory regions of RefSeq Gene Orthologs.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20110518150753"><span>IKMC -- International Knockout Mouse Consortium web portal</span></a></div><p>Find information about mutated mouse genes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209411604"><span>IMG/M -- Integrated Microbial Genomes/Metagenomes</span></a></div><p>A data management and analysis system for metagenomes</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1234976694"><span>ISED -- Influenza sequence and epitope database.</span></a></div><p>Search for influenza sequence, vaccine, and drug resistance information.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20140710115515"><span>LAMDHI: The Search for Animal Models Starts Here</span></a></div><p>LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1228843803"><span>MANTIS -- a phylogenetic framework for multi-species genome comparisons</span></a></div><p>The missing link between multi-species full genome comparisons and functional analysis.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1099578148"><span>MBGD -- Microbial genome database for comparative analysis</span></a></div><p>Conduct comparative analysis of completely sequenced microbial genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1221077729"><span>MEGA -- Molecular Evolutionary Genetics Analysis</span></a></div><p>A biologist-centric software for evolutionary analysis of DNA and protein sequences.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174596756"><span>MamPol -- a database of nucleotide polymorphism in the Mammalia class</span></a></div><p>Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1266437314"><span>MicrobesOnline -- Prokaryotic Genome Database</span></a></div><p>Find information about 1000s of microbial genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1208461006"><span>Narcisse -- a mirror view of conserved syntenies</span></a></div><p>A database dedicated to the study of genome conservation.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1219772764"><span>OMA -- the Orthologous MAtrix project</span></a></div><p>Explore orthologous relations across 352 complete genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209738741"><span>OPTIC -- orthologous and paralogous transcripts in clades</span></a></div><p>Browse complete genomes in several clades.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209573208"><span>OrthoDB -- the hierarchical catalog of eukaryotic orthologs</span></a></div><p>Find groups of orthologous genes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1221231200"><span>OrthoMaM -- orthologous mammalian markers</span></a></div><p>A database of orthologous genomic markers for placental mammal phylogenetics.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1100009979"><span>PEDANT -- Protein Extraction, Description and ANalysis Tool</span></a></div><p>Conduct genome wide functional and structural analysis.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174489475"><span>PReMod -- a database of genome-wide mammalian cis-regulatory module predictions</span></a></div><p>Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1151083092"><span>PhenomicDB -- Comparison of phenotypes of orthologous genes in human and model organisms</span></a></div><p>Compare phenotypes of a given gene or gene set in different model organisms.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1190899370"><span>Phylemon -- A suite of web tools for molecular evolution, phylogenetics and phylogenomics</span></a></div><p>Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1232555615"><span>PhyloPat -- the phylogenetic pattern database</span></a></div><p>Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174510223"><span>Pristionchus.org -- a genome-centric database of the nematode satellite species Pristionchus pacificus</span></a></div><p>Search for genomic information on nematode satellite species Pristionchus pacificus.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1236367352"><span>ProtClustDB -- NCBI Protein Clusters Database</span></a></div><p>Find information about related protein sequences.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209410278"><span>ProtozoaDB -- database of protozoan genomes</span></a></div><p>Database hosting genomics and post-genomics data from multiple protozoans.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1232554690"><span>Pseudofam -- the pseudogene families database</span></a></div><p>A database of pseudogene families based on the protein families from the Pfam database.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20110518151439"><span>RIDM - RIKEN Integrated Database of Mammals</span></a></div><p>Find genomic information about mammals.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1272562567"><span>RegPrecise -- Regulon Prediction Database</span></a></div><p>Find information about predicted regulons in prokaryotic transcription regulation.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1272477473"><span>SALAD -- Surveyed contained motif ALignment diagram and the Associating Dendrogram</span></a></div><p>Perform systematic comparison of proteome data among species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1229010765"><span>SGN -- SOL Genomics Network</span></a></div><p>A comparative map viewer dedicated to the biology of the Solanaceae family.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1256669040"><span>ShotgunFunctionalizeR -- R-package for functional comparison of metagenomes</span></a></div><p>Analyze data from functional analysis on fragmented microbial genetic material.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1256238439"><span>SnoopCGH -- Comparative Genomic Hybridization software</span></a></div><p>Visualize and explore comparative genomic hybridization data sets.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174489598"><span>SwissRegulon -- a database of genome-wide annotations of regulatory sites</span></a></div><p>Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1229013521"><span>TaxonGap -- a visualization tool for intra- and inter-species variation among individual biomarkers</span></a></div><p>Compare and select individual biomarkers.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1106063477"><span>The Adaptive Evolution Database (TAED) -- a phylogeny based tool for comparative genomics</span></a></div><p>Search for information on adaptive evolution in gene families of higher plants and chordate.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1216742716"><span>The CGView Server -- a comparative genomics tool for circular genomes</span></a></div><p>Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1099663588"><span>The ERGO -- Genome analysis and discovery system</span></a></div><p>Conduct a comprehensive analysis of genes and genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1177611772"><span>The Macaque Genome: Interactive Poster and Teaching Resource</span></a></div><p>An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1103816940"><span>The TIGR Gene Indices -- clustering and assembling EST and known genes and integration with eukaryotic genomes</span></a></div><p>Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1043767169"><span>UniGene</span></a></div><p>Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1216738072"><span>Uprobe -- universal overgo hybridization-based probe retrieval and design</span></a></div><p>A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1098205291"><span>VISTA -- Computational Tools for Comparative Genomics</span></a></div><p>Comprehensive suite of programs and databases for comparative analysis of genomic sequences.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20110518144404"><span>cBARBEL -- Catfish Breeder and Researcher Bioinformatics Entry Location</span></a></div><p>Find information about ictalurid catfish.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209738040"><span>eggNOG -- evolutionary genealogy of genes: Non-supervised Orthologous Groups</span></a></div><p>Discover orthologous groups of genes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1234370319"><span>metaTIGER -- a metabolic gene evolution resource</span></a></div><p>Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1138901833"><span>xBASE -- a collection of online databases for bacterial comparative genomics</span></a></div><p>Conduct bacterial comparative genomics.</p></div>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/22073/bcil-bioinformatics-bitp-application</guid>
	<pubDate>Fri, 17 Apr 2015 04:34:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/22073/bcil-bioinformatics-bitp-application</link>
	<title><![CDATA[BCIL Bioinformatics BITP Application !!]]></title>
	<description><![CDATA[<p>BCIL Bioinformatics BITP Application Form 2015 logoGrab latest Information! Biotech Consortium India Limited has announced a notification for offering admission in Biotech Industrial Training Program. The organization has invited online application from 7th April 2015 BCIL Admission 2015. BCIL has conducted an entrance exam which is scheduled on 20th June 2015. Candidates those who are looking for this program just go for it and don&rsquo;t miss this opportunity.<br /><br />To apply for Biotech Industrial Training Programme the candidates should have 50% marks in B.Tech/BE/M.Tech Degree in Bio technology, bio process technology and other related disciplines form any recognized institution. The organization has decided application fee of Rs.500/- for all candidates and that should be paid through demand draft. Applicants who satisfy the organization requirement, they can take their steps forward.<br /><br />Candidates should submit the online application before 10th May 2015. After registering the online application you need to take the hard copy of it and send through post. Print out of this application should be reached before 15th May 2015. All the latest updates like selection process, exam syllabus and other related information are updated soon at the main URL of the department and aspirants should keep in touch with this site. Further details of BCIL Bioinformatics BITP Application Form 2015 are explained below.<br /><br />Organization: Biotech Consortium India Limited<br /><br />Website URL: www.bcil.nic.in<br /><br />Location: New Delhi<br /><br />Course Name: Biotech Industrial Training Program<br /><br />Exam Name: BCIL Entrance Exam<br /><br />Educational Details: Applicants should complete their B.Tech/M.Tech/BE programs in Neuro- Science, Agricultural, Bio technology, bio process technology and other related disciplines having 50% aggregate from any authorized university.<br /><br />Application Fee: For all candidates application fee is Rs.500/- and it will be paid through Demand Draft drawn in favour of BCIL, New Delhi.<br /><br />How to Apply: Candidates who are willing to apply for this program they can apply through online mode. Then send the hard copy of registered application form to through post.<br /><br />Important Dates<br /><br />Opening Date of Submission Online Application Form: 7h April 2015<br /><br />Closing Date of Submission of Online Application Form: 10th May 2015<br /><br />Last Date of Receipt of Application Form: 15th May 2015<br /><br />Exam Date: 20th June 2015</p><p>More at http://bcil.nic.in/default.htm</p>]]></description>
	<dc:creator>Pranjali Yadav</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/35395/comprehensive-list-of-visualization-tools-for-biological-pathways</guid>
	<pubDate>Tue, 30 Jan 2018 06:01:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/35395/comprehensive-list-of-visualization-tools-for-biological-pathways</link>
	<title><![CDATA[Comprehensive list of visualization tools for biological pathways]]></title>
	<description><![CDATA[<p>The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads to a change of state in the cell. Pathways come in different flavors, depending on their functions in the cell &ndash; the three main types are metabolic pathways, gene regulatory pathways, and signaling pathways. These biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization.</p><p><img src="https://photos-1.dropbox.com/t/2/AABemz29qAuSTqSzr5mEsQE7JIMxZlU1CBy0E5n0yUVYbA/12/85115969/png/32x32/1/_/1/2/pathway.png/EOfXoUIYrJ8CIAcoBw/01qsT2eykyPvSH-rNpy3cqioDzZPc4i-xULG3BEZvCk?preserve_transparency=1&amp;size=1280x960&amp;size_mode=3" width="800" height="533" alt="image" style="border: 0px;"></p><p>Following are the comprehensive list of visualization tools for biological pathways:</p><p>BiNA</p><p>Drawings of metabolic networks supporting hiding of cofactors and drawing of chemical structures</p><p>http://bina.unipax.info/</p><p>BioTapestry</p><p>Interactive tool for building, visualizing and sharing gene regulatory network models over the web</p><p>http://www.biotapestry.org/</p><p>Caleydo</p><p>Visual analysis framework targeted at biomolecular data. Visualization of interdependencies between multiple datasets</p><p>http://www.caleydo.org/</p><p>CellDesigner</p><p>A modeling tool for biochemical networks</p><p>http://www.celldesigner.org/</p><p>Edinburgh Pathway Editor</p><p>Edit and draw pathway diagrams</p><p>http://epe.sourceforge.net/SourceForge/EPE.html</p><p>GenMAPP</p><p>Visualization of gene expression and other genomic data on maps representing biological pathways and groupings of genes</p><p>http://www.genmapp.org/</p><p>Ingenuity IPA</p><p>Data integration platform and manually annotated pathways</p><p>http://tinyurl.com/IngenuityPath</p><p>JDesigner</p><p>Graphical modeling environment for biochemical reaction networks</p><p>http://jdesigner.sourceforge.net/Site/JDesigner.html</p><p>KaPPA View</p><p>Plant pathways</p><p>http://kpv.kazusa.or.jp/</p><p>KEGG Atlas</p><p>Interactive Kyoto Encyclopedia of Genes and Genomes pathways</p><p>http://www.genome.jp/kegg/</p><p>Omix&nbsp;</p><p>Visualizing multi-omics data in metabolic networks</p><p>https://www.omix-visualization.com</p><p>PathVisio&nbsp;</p><p>Biological pathway analysis software that allows drawing, editing and analysis of biological pathways</p><p>http://www.pathvisio.org/</p><p>VitaPad&nbsp;</p><p>Application to visualize biological pathways and map experimental data to them</p><p>http://tinyurl.com/vitapad/</p><p>Web tools for pathways</p><p>ArrayXPath&nbsp;</p><p>Mapping and visualizing microarray gene-expression data and integrated biological pathway resources using SVG</p><p>http://tinyurl.com/ArrayXPath/</p><p>GEPAT&nbsp;</p><p>Integrated analysis of transcriptome data in genomic, proteomic and metabolic contexts</p><p>http://gepat.sourceforge.net/</p><p>iPath&nbsp;</p><p>Web-based tool for the visualization, analysis and customization of pathway maps</p><p>http://pathways.embl.de/</p><p>Kegg-Based Viewer&nbsp;</p><p>KEGG-based pathway visualization tool for complex high-throughput data</p><p>http://www.g-language.org/data/marray/</p><p>MapMan&nbsp;</p><p>User-driven tool that displays large datasets onto diagrams of metabolic pathways or other processes</p><p>http://mapman.gabipd.org/web/guest/mapman</p><p>MetPA&nbsp;</p><p>Analysis and visualization of metabolomic data within the biological context of metabolic pathways</p><p>http://metpa.metabolomics.ca</p><p>Omics Viewer&nbsp;</p><p>Data mapping on BioCyc pathways (collection of 5500 pathway/genome databases)</p><p>http://www.biocyc.org/</p><p>Pathway Explorer</p><p>Interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them</p><p>http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml</p><p>Pathway projector&nbsp;</p><p>Zoomable pathway browser using KEGG atlas and Google Maps API</p><p>http://www.g-language.org/PathwayProjector/</p><p>PATIKA&nbsp;</p><p>Integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework</p><p>http://www.cs.bilkent.edu.tr/~patikaweb/</p><p>Reactome SkyPainter&nbsp;</p><p>Visualization of over-represented pathways and reactions from gene lists</p><p>http://www.reactome.org/skypainter-2</p><p>WikiPathways</p><p>Wiki-based, open, public platform dedicated to the curation of biological pathways by and for the scientific community</p><p>http://www.wikipathways.org/</p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22024/research-associate-bioinformatics-job-position-in-indian-agricultural-statistics-research-institute-iasri-pusa-new-delhi</guid>
  <pubDate>Tue, 14 Apr 2015 11:57:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI), Pusa, New Delhi]]></title>
  <description><![CDATA[
<p>Indian Agricultural Statistics Research Institute is inviting applications from indian citizens for recruiting following posts:</p>

<p>Vacancies:<br />Research Associate-02<br />Age Limits:<br />Candidates age limit should be not more than 40 years as on date of interview.<br />Qualification:<br />Candidates should possess Ph.D in Bioinformatics/Agricultural Statistics/Statistics/Computer Science/Computer Application or equivalent.<br />Selection Process:<br />Selection will be based on interview.<br />How to Apply:<br />Eligible candidates may attend for interview along with application in prescribed format, recent passport size photograph pasted on the application form, bio-data, original certificates and self attested copies of relevant documents, all experience certificates, testimonials etc, held at Indian Agricultural Statistics Research Institute, Pusa, New Delhi on 18-04-2015 at 10:30 AM.<br />Last Date:<br />18-04-2015</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</guid>
	<pubDate>Tue, 08 May 2018 04:27:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</link>
	<title><![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]></title>
	<description><![CDATA[<p><strong>HISAT2</strong><span>&nbsp;is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs&nbsp;</span><a href="http://dl.acm.org/citation.cfm?id=2674828">[Sir&eacute;n et al. 2014]</a><span>, we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).&nbsp;</span></p>
<p><span>more at&nbsp;https://ccb.jhu.edu/software/hisat2/index.shtml</span></p><p>Address of the bookmark: <a href="https://github.com/infphilo/hisat2" rel="nofollow">https://github.com/infphilo/hisat2</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/22044/binc-sample-question-paper</guid>
	<pubDate>Thu, 16 Apr 2015 09:12:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/22044/binc-sample-question-paper</link>
	<title><![CDATA[BINC Sample Question Paper !!!]]></title>
	<description><![CDATA[<p>BINC sample question paper for round ONE.</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/22044" length="1260" type="text/plain" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38743/molinspiration-broad-range-of-cheminformatics-software-tools-supporting-molecule-manipulation</guid>
	<pubDate>Sun, 20 Jan 2019 05:32:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38743/molinspiration-broad-range-of-cheminformatics-software-tools-supporting-molecule-manipulation</link>
	<title><![CDATA[molinspiration: broad range of cheminformatics software tools supporting molecule manipulation]]></title>
	<description><![CDATA[<p><span>Molinspiration offers&nbsp;</span><a href="https://www.molinspiration.com/products.html">broad range of cheminformatics software tools</a><span>&nbsp;supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Our products support also fragment-based virtual screening, bioactivity prediction and data visualization. Molinspiration tools are written in Java, therefore can be used practically on any computer platform.</span></p><p>Address of the bookmark: <a href="https://www.molinspiration.com/" rel="nofollow">https://www.molinspiration.com/</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/22068/binc-examination-2015</guid>
	<pubDate>Fri, 17 Apr 2015 03:34:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/22068/binc-examination-2015</link>
	<title><![CDATA[BINC examination 2015 !!!]]></title>
	<description><![CDATA[<p>BioInformatics National Certification (BINC) Examination 2015 organized by Department of Biotechnology, Government of India, New Delhi Pondicherry University, Puducherry</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/22068" length="281577" type="application/pdf" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44288/upset-plots</guid>
	<pubDate>Fri, 24 Mar 2023 22:30:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44288/upset-plots</link>
	<title><![CDATA[Upset plots !]]></title>
	<description><![CDATA[<p>Upset plots are a type of visualization used to analyze the intersection of sets or categories. They are particularly useful for displaying data with multiple categories and analyzing their overlaps.</p>
<p>In an upset plot, each row represents a category or set, and each column represents a data point. The length of the bar for each category indicates the number of data points that belong to that category. The plot also shows the intersections between categories, represented by overlapping bars.</p>
<p>Upset plots are useful for visualizing complex data with multiple categories and intersections, and can help identify patterns and relationships between categories. They are often used in fields such as bioinformatics, where they can be used to analyze gene expression data or to compare the results of different experimental conditions.</p>
<p>https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions</p><p>Address of the bookmark: <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions" rel="nofollow">https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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