Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data on remote servers while offering flexibility similar to popular GUI viewers like IGV.

Documentation is at readthedocs/asciigenome.

Address of the bookmark: https://github.com/dariober/ASCIIGenome

Studentship and Traineeship in Bioinformatics

Applications are invited on plain paper from suitable candidates for Studentship and Traineeship (One each) at Bioinformatics Sub-Center as detailed below:

1. Studentship: Studentship is for those who have completed M. Sc. Degrees in Life Science.

Number of seats : One

Duration : Six months

Eligibility : Passed M.Sc. degree in Life Sciences.

Fellowship : Rs. 5000/- (Five thousand only) per month

2. Traineeship: Traineeship is for those who have completed M. Sc. Degrees in Life Science/Registered Ph. D. student in Life Sciences.

Number of seats : One

Duration : Six months

Eligibility : Passed M.Sc. degree in Life Sciences/ Registered Ph. D. student in Life Sciences

Fellowship : Rs. 5000/- (Five thousand only) per month

Preferences will be given to person who has experience in Bioinformatics and Computer
sciences. The application along with detailed bio-data should reach the undersigned, on or before 25th August 2014. Both, the studentship and the traineeship are temporary, will be discontinued after the six months from the date of Joining. It may be discontinued in-between without any notice, if the work is not found satisfactory.

Advertisement www.bioinfobubpl.nic.in/Advertisement_st.pdf

https://github.com/marbl/meryl

Address of the bookmark: https://github.com/marbl/merqury

• Draft assembly fasta file
• Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)

Address of the bookmark: https://github.com/bcgsc/ARCS/

Walk in interview for guest faculty in Pondicherry University, India. For more information please visit http://www.bicpu.edu.in/bioinfor140814.pdf

usage:   canu [-correct | -trim | -assemble | -trim-assemble] \
              [-s ] \
               -p  \
               -d  \
               genomeSize=[g|m|k] \
               -maxThreads=2 \
               useGrid=false \
              [other-options] \
               read_file.fastq.gz

A default Canu run produces usually high quality assembly, example of a command that was used for testing can be found below. However, there are still a lot of parameters that are possible to tweak. For example if we desire to assemble haplotypes separately of if we want to smash them together, we can alternate the error correction process.

canu -p test_asmbl \
     -d asm_test3 \
     genomeSize=2m \
     -maxThreads=2 useGrid=false \
     -pacbio-raw \ ~/pacbio/dna/sample_reads.fastq.gz

There is a brilliant section in documentation about parameter tweaking.

The output directory contains will contain many files. The most interesting ones are:

• *.correctedReads.fasta.gz : file containing the input sequences after correction, trim and split based on consensus evidence.
• *.trimmedReads.fastq : file containing the sequences after correction and final trimming
• *.layout : file containing informations about read inclusion in the final assembly
• *.gfa : file containing the assembly graph by Canu
• *.contigs.fasta : file containing everything that could be assembled and is part of the primary assembly

The basic stats of assembly can be read from reports generated by the assembler, or calculated using standard UNIX command line tools.

More at https://canu.readthedocs.io/en/latest/faq.html

DNAApp: for iPhone/iPad

This is an iOS app that allows for the opening and analysis of DNA sequencing files - ab1. It includes handy tools such as "Reverse Complement", "Jump to", "Copy and Paste sequences", fast and end scrolling, "Chromatogram adjustments", and "Searching for segments" functions.
When used in combination with other zip apps, and also web-tools like Blast, this app allows you to analyze, and also determine the quality of your sequencing files.
This app works with cloud storage access like Dropbox to your sequencing files.
This is now compatible with the new update for iOS 7.1.
Demo video can be found at: https://www.youtube.com/watch?v=mXeo9hXdZgM 

More @ https://itunes.apple.com/us/app/dnaapp/id854944694?mt=8

DNAApp: For android

This is the first android app that allows for the opening and analysis of DNA sequencing files - ab1. It includes handy tools such as "Reverse Complement", "Jump to", fast and end scrolling, "Chromatogram adjustments", amino acid translations, "export to fasta", and "searching for segment" function.

• When used in combination with other zip apps, and also web-tools like Blast, this app allows you to analyze, and also determine the quality of your sequencing files.
• This app works with cloud storage access like Dropbox to your sequencing files.
• This is now compatible with the new update for Android 4.4.2.

More @  https://play.google.com/store/apps/details?id=bii.seqdatreader&hl=en

BioGene:iPhone/iPad

BioGene is an information tool for biological research. Use BioGene to learn about gene function. Enter a gene symbol or gene name, for example "CDK4" or "cyclin dependent kinase 4" and BioGene will retrieve its gene function and references into its function (GeneRIF).

• BioGene was produced in affiliation with the Computational Biology Center at Memorial Sloan-Kettering Cancer Center with primary information from Entrez Gene at the NCBI.

More @  https://itunes.apple.com/us/app/biogene/id333180084?mt=8

Mentha - the interactome browser: Android

About: mentha - the interactome browser, is a project that offers protein-protein physical/enzymatic interaction information from various sources. For more details about mentha, visit mentha's website. This client application is an independent project. This application is designed to allow you to search proteins on the go.

Key features (Also in website):

• Search proteins by UniProt IDs, gene name or keywords
• Collect proteins from different queries.
• Spot common interactors in clusters.
• Easily distinguish between proteins from Homo sapiens and other organisms (Yellow rounded rectangles)
• Click on edges(links) to get scientific evidence.
• Click on proteins to see descriptions.

More @  https://play.google.com/store/apps/details?id=com.sinnefa.mentha&hl=en

GeneIndex: iPhone/iPad

GeneIndex quickly provides information about genes from various sources. It also includes a RSS reader for journal feeds as well as a PubMed viewer.

Key Features:

• Look up genes by symbol or description.
• Gene indexes for many mammals, plants, invertebrates, and bacteria.
• Link to gene info on websites.
• Download files for offline use. (.pdf, .mp3, .m4v, .doc, .ppt, .xls )
• transfer files via open in, email, or iTunes file sharing
• View RSS feeds for journals
• Query GeneRIF interactions, COSMIC mutations, and CNV data for cell lines.
• Does not require a network connection for local databases.
• View and search PubMed in table view.

GeneIndex provides a convenient and portable way to lookup gene symbols while at a seminar, conference, or lab meeting. Genes are linked to common life science websites such as NCBI, COSMIC, KEGG, PubMed, SymAtlas, UCSC genome browser, Pathway Commons, Genatlas, Wikipedia, HUGO, and OMIM. GeneRIF gene interactions can also be queried.

• Keep current on the scientific literature. GeneIndex includes a RSS reader and web browser for browsing popular journals like Nature, Science, and Cell. You can also add your own RSS feeds. PDFs and podcasts can be saved as files that you can view on the device or email as attachments.
• Examine the status of genes in common cell lines. A subset of COSMIC containing cell lines can be queried for mutations. Copy Number Variation (CNV) plots from cell lines profiled by GSK and Sanger are also linked to genes.

More @  https://itunes.apple.com/us/app/geneindex/id319769866?mt=8

Genome Voyager: iPad

Gain first hand experience identifying the genomic basis of disease by analyzing cases with whole genome sequencing data that have been published for research and learning purposes.

• Visualize whole human genome sequencing data including small variations, copy number variations (CNVs), and loss of heterozygosity (LOH) events
• Quickly find variants of interest by filtering variants based on associated genes, functional impact, allele frequency in data sets, and cross-references with various genomic databases.
• Collaborate on variant assessments with other researchers and academics to improve knowledge of both pathogenic and benign variants.
  To use Genome Voyager, users must join Genome Voyager’s community of researchers and academics. Visit http://voyager.completegenomics.com to signup.

More @  https://itunes.apple.com/us/app/genome-voyager/id637353801?mt=8

YeastGenome: iPhone/iPad

Use YeastGenome to quickly find fundamental information about Saccharomyces cerevisae genes and chromosomal features. Search gene names, gene descriptions or browse the database to find information about your favorite gene, as well as more detailed information such as Gene Ontology, mutant phenotype, and protein and genetic interaction data.
YeastGenome contains the latest from the Saccharomyces Genome Database (www.yeastgenome.org) in an on bound app database. As more detailed information is presented the app switches to web services access to SGD, and then for even more details provides complete information via hyperlinks to the appropriate SGD database pages.

Key features:

• Search using gene name or keywords
• Browse by feature type
• Save your favorite features
• Can be used in airplane mode
• Email information about features to collaborators

What's New in Version 1.8.1

• This update is required to provide continued functionality. Some of the data provided by this app accesses the SGD service using a method that is changing in May 2013. This version provides changes to allow access to continue. The on board database of yeast gene information has also been updated to March 2013.

More @  https://itunes.apple.com/us/app/yeastgenome/id520868597?mt=8

SNPdbe: iPhone/iPad

SNPdbe — SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; ‘human’ being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt.

More @  https://itunes.apple.com/us/app/snpdbe/id588289719?mt=8

SimGene: iPhone/iPad / Android

SimGene: for iPhone/iPad

SimGene is an iPhone/iPad/iPod touch application designed for molecular biologists, bioinformaticians and medical researchers. The application interfaces with Simbiot, Ensembl, NCBI, Gene Ontology, KEGG Pathways, PubMed, Genomic Variations and many other databases to retrieve up-to-date annotation information for over 30 species, based on gene symbol search. The application provides gene and transcript cross reference information for NCBI, Ensembl, RefSeq and UniProt. SimGene also contains an integrated genome browser with information on genes, transcripts, exons and SNPs.

More @  https://itunes.apple.com/us/app/simgene/id427772349?mt=8

SimGene: for Android

bioinformaticians and medical researchers. The application interfaces with Simbiot,Ensembl, NCBI, Gene Ontology, KEGG Pathways, PubMed, Genomic Variations andmany other databases to retrieve up-to-date annotation information for over 30species, based on gene symbol search. The application provides gene and transcriptcross reference information for NCBI, Ensembl, RefSeq and UniProt. SimGene alsocontains an integrated genome browser with information on genes, transcripts,exons and SNPs.

More @  https://play.google.com/store/apps/details?

TimeTree: iPhone/iPad

TimeTree is a public knowledge-base for information on the evolutionary timescale of life. This application allows easy exploration of the thousands of divergence times among organisms in the scientific literature. A tree-based (hierarchical) system is used to identify all published molecular time estimates bearing on the divergence of two chosen organisms, such as species, compute summary statistics, and present the results. Names of two taxa to be compared are entered in the search window and the results are presented on a set of self-explanatory tabs.

• TimeTree 3.0 was released September 27, 2011 with new data from 1209 studies including 25342 time nodes. We will be adding more data in the future as it comes in from researchers.
• TimeTree is jointly directed by Blair Hedges (Pennsylvania State University) and Sudhir Kumar (Arizona State University). This project has been supported, in part, by grants from the National Science Foundation, National Institutes of Health, NASA Astrobiology Institute, and Science Foundation of Arizona.

More @  https://itunes.apple.com/us/app/timetree/id372842500?mt=8

GeneGroove: iPhone/iPad

GeneGroove is the first application to create a music melody from DTC-Genomics data. If you own 23andMe (Mountain View, CA) personal genomic results, GeneGroove will create for you a unique melody intimately based on your 23andMe genome informations. The music in you.

• After uploading your 23andMe raw data onto your iPhone via iTunes, GeneGroove will analyze your genome informations and generate a unique identifier key. This key, called the GeNumber, will embed the uniqueness of your genome data while keeping your privacy safe, and will be used by GeneGroove to generate your music melody.
• The GeNumber doesn't contain anymore genomic information but it is based on your genome and it is unique, it is yours. It will be used in upcoming Portable Genomics applications to mix and remix music, manipulate sounds and share your art with your friends and family.

More @  https://itunes.apple.com/us/app/genegroove/id492247404?mt=8

In this report, we compare and evaluate several genome assembly software based on TSG technology. The experimentation has been performed on 4 reference genomes and the results evaluated with the QUAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 software use only long reads, while the 3 last software can merge long and short reads

Our present objectives is to identify and isolate the substances secreted by Spalax cells, resolve with which components they interact that are active only on cancer cells, in order to unravel the biological mechanisms and pathways that evolved in Spalax cell machinery and ultimately lead to the death of cancer-cells. The study could attest to be a breakthrough in cancer research, using the long lived, hypoxia- and cancer-tolerant Spalax as a significant biological resource for biomedical research that hopefully could open new horizons in treatment and prevention of cancer in humans.

Contact: The applications should be submitted, together with extended CV and bibliography, summary of past accomplishments, and contact information of 3 referees, to Prof of Research Aaron Avivi (aaron@research.haifa.ac.il) AND Dr. Imad Shams (imadshams@gmail.com). (http://bit.ly/1lywShk) aaron@research.haifa.ac.il

More at http://evolution.haifa.ac.il/index.php/29-people/personal-websites/77-personal-site-avivi

Address of the bookmark: http://genomearchitect.github.io/