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Downloads & Upgrades: iReport; Velvet 1.2.02; UCSC Genome Browser; Labguru app; MetaFlux; Galaxy; CummeRbund; dbSNP 136


Ingenuity has released iReport, a reporting tool for statistical analysis and biological interpretation of gene expression data.

Users upload their data to Ingenuity's website and receive a customized report that identifies differentially expressed genes, along with diseases, functions, biological processes, and pathways that are most affected by the experiment. It also allows researchers to examine supporting literature evidence, take notes, share reports, and export images for publication.

Ingenuity's iReport works with microarray, RNA-seq, qPCR, and other -omics platforms and is priced at $495.

Velvet 1.2.02 is available here.

The release includes updates to the Columbus module, a completed binary file module, as well as changes to the SAM/BAM parser so that it now catches some minor exceptions in reads that were previously undetected

This week, the genome browser team at the University of California, Santa Cruz, said that the UCSC Genome Browser now includes a genome assembly for the tammar wallaby, Macropus eugenii.

Separately, the team also released a browser for the C. elegans genome.

BioData has released a free iPad app for users of Labguru, the company's research management web application for academic labs.

The app provides relevant information from experiments planned and tracked by the desktop version of Labguru so that users can execute protocols and collect data at the bench. It also lets users keep track of their experiments' progress and maintains a list of currently running experiments and associated countdown timers, among other features.

This week, SRI released MetaFlux, a software tool for constructing genome-scale models of metabolic networks.

According to its developers, MetaFlux combines flux balance analysis — a mathematical method to analyze metabolism — with pathway databases that contain information about interactions between proteins and small molecules. It generates models directly from pathway/genome databases, which can be constructed, queried, and visualized using SRI's Pathway Tools software. MetaFlux can also suggest additional reactions, nutrients, and secreted metabolites to complete a model.

The tool can be used to design drugs for disease-causing bacteria and to metabolically engineer bacteria to make chemicals and fuels.

It is available to academic users for free while commercial users are charged a fee.

The Galaxy development team has released an updated version of the platform.

Galaxy now includes support for TopHat 1.4.0, Cufflinks, Python, SAMTools, FASTQC, and Picard, among others. Additionally, Galaxy tool sheds now support sharing of workflows as well as tools, and it includes new Trackster features and performance upgrades among other updates.

CummeRbund 1.1.1 is available here.

The release includes several bug fixes and some updates including a method for retrieving of significant features from pairwise tests and an approach to constrain plot dimensions.

The National Center for Biotechnology Information has released dbSNP Build 136 for Arabidopsis, chimpanzee, macaque, nematode, orangutan, pig, rat, and zebrafish

The complete build summary for 136 is available here

The complete data for build 136 can be found here

The Scan

Gap in COVAX Doses

BBC News reports that COVAX is experiencing a vaccine shortfall, as the Serum Institute of India has paused exports.

Sanofi, GSK Report Promising Results

The Wall Street Journal reports that the candidate SARS-CoV-2 vaccine from Sanofi and GlaxoSmithKline has had encouraging early results.

Influence of Luck

The New York Times examines how the US avoided variant-fueled increases in COVID-19 cases.

PLOS Papers on Retina GWAS, Hantaan Virus, COVID-19 Phenome-Wide Association Study

In PLOS this week: genome-wide association study of retinal morphology, analysis of hantaan virus found in a mouse, and more.