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Downloads & Upgrades: Jan 11, 2009

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Ingenuity Systems has released IPA 7, the new version of its semantically oriented data-analysis platform. The company said the new software has “contextual data-analysis” functionality, a series of biological filters, and other tools that help users search and analyze experimental results. Among the new features, the company said, are new reporting tools and signaling pathways, more chemical content, and microRNA target information.


Open Discovery is a new Live Linux software package developed by V. Umashankar and Kala Bharath at the Department of BioInformatics at SRM University in Chennai, India, and available free to download here.

The platform includes bioinformatics tools for sequence and phylogenetic analysis, molecular dynamics, modeling, and docking.

Open Discovery developers said in a release that it is capable of booting from USB drives with changes that persist over reboot, so users can modify and store data on the USB drive.


SoftGenetics announced a new module to enable small RNA molecule analysis from short-read sequences. The module works in part with NextGene’s Condensation Tool, using reads from second-generation sequencing systems “to statistically polish the data and increase the base call accuracy up to 99.5 percent,” the company said in a statement.

The company said that this analysis module is compatible with all currently available second-generation sequencing systems and contains embedded applications for SNP and indel detection, transcriptome analysis, ChIP-Seq, DGE/SAGE, and de novo assembly.

SoftGenetics also announced an upgrade to its GeneMarker software that adds a module that helps wildlife researchers to identify kinships in natural populations.

The company said in a statement this tool is the first to integrate fragment analysis, short tandem repeats, microsatellite data, and kinship/paternity analysis.

Kinship analyses are tools used to track wildlife population movement and inbreeding and play a role in animal breeding, husbandry, and aquaculture.

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The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.