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Downloads and Upgrades: Strand Life Sciences, SMRTAnalysis 2.2, Illumina's BaseSpace, and more

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Strand Life Sciences has released the StrandOmics software which provides tools for clinical interpretation and reporting of genomic variants. The system includes a proprietary knowledgebase that associates DNA variants with clinical phenotypes along with literature references.

The company has also launched Avadis-NGS Server Edition, which supports collaborative analytics and storage for next-generation sequencing data. The solution works on a variety of hardware platforms and can be configured to research and clinical labs' needs.

The company said that both solutions are part of the technology suite that will support projects at Strand Centers for Genomics and Personalized Medicine. Strand recently signed a deal with BioHealth Innovation to expand the service into the US.

Also this week, Strand announced that it has been awarded a patent for it's in silico method of assessing the hepatoxicity of new drug compounds. The company's method has been implemented in a rat-based virtual liver model, which is being used in the pharmaceutical industry. Strand has also released a human version of the virtual liver model.


Pacific Biosciences has released a new version of its SMRT Analysis software, which is used to analyze data from the company's Single Molecule, Real-Time DNA Sequencing platform.

SMRTAnalysis 2.2 includes enhanced functionality that supports full-length transcript/isoform sequencing, and human leukocyte antigen (HLA) haplotype phasing.


Illumina has added new applications specifically for oncology to the list of Core Apps for its BaseSpace infrastructure. The list includes TopHat and Cufflinks apps and an RNA Express app which support transcriptome data analysis; and a Tumor Normal app for somatic variant calling.

The company also said that it is developing applications for handling data from Illumina’s TruSight Tumor Sequencing panel and TruSeq Amplicon Cancer panel, as well as an exome version of the Tumor Normal App for analyzing variants in Nextera Rapid Capture Enrichment data.


Qiagen has launched the CLC Cancer Research Workbench, a bioinformatics software suite for analyzing, visualizing, and interpreting NGS data in cancer research. The system includes tools for identifying prognostic markers, sub-clonal somatic mutations, inherited traits, biomarkers for drug response, and for determining new oncogenes. It also lets users compare their results to information in public databases such as COSMIC, ClinVar as well as to information in their internal repositories.


Genedata has released Genedata Biologics 4.0, the latest version of its enterprise workflow support and data management solution for biologics research and development.

This version of the software includes tools for systematically designing, cloning, expressing, purifying, and testing bi- and multi-specific antibodies, among other features.


Cancer Genetics and Biodiscovery said this week that they have expanded the Nexus Copy Number Discovery platform to include tools for identifying predictive biomarkers of cancer outcomes.

The Nexus Copy Number software offers statistical tools for copy number and sequence variation analysis and visualization from microarrays and next generation sequencing.


SRI International has released BioCyc 18.0 with updates to the EcoCyc, and MetaCyc websites. The release includes downloadable data files and a downloadable Pathway Tools software/database bundle.


BioJava Legacy 1.8.5 is available here. Among other changes, the release includes bug fixes and updated dependency versions.


Reactome 48 is available here.

Topics with new or revised events include cellular response to stress, cell cycle, development, disease, gene expression, metabolism of proteins, and signal transduction.


The Scan

Booster Push

New data shows a decline in SARS-CoV-2 vaccine efficacy over time, which the New York Times says Pfizer is using to argue its case for a booster, even as the lower efficacy remains high.

With Help from Mr. Fluffington, PurrhD

Cats could make good study animals for genetic research, the University of Missouri's Leslie Lyons tells the Atlantic.

Man Charged With Threatening to Harm Fauci, Collins

The Hill reports that Thomas Patrick Connally, Jr., was charged with making threats against federal officials.

Nature Papers Present Approach to Find Natural Products, Method to ID Cancer Driver Mutations, More

In Nature this week: combination of cryogenic electron microscopy with genome mining helps uncover natural products, driver mutations in cancer, and more.