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Illumina, Dell EMC, QIAGEN, and More: News from November 2016



November 30, 2016| News, products, and partnerships from around the bio-IT community including news from Illumina, Dell EMC, QIAGEN, and more.

Honeywell announced the launch of a new business, Honeywell Research Chemicals, that will now include several brands and solvent and inorganic chemical products that were acquired from Sigma-Aldrich in December 2015. Honeywell Research Chemicals combines more than 200 years of industry expertise and experience with a level of customization that meets the fast-changing needs of advanced researchers, who require a reliable supply of critical reagents and solvents in the analytical testing, drug discovery and applied materials sectors. Press release

The InfiniBand Trade Association announced the public availability of the InfiniBand Architecture Specification Volume 2 Release 1.3.1 and a Virtualization Annex to the InfiniBand Architecture Specification Volume 1 Release 1.3. The new Volume 2 specification release expands interoperability and performance management functionality across the InfiniBand ecosystem for both high performance computing (HPC) and enterprise data center networks. The Virtualization Annex extends support for multiple virtualized endpoints within InfiniBand hardware. Both of these publications will be essential to expanding the performance and scalability of future data centers.

SoftGenetics announced the latest release of their NextGENe software for rapid analysis of next generation sequencing. Version 2.4.2 includes several additional unique applications which were developed in collaboration with user groups. A key application, the new Batch CNV Tool, developed in collaboration with Bekim Sadikovic, Molecular Diagnostics Division, London Health Sciences Centre, was developed to provide a robust NGS alternative to costly and time consuming MLPA analysis. Sadikovic’s laboratory has shown that the technique is 100% concordant with MLPA analysis, and is using the new capability to screen for copy number variations, dramatically reducing analysis time while significantly decreasing costs. Additionally, Tracey Lewis, ARUP laboratories, validated NextGENe software’s Case Control capability for use in clinical applications. (see poster presented at ASHG conference.) Developed in collaboration with New England BioSystems, NextGENe software’s new UMI (Unique Molecular Identifier) Tool effectively removes duplicate reads providing increased analysis accuracy by processing only a single read of a group sharing the same molecular identifier. The UMI Tool can be used to remove duplicate reads from most commercially available chemistries which include UMIs. However, the new NextGENe software version includes Templates for analysis of the NEBNext Direct Cancer HotSpot Panel and Direct BRCA Panel, which permits one‐click analysis of these chemistries. The NextGENe Viewer is now available in 64‐bit version. The 64‐bit version dramatically increases the Viewers speed and capacity, allowing faster refresh and scrolling when reviewing NGS data. Press release

Edison T. Liu of The Jackson Laboratory (JAX) has been named a Fellow of the American Association for the Advancement of Science (AAAS). Elected by his peers, Liu was recognized for his distinguished contributions to cancer biology, particularly the molecular analysis of breast cancer, and to the global advancement of human genomics. “I am honored to be elected as an AAAS Fellow, and to be included in this distinguished group of leaders dedicated to advancing science,” said Liu in a written statement. “This is a pivotal moment in medical science – one where the global community can work together as never before in improving human health.” Liu will be one of the plenary keynote speakers at the 2017 Bio-IT World Conference & Expo in Boston, May 23-25.

Published today in the open-access journal GigaScience, is an article that presents the genome sequence of Ginkgo biloba, the oldest extant tree species. The research was carried out by a team of scientists at BGI, Zheijiang University, and the Chinese Academy of Sciences, who tackled and analyzed an exceptionally large genome, totalling more than 10 billion DNA “letters”. Ginkgo is considered a “living fossil,” meaning its form and structure have changed very little in the 270 million years since it first came into existence. Given its longevity as a species and unique position in the evolutionary tree of life, the ginkgo genome will provide an extensive resource for studies concerning plant defenses against insects and pathogens, and research investigating early events in tree evolution and in evolution overall. Press release

Genocea presented new findings supporting the potential of ATLAS, the Company’s proprietary rapid antigen identification screening system, to identify clinically meaningful personalized neoantigens that could guide development of neoantigen vaccines. This study, conducted in collaboration with Memorial Sloan Kettering Cancer Center (MSK), analyzed neoantigens in one non-small cell lung cancer (NSCLC) patient successfully treated with pembrolizumab (KEYTRUDA). Genocea’s proprietary ATLAS technology comprehensively re-creates a patient’s actual T cell immune response to cancer ex vivo. This means ATLAS can potentially identify – not just predict – targets to which patient T cells are responding to kill a tumor. It may also allow ATLAS to distinguish between neoantigen candidates that stimulate productive T cell responses and those that are irrelevant or are associated with inhibitory responses. Press release

A diverse group of scientists have come together at the first sbv IMPROVER Datathon in order to share a large dataset among a diverse group of scientists, encourage them to expand computational analytics strategies, create customizable analytical tools, and demonstrate reproducibility in a complex, multi-endpoint toxicological study, and explore new ways of collaborating across disciplines and approaching large datasets.

The Datathon was a working session in which participants collaborated to turn datasets into scientific insight. Data was provided to teams who then developed research questions and preliminary findings. In advance of the event, the sbv IMPROVER team prepared protocols to explore the dataset, which enabled participants to access the data as well as to understand and design novel workflows which connect the data to analytics. Custom analytics modules (called “gadgets”) for data exploration, visualization and comparison, were built for the Datathon, enabled by an open connectivity platform technology called Garuda. This community-built open platform provides a unique framework to dynamically connect data with publicly available tools or participant developed algorithms.

Cycle Computing announced that Dell EMC will offer its software and services as an option with Dell EMC HPC Systems. Cycle Computing’s CycleCloud provides an optimized experience for users, maximizing the value of internal infrastructure and harnessing the emerging value of public cloud. It is a single tool and user interface that reduces time and complexity for admins and IT and is the first solution of its kind to solve the problems of zero queue and unlimited scale required with Big Compute, while addressing the entire workflow requirement of an enterprise including its data movement, orchestration, security, cost control, and back-up. “At Dell EMC, we are constantly looking for the best ways to serve our customers, and Cycle Computing is a valuable addition to our HPC offerings,” said Jim Ganthier, senior vice president, Validated Solutions, and HPC organization, Dell EMC. “With Cycle, Dell EMC will be the first to offer ‘crate to cloud’ for HPC in a matter of hours and will help our customers accelerate time to results while reducing cost and complexity.” Press release

Dotmatics announced Vortex for Bioinformatics, an easy-to-use program designed to allow all bioscientists to analyze and visualize their data to make better-informed decisions. Built into the long established and widely used Vortex program, Vortex for Bioinformatics can handle whole genome, antibody, protein and peptide data types and can scale to handle massive amounts of data including whole genomes on a laptop. With novel methods to relate biologic structure and sequence to activity, Vortex for Bioinformatics helps users understand assay results and drive forward the design of biologics with high performance analysis and visualization. Press release

Transcriptic announced the closing of a $13.4 million Series A-1 investment. The new funding was led by Data Collective, along with new investors Digital Science and WuXi AppTec. Existing investors, including AME Cloud Ventures, and others also contributed to the round. Transcriptic will utilize the new capital to drive the company’s product, team and expansion plans. Since the company launched in 2012, the company has executed experiments for individual researchers, institutions and large pharmaceutical businesses. The new funds will allow the company to grow its team to accommodate further growth, extend the capabilities of its innovative platform, and deliver on its vision of using its automated platform to dramatically increase research productivity. Press release

Seven Bridges and SolveBio announced the integration of their complementary platforms for genomic data analysis. The integration of Seven Bridges’ platform for cloud-based biomedical data analysis with SolveBio enables biotech and pharmaceutical researchers to seamlessly transition from the analysis of large NGS datasets to clinical analysis and interpretation, speeding the progress of their precision medicine initiatives. This integration is available in Seven Bridges’ Public Apps repository today, meaning any joint customer may immediately use this end-to-end workflow. “Through the integration of our respective platforms, Seven Bridges and SolveBio are helping to accelerate the pace of precision medicine research from ‘bench to bedside,’” said James Sietstra, President of Seven Bridges in a written statement. “Seven Bridges brings the scale of the cloud and national-scale genomic datasets, while SolveBio’s deep knowledge base and contextual intelligence tools help researchers take their work to the next level in discovering new treatments for patients.” Press release

Box announced its deepened commitment to support digital transformation at life sciences organizations across the globe, with new customers Daichi Sankyo and Shionogi, as well as new Independent Software Vendors (ISVs) and systems integrators such as CHITA, Prolifiq, USDM, and CTCLS. With Box for life sciences, organizations of all sizes can safeguard their most sensitive content, while securely collaborating between teams and with outside vendors and partners, protecting IP and maintaining the highest level of compliance. Blog

Illumina announced the launch of TruSight Tumor 170, a 170 gene next-generation sequencing solution to support the transformation of the tumor-profiling paradigm from a series of single-gene tests to a multi-analyte approach, providing a more thorough picture of a tumor’s genomic landscape. TruSight Tumor 170 offers an integrated DNA and RNA enrichment-based workflow, targeting cancer-related genetic aberrations, including small variants, gene amplifications, gene fusions, and splice variants. With optimized bioinformatics tools and automation options, laboratories can implement the assay on an in-house, research use only NextSeq instrument. Designed to support limited nucleic acid input from formalin-fixed, paraffin-embedded (FFPE) samples, TruSight Tumor 170 facilitates efficient evaluation of biomarkers. Press release

ZEISS introduces a new system for automated microscopy in life sciences research. ZEISS Celldiscoverer 7 combines the user-friendly automation features of a boxed microscope with the image quality and flexibility of a classic inverted research microscope. Scientists acquire better data in shorter times with 2D or 3D cell cultures, tissue sections or small model organisms. Press release

QIAGEN announced the validation of new and improved sequencing  chemistry for its GeneReader NGS System, the world’s first complete Sample to Insight solution, making the benefits of next-generation sequencing (NGS) accessible to any laboratory. QIAGEN published new, excellent performance data of the QIAGEN GeneReader NGS System using the new sequencing chemistry and QIAGEN’s GeneRead QIAact Actionable Insights Tumor Panel. Data generated from the GeneReader NGS System with the new chemistry showed 100% concordance with results of QIAGEN’s FDA approved therascreen KRAS RGQ PCR assay, the company’s CE-labeled therascreen RAS Extension Pyro Assay as well as with an alternative next-generation sequencing (NGS) sequencer from another vendor. In this study, 42 metastatic colorectal cancer FFPE samples were tested with previously confirmed RAS mutational status. Press release

FlyElephant announces the start of the cooperation with HPC HUB. HPC HUB is a developer of complex software and hardware solutions in high performance computing for resource intensive tasks for science and business, and provides cloud computing model services. The current HPC HUB`s products are based on complete and container systems virtualization, the resource management system OpenStack, the distributed storage Ceph and the clustered file system GFS2. Press release

Recursion Pharmaceuticals has adopted Bokeh––a Continuum Analytics open source visualization framework that operates on the Anaconda platform. Bokeh on Anaconda makes it easy for biologists to identify genetic disease markers and assess drug efficacy when visualizing cell data, allowing for faster time-to-value for pharmaceutical companies. By combining interactive, layered visualizations in Bokeh on Anaconda to show both healthy and diseased cells along with relevant data, biologists can experiment with thousands of potential drug remedies and immediately understand the effectiveness of the drug to remediate the genetic disease. Biologists realize faster insights, speeding up time-to-market for potential drug treatments. Press release

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