Amazon Genomics CLI is Open Source, UK Biobank's Research Analysis Platform Live, More – Bio-IT World

October 7, 2021 | New leadership at JAX, Illumina expands into Latin America, PacBio partners with The European Reference Genome Atlas, UK Biobank’s Research Analysis Platform is now live, and BC Platforms seeks to build the largest integrated clinical and genomics data biobank in Africa. Plus: new products from MemVerge, Quantum, Pure Storage, Sensyne Health, and more.

Paradigm4 has launched flexFS, its innovative, elastic cloud file system for flexible and more resource efficient data storage and scalable computing. flexFS increases data agility and reduces the costs of working with large multi-omics and multiple imaging modalities data sets. It delivers optimal performance for data staging, data migration, and compute-intensive analytics and machine learning. flexFS serves up industry-leading aggregate throughput, which can materially reduce compute costs by lowering “time-to-compute”. flexFS is easy-to-use, secure, and cloud portable. As a POSIX-compatible file system, flexFS automatically interoperates with existing software, tools, and processes. Each volume can be shared by thousands of hosts concurrently. The aggregate throughput of flexFS increases as cluster size increases, where other solutions’ throughput may remain constant. A usage-based cost structure makes flexFS less expensive and more efficient to deploy than solutions where the amount of storage must be provisioned upfront for the maximum usage mark. flexFS also has always-on encryption during transit and at rest, as well as an optional end-to-end encryption layer, ensuring that metadata and file block data are always secure. Press release.
BICO Group AB has entered into an agreement with the shareholders of QInstruments GmbH to acquire all outstanding shares, on a cash- and debt-free basis, and under the assumption that the working capital at closing equals the normalized working capital, to a purchase price of 61.25 million euro, of which 3 million euro will be paid upon achievement of predetermined revenue and EBITDA milestones. Approximately 13% of the purchase price will be paid in newly issued shares of series B in BICO (the “Consideration Shares”), and the remaining part will be paid in cash. QInstruments’ equipment enables precision temperature control and mixing of molecular samples and are highly modular and customizable for easy integration into existing devices and workflows. The company’s products are used by Pfizer, Roche, Illumina, Bayer, Merck, Novartis, and others to support COVID-19 diagnostics, RNA/DNA extraction workflows, high-throughput drug screening, and key genomics and life science applications. QInstruments will join BICO’s Bioautomation business area and strengthen the company’s ability to improve workflows for other BICO subsidiaries as well as those of our customers. Press release.

The Jackson Laboratory, an independent, nonprofit biomedical research institution, today announced the appointment of Lon Cardon, Ph.D., FMedSci, a pioneer in human genetics and drug discovery, as its next president and chief executive officer. Effective on November 29, Cardon will succeed current President and CEO Edison Liu M.D. who will step down after a decade of leadership. Liu will continue to serve as a JAX professor studying the functional genomics of cancer with a focus on breast cancer. Press release.

Quantum Corporation has announced two innovations aimed at organizations generating, storing, and managing huge amounts of data. Quantum is introducing ActiveScale Cold Storage, a new class of storage that combines advanced object store software with hyperscale tape technology to provide secure, highly durable, and extremely low-cost storage for archiving cold data. In addition, Quantum is offering a new line of fully managed Object Storage Services to bring the cloud experience to wherever data lives and accelerate digital transformation. These new offerings reduce cold storage costs by 80%, enable organizations to maintain control of their most valuable data assets, and unlock value in cold data over years and decades without expensive access fees. The world has entered a new era of data, as the quantity of unstructured data generated globally continues to grow exponentially. The gap between data growth and storage budgets is widening, and it is estimated that 60% of the data generated will be “cold” – inactive data that must be stored, protected, and remain accessible for years or decades because of compliance requirements and the immense value it contains. To address this pressing challenge, Quantum is introducing ActiveScale Cold Storage – a new class of object storage designed for cold data, built on hyperscale architectures, and offered as-a-service from Quantum. ActiveScale Cold Storage combines object storage software with two-dimensional erasure coding and Quantum Scalar tape storage to create a new class of storage that is secure, highly durable, and extremely low-cost. Press release
OpGen has received 510(k) clearance by the U.S. Food and Drug Administration (FDA) to market the Acuitas AMR Gene Panel, and is finalizing preparations for its swift commercial launch in the U.S. The Acuitas AMR Gene Panel detects 28 genetic antimicrobial resistance (AMR) markers in isolated bacterial colonies from 26 different pathogens. The company believes the panel provides clinicians with a valuable diagnostic tool that informs about potential antimicrobial resistance patterns early and supports appropriate antibiotic treatment decisions in this indication. The Acuitas AMR Gene Panel expands the diagnostic capability of clinicians to rapidly and simultaneously test for select drugs in 9 classes of antibiotics, including aminoglycosides, carbapenems, cephalosporins, fluoroquinolones, penicillins, polymyxins, sulfonamides, trimethoprim, and vancomycin, to aid in the identification of potentially antimicrobial-resistant organisms that might otherwise escape detection and hence can prevent prolonged inappropriate treatment of patients. Press release
Illumina announced the creation of Illumina Colombia S.A.S. and Illumina México Productos de Biotecnología marking our commitment to expand genomics in Latin America and increase the level of support for our local customers and partners. The entities will help advance Illumina’s clinical business in Colombia and México, with a focus on key healthcare systems and hospitals. In addition, the entities will support local and nearby Illumina channel partners across Latin America, including countries in the Caribbean, Central America and South America. The entities will ensure Illumina’s customers are able to keep their instruments functional and receive the very best training on the latest products. Looking ahead, these new entities will work closer with Illumina customers and channel partners to execute key local partnership, not only in those countries, but throughout Latin America. Press release.

UPM Biomedicals is pleased to announce that it has entered into an agreement with PerkinElmer Health Sciences. PerkinElmer will act as a distributor of the UPM GrowDex and GrowDase range of products. This new collaboration will offer researchers a complete solution for high throughput screening (HTS) of 3D cell cultures in early drug discovery, bringing together PerkinElmer’s cell imaging and automation solutions and knowledge with UPM’s animal-free 3D reagent offerings and expertise. UPM’s nanofibrillar cellulose GrowDex hydrogels create an environment that resembles the conditions inside the human body, and can be effectively handled at room temperature, making them well suited for scale up and automation without compromising performance. Combined with GrowDase, which enables effective one-step recovery of cells for downstream processing applications, this provides an ideal solution for high throughput 3D cell culture applications, offering more reproducible and reliable results to help predict how drugs will work in vivo. Press release.

Pure Storage has unveiled two new solutions to bring infrastructure operations and applications closer together: Pure Fusion, a new autonomous storage-as-code platform, and Portworx Data Services, a Database-as-a-Service platform for Kubernetes. Pure Fusion is an industry-first self-service, autonomous storage platform that marries the best of enterprise storage with the agility and scalability of the cloud. Pure Fusion delivers a SaaS management plane that pools storage arrays into availability zones and automates previously complex tasks such as workload placement, workload mobility, and fleet rebalancing. It also includes a new API framework that enables both storage teams and end users to operate in an on-demand, storage-as-code model that integrates with the developer tools they use today. Press release. Portworx Data Services is the industry’s first Database-as-a-Service (DBaaS) Platform for Kubernetes. Portworx Data Services delivers automated DBaaS management. With the click of a button, DevOps engineers can deploy a managed, production-grade data service on Kubernetes from the industry’s broadest catalog of options for SQL, NoSQL, search, streaming, and more, with fully automated Day-2 operations. Press release.

The Amazon Genomics CLI is an open source project and is now generally available. Researchers can use it with publicly available workflows as a starting point and develop analyses on top of these. Amazon Genomics CLI simplifies and automates the deployment of cloud infrastructure, providing users with an easy-to-use command line interface to quickly setup and run genomics workflows on AWS. By removing the heavy lifting from setting up and running genomics workflows in the cloud, software developers and researchers can automatically provision, configure and scale cloud resources to enable faster and more cost-effective population-level genetics studies, drug discovery cycles, and more. Amazon Genomics CLI lets users run workflows on an optimized cloud infrastructure which includes improvements to genomics workflow engines to make them integrate better with AWS, removing the burden to manually modify open-source tools and tune them to run efficiently at scale. These tools work seamlessly across Amazon Elastic Container Service (Amazon ECS), Amazon DynamoDB, Amazon Elastic File System (Amazon EFS), and Amazon Simple Storage Service (Amazon S3), helping users scale compute and storage and at the same time optimize costs using features like EC2 Spot Instances. Amazon Blog.

Pacific Biosciences has announced a partnership with The European Reference Genome Atlas (ERGA) consortium to support its efforts in understanding and protecting biodiversity by generating high-quality reference genomes for European plant and animal species. PacBio’s HiFi Sequencing technology allows scientists to take the first important step by reliably generating high-quality genetic maps of each plant and animal species. Studies have shown that reference-quality genomes provide the most complete insight into the genetic basis that forms each species. ERGA seeks to increase coordination across all countries of the European continent, in tandem with international partners, to generate reference-quality, complete and error-free genome assemblies for at least 200,000 plant and animal species across Europe. Press release.

NervGen Pharma Corp., a clinical stage biotech company dedicated to developing innovative solutions for the treatment of nervous system damage, has announced a partnership with Imeka Solutions, currently the only neuroimaging company that combines artificial intelligence and diffusion imaging to obtain high resolution images of white matter in the brain. NervGen intends to utilize Imeka’s imaging technology as a sensitive pharmacodynamic biomarker for its lead compound, NVG-291, in its Phase 1b/2 clinical trials. Additionally, the companies are submitting non-dilutive grants that support combining their technologies in preclinical and clinical studies for various conditions related to central nervous system damage. Press release
UK Biobank, a large-scale biomedical database and research resource, has launched a uniquely powerful and innovative research platform that allows approved researchers to access and analyze the entire UK Biobank database securely, in the cloud, from anywhere in the world. It is designed to accommodate the vast and increasing scale of genomics and healthcare data pertaining to UK Biobank’s 500,000 participants. This new Research Analysis Platform (RAP), enabled by DNAnexus and powered by Amazon Web Services (AWS), exponentially increases the scale and accessibility of the world’s largest and most comprehensive biomedical database for researchers around the world to advance understanding of human disease. While the growth of the UK Biobank resource has created an unparalleled opportunity for medical research there have been some limitations with collating, storing, and accessing data at this scale. The new cloud-based platform removes these barriers and will accelerate both the speed and scale of health-related research. Press release.

ACD/Labs has announced its annual updates across its Spectrus and Percepta platform applications. The v2021 release delivers new features and enhancements for ACD/Labs software users while aligning with current scientific IT trends. Key highlights include broader integration with laboratory hardware and software for a better-integrated lab, expanded support for processed data from chromatography data systems (CDSs), ability to integrate data from process chemistry sensors and probes for improved data capture enabling data-driven decisions, democratized knowledge & accessible data with Spectrus, support for a broader range of data types and structures (biologics, antibody-drug conjugates, and other complex molecules), improved search capabilities for numerical data and chemical/biochemical structures, faster data access across geographic locations, expansion of functionality in browser-based applications, improved tools for systems admins, and soon-to-be-released Spectrus JS—the first browser-based application for processing and analysis of NMR data. Press release
MemVerge has announced its Memory Machine Big Memory virtualization software has been selected by Penn State Huck Institutes of the Life Sciences to speed the genomic analytic processing for plant DNA research to develop more sustainable plant products. Using MemVerge Memory Machine memory virtualization software, Penn State has been able to accelerate discovery for its plant DNA research. Memory Machine software provided scientists at Penn State with transparent access to virtualized DRAM and PMem memory and ZeroIO Snapshot technology. The in-memory snapshot technology allows researchers to roll back workloads quickly to specific points in time for adaptive analyses and ensure resilience with lightning-fast crash recovery. This allows new genomic testing to continue without downtime. Press release
Genomenon, an AI-driven genomics company, today announced a collaboration with Alexion, AstraZeneca Rare Disease that will make critical information needed for the diagnosis and treatment for a set of rare diseases more readily accessible. The goal of this collaboration is to empower genetic testing labs with the data they need to diagnose patients suffering from rare diseases. The collaboration with Alexion was born out of Genomenon’s mission to ensure that no rare disease patient goes undiagnosed and untreated. Working with Alexion, Genomenon is using its AI-driven genomic technology to produce a complete “Genomic Landscape” for an initial group of rare diseases that includes Wilson disease, Complement-Mediated Thrombotic Microangiopathy (CM-TMA), Lysosomal Acid Lipase Deficiency (LAL-D), and Hypophosphatasia (HPP). The expertly curated genetic datasets for these rare conditions, along with information on available therapies or clinical trials, will then be made available to doctors, researchers, and clinicians through Genomenon’s Mastermind Genomic Search Engine. Press release
Deepcell, a life science company pioneering AI-powered cell classification and isolation for cell biology and translational research, has entered into an agreement with Stanford University to provide data to Tabula Sapiens, part of a breakthrough scientific program supported by the Chan Zuckerberg Initiative’s single-cell biology program and the Chan Zuckerberg Biohub. The Tabula Sapiens program is aimed at creating a benchmark human cell atlas of 2 million cells collected from 25 organs of eight people. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects and allows detailed analysis and comparison of cell types that are shared between tissues. This work is aimed at creating a detailed portrait of cell types as well as a view of their distribution and variation across tissues and within the endothelial, epithelial, stromal, and immune compartments. Through this initiative, scientists will use Deepcell’s platform to generate single-cell morphology data that will be shared publicly with the research community via Tabula Sapiens. As a result of this collaboration, the Deepcell platform will expand the company’s Deep Cell Atlas, setting the basis for new discoveries in cell biology through AI-powered cell morphology. Press release
SAS and the University of North Carolina at Chapel Hill are teaming up to transform the drug development process to prevent infectious disease threats from turning into a pandemic like COVID-19. The partnership is focused on the work of the University’s Rapidly Emerging Antiviral Drug Development Initiative (READDI) which is developing broad spectrum antiviral drugs to have on the shelf to prevent future pandemics. To advance their work, SAS research and development teams are applying advanced machine learning techniques to integrate multiple biological data sets from the deep lung environment of severely ill COVID-19 patients. These analyses will be used by Carolina researchers to identify targets for new COVID-19 antiviral drugs. While the initial focus of the joint team is on addressing new treatments for COVID-19, READDI and SAS will continue to work together to meaningfully accelerate drug discovery for other antiviral drugs. Press release., the life science industry’s leading R&D marketplace, has completed the acquisition of InsideScientific, an online educational platform for life science researchers. The acquisition enables to offer a full suite of science-based content and event production services—such as webinars, virtual events, podcasts, and training programs—to its existing global network of researchers and service providers. operates online marketplaces for 24 of the world’s top 30 pharmaceutical companies, over 80 biotech companies and the US National Institutes of Health (NIH). Press release
COMPASS Pathways, a mental health care company dedicated to accelerating patient access to evidence-based innovation in mental health, has acquired an intellectual property (IP) portfolio including patent applications covering a variety of psychedelic and empathogenic substances. The IP was developed together with inventor Matthias Grill PhD, founder and CEO of MiHKAL GmbH in Basel, Switzerland, who will be working with COMPASS on an exclusive research project to develop new product candidates. The substances covered in the IP portfolio include a variety of psychedelic and empathogenic compounds, some of which are prodrugs—pharmacologically inactive compounds which are metabolized inside the body to produce an active drug. The new substances include novel derivatives of known compounds, increasing the confidence in therapeutic effects and safety profile while offering optimized characteristics. Press release
Cresset Discovery Services is collaborating with the University of Newcastle, Australia, to focus on drug reprofiling against oncology targets. The work will build on research led by award-winning molecular biologist, Associate Professor Nikola Bowden. Nikola is co-Director of the Centre for Drug Repurposing and Medicines Research and leads the DNA repair group. The overall aim of her research is to deliver personalized diagnosis and treatment to cancer patients, with a focus on DNA repair and drug repurposing in melanoma and ovarian cancer. Repurposing existing drugs offers a promising solution to cancer patients in need of more immediate treatment. Having prior knowledge of a drug’s safety, dosing and side effects can significantly shorten research and development timelines. Press release.

Sensyne Health has launched SENSIGHT, an AI enabled global data analytics platform for the healthcare and life sciences sectors. SENSIGHT is built on a rapidly growing deep and broad set of anonymized and de-identified patient data derived from the research partnerships Sensyne has entered into with NHS Trusts and US health systems that currently covers 22.5 million patients across a range of disease areas. The power and affordability of the SENSIGHT platform represents a disruptive shift in how the life science and healthcare communities will access and leverage clinical data insights, collaborate with their colleagues, and advance the state of care and discovery. The platform provides clinicians, research academics and life science professionals with an instant AI research capability to analyze health insights across a curated common data environment, underpinned and protected by a rigorous information governance and security framework. No direct patient data is, or ever will be, shared on SENSIGHT. The platform instead rapidly interrogates Sensyne’s deep diverse datasets and delivers intelligent analytics and data-driven insights, not the data itself. Subscribers will be screened to ensure legitimate interest, with only those in accredited companies and organizations being accepted. Researchers can communicate and collaborate with each other on the platform, creating a virtual scientific research network that connects professionals across the healthcare and life sciences industries creating a community with common interests in particular research fields or areas of unmet medical need. Press release
IBM Research and Arctoris are investigating the application of AI and automation to accelerate closed loop molecule discovery. IBM Research has developed RXN for Chemistry, an online platform leveraging state-of-the-art Natural Language Processing (NLP) architectures to automate synthetic chemistry. Representing chemical reactions via SMILES (Simplified Molecular Input Line Entry System), the system performs highly accurate reaction predictions using its powerful AI. Optimized synthetic routes are then used as input for RoboRXN, an automated platform for molecule synthesis. Arctoris has developed Ulysses, an end-to-end automated platform for drug discovery research. The platform ensures accuracy, precision, and reproducibility by leveraging robotic experiment execution and digital data capture technologies across cell and molecular biology and biochemistry/biophysics. Experiments conducted with Ulysses generate more than 100 times more datapoints per assay compared to industry standard, leading to deeper insights and accelerated progress compared to manual methods. The two platforms are now being combined for the first time in a research collaboration that will see new small molecule inhibitors for undisclosed targets being designed, made, tested, and analyzed (DMTA) in an autonomous, closed loop approach. Concretely, IBM Research will design and synthesize novel chemical matter (Design, Make), to be profiled and evaluated by Arctoris (Test, Analyze), with the resulting data informing the subsequent iteration of the DMTA cycle. Press release
BC Platforms has announced a new collaboration with the African Institute of Everyone Genome (AiEG), a South African genomic company focusing on building the largest integrated clinical and genomics data biobank in the African continent. As part of the collaboration, BCP’s platform will enable RWD research involving 10M+ consenting patient genomes from all 54 African countries, to be collected by AiEG over a period of 10-15 years. The main goal of the research will be to enable drug development and clinical research for patients in sub-Saharan Africa. As part of the Strategic Data Partnership with AiEG, BC Platforms is providing a cloud-based, scalable Discovery and Research Platform, made available to AiEG and commercial researchers via Microsoft Azure. AiEG has built a large footprint of public and private healthcare entities and experienced research clinicians who consent patients for sharing clinical and genomic data for research. The first pilot cohort of patients are anticipated to be engaged in October 2021. BCP’s role will enable research collaborations with drug developers, data management, and preparation of analysis-ready datasets and leading with global best practices in patient data privacy and security. Press release
Agenus, an immuno-oncology company, has launched SaponiQx, a subsidiary of Agenus, dedicated to driving innovation in novel adjuvant discovery and vaccine design, and its partnership with Ginkgo Bioworks, Inc., the leading horizontal platform for cell programming. Ginkgo, which recently announced a business combination with Soaring Eagle Acquisition Corp., is enabling customers across industries to improve products and manufacturing processes, and increase efficiency and sustainability, by making biology easier to engineer. SaponiQx is building an innovative adjuvant platform to deliver both sustainable manufacturing approaches and a secure supply of known adjuvants, as well as discover novel adjuvants and develop new, more effective vaccines utilizing optimized antigen-adjuvant pairings. Ginkgo’s experience in metabolic engineering, enzymatic diversification, and process optimization can be applied to discover novel adjuvants and improve current manufacturing processes that can then be applied toward developing better-integrated vaccines. Press release
Thermo Fisher Scientific’s new TSQ Plus triple quadrupole mass spectrometer (MS) portfolio increases workflow throughput through superior data acquisition and polarity switching speeds. The improved low-mass product ion transmission efficiency enhances sensitivity for key target applications. The new portfolio, which consists of the TSQ Altis Plus, TSQ Quantis Plus and TSQ Fortis Plus MS, can be used across a range of applications, from targeted quantitation to cutting-edge research. Intuitive mass calibration routines and method optimization, in combination with market-leading chromatography and data processing software solutions, offers improved ease of use to address future analytical challenges. Press release
Selecta Biosciences, a biotechnology company leveraging its clinically validated ImmTOR platform to develop tolerogenic therapies that selectively mitigate unwanted immune responses, and Cyrus Biotechnology, a leading protein design company, have announced a protein engineering collaboration combining Selecta’s ImmTOR platform with Cyrus’ ability to radically redesign protein therapeutics. The lead program in the collaboration is a proprietary interleukin-2 (IL-2) protein agonist designed to selectively promote expansion of regulatory T cells (Treg) for the treatment of patients with autoimmune diseases and other deleterious immune conditions. Novel IL-2 approaches and technologies are driving innovation in the therapeutic development space. The IL-2 pathway influences critical aspects of both immune stimulation and immune regulation, through the development and expansion of regulatory T cells (Treg). Press release
Illumina and Merck have announced a partnership to develop and commercialize tests that identify genetic mutations used in the assessment of homologous recombination deficiency (HRD). Patients whose tumors are HRD-positive may be eligible for targeted treatment by a class of precision medicines called PARP inhibitors. The HRD tests will leverage Illumina’s TruSight Oncology 500 (TSO 500) content, enabling the most comprehensive genomic profiling assays in a single workflow. This strategic partnership builds on an initial study conducted with Merck and leverages Illumina’s relationship with Myriad Genetics to expand international access to the proprietary technology in Myriad’s FDA approved myChoice CDx companion diagnostic test. Illumina will develop a new HRD CDx test for the EU and the UK to aid in the identification of ovarian cancer patients with positive HRD status who are eligible for treatment with LYNPARZA (olaparib), a first-in-class PARP inhibitor, jointly developed and commercialized by Merck and AstraZeneca. In addition, Illumina will develop and commercialize a research use only (RUO) HRD assay that will be add-on content for the TSO 500 RUO panel. Illumina plans to launch this product globally, excluding the United States and Japan. Press release.

FUJIFILM Recording Media U.S.A., Inc. is pleased to announce the launch and availability of its FUJIFILM LTO Ultrium 9 Data Cartridge (LTO-9). Fujifilm’s LTO-9 complies with the ninth generation LTO Ultrium standards for magnetic tape storage media, marking a new standard of performance for backing up and archiving large volumes of data. Fujifilm’s LTO-9 uses proprietary technology to offer up to 45TB of storage capacity (18TB for non-compressed data), a 50% increase from the previous generation of LTO tape. Magnetic tape is increasingly recognized as an ideal storage media for long term archival of high-volume data, safely at low-cost. In addition, tape has a significantly lower environmental impact as there is no need to have it constantly powered-on during data storage, thereby reducing CO2 emissions generated during its lifecycle by 95% when compared to hard disk drives (HDDs). Press release.
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