A unified encyclopedia of human functional DNA elements

Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the target cell type. Here we present annotations of 164 human cell types using 1615 data sets. To produce these annotations, we automated the label interpretation step to produce a fully automated annotation strategy. Using these annotations, we developed a measure of the importance of each genomic position called the “conservation-associated activity score.” We further combined all annotations into a single, cell type-agnostic encyclopedia that catalogs all human regulatory elements.

Spotlight

LeanTaaS

LeanTaaS is a software company that uses lean principles, machine learning, and predictive analytics to digitally transform core operational processes in healthcare. This transformation increases patient access, decreases wait times, improves staff satisfaction, reduces healthcare delivery costs, and improves operational performance. LeanTaaS's cloud-based iQueue platform mathematically matches the demand for expensive, constrained healthcare resources – operating rooms, infusion chairs, imaging assets, inpatient beds, etc.

OTHER ARTICLES
MedTech

Biotech in 2022

Article | July 11, 2022

The robust global channel of more than, 800 gene and cell curatives presently in trials will produce clinical readouts in 2022, revealing what lies ahead for advanced curatives. The impact will be felt in 2022, no matter how you slice it. Eventually, how well industry and non-supervisory bodies unite to produce new frameworks for advanced therapies will shape the year 2022 and further. Pacific Northwest talent will continue to contribute to the advancement of gene and cell curatives in both the short and long term, thanks to its deep pool of ground-breaking scientific developers, entrepreneurial directorial leadership, largely skilled translational scientists, and endured bio manufacturing technicians. We may see continued on-life science fund withdrawal from biotech in 2021, but this can be anticipated as a strong comeback in 2022 by biotech industry, backed by deep-pocketed life science investors who are committed to this sector. A similar investment, combined with pharma's cash-heavy coffers, can result in increased junction and acquisition activity, which will be a challenge for some but an occasion for others. Over the last five years, investment interest in Seattle and the Pacific Northwest has grown exponentially, from Vancouver, British Columbia, to Oregon. The region's explosive portfolio of new biotech companies, innovated out of academic centres, demonstrates the region's growing recognition of scientific invention. This created a belief that continued, especially because Seattle's start-ups and biotech enterprises are delivering on their pledge of clinical and patient impact. Talent and staffing will continue to be difficult to find. It's a CEO's market, but many of these funds' return, and are not rising in proportion to the exorbitant prices they're paying to enter deals. This schism has become particularly pronounced in 2021. Hence, everyone in biotech is concerned about reclamation and retention.

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Medical

Next-Gen Genetics Cancer Therapies Creating Investment Prospects

Article | August 16, 2022

Genetic therapeutics such as genetic engineering and gene therapy are increasingly emerging as one of the most influential and transformed biotechnological solutions around the globe in recent times. These genetic solutions are being assessed across various medical domains, including cancer treatment, neurology, oncology, and ophthalmology. Citing the trend, the genetics industry is estimated to experience a tsunami of approvals, with over 1,000 cell and gene therapy clinical trials currently underway and over 900 companies worldwide focusing on these cutting-edge therapies. Growing Cancer Encourages Advancements in Genetic Technologies With the surging cases of cancers such as leukemias, carcinomas, lymphomas, and others, patients worldwide are increasing their spending on adopting novel therapeutic solutions for non-recurring treatment of the disease, such as gene therapy, genetic engineering, T-cell therapy, and gene editing. As per a study by the Fight Cancer Organization, spending on the treatment of cancer increased to $200.7 billion, and the amount is anticipated to exceed $245 billion by the end of 2030. Growing revenue prospects are encouraging biotechnology and biopharmaceutical companies to develop novel genetic solutions for cancer treatment. For instance, Bristol-Myers Squibb K.K., a Japanese pharmaceutical company, introduced a B-cell maturation antigen (BCMA)-directed chimeric antigen receptor (CAR) T cell immunotherapy, Abecma, for the treatment of relapsed or refractory (R/R) multiple myeloma in 2022. Amid a New Market: Genetics Will Attract Massive Investments Despite several developments and technological advancements, genetics is still considered to be in a nascent stage, providing significant prospects for growth to the companies that are already operating in the domain. Genetics solutions such as gene therapies, gene editing, and T-cell immunotherapy are emerging as highly active treatments across various medical fields, resulting in increasing research and development activities across the domain, drawing significant attention from investors. Given the potential of genetic treatments and the focus on finding new ways to treat cancer and other related diseases, it's easy to understand why companies are investing in the domain. For instance, Pfizer has recently announced an investment of around $800 million to construct development facilities supporting gene therapy manufacturing from initial preclinical research through final commercial-scale production. Due to these advancements, cell and gene therapies are forecast to grow from $4 billion annually to more than $45 billion, exhibiting growth at a 63% CAGR. The Future of Genetics Though there is a significant rise in advancement in genetic technologies and developments, the number of approved genetic treatments remains extremely small. However, with gene transfer and CRISPR solutions emerging as new modalities for cancer treatment, the start-up companies will attract a growing amount and proportion of private and public investments. This is expected present a tremendous opportunity for biopharma and biotechnology investors to help fund and benefit from the medical industry's shift from traditional treatments to cutting-edge genetic therapeutics in the coming years.

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Research

Advancement in Genomics Accelerating its Penetration into Precision Health

Article | July 11, 2022

Genomics is an interdisciplinary field of biology emphasizing the structure, editing, evolution, function, and mapping of genomes. It is creating deeper inroads across the precision health domain with the increasing introduction of advanced technologies such as quantum simulation, next-generation sequencing (NGS), and precise genome manipulation. As precision health focuses on providing the proper intervention to the right patient at the right time, genomics increasingly finds applications in human and pathogen genome sequencing in clinical and research spaces. Rising Hereditary Diseases Burden Paving the Way for Genomics in Precision Health In the last few years, a significant surge in the prevalence of diseases and ailments such as diabetes, obesity, baldness, and others has been witnessed across the globe. A history of family members with chronic diseases, such as cancer, diabetes, high blood pressure, hearing issues, and heart disease, can sometimes continue into the next generation. Hence, the study of genes is extensively being conducted for predicting health risks and early treatment of these diseases. It also finds use in CRISPR-based diagnostics and the preparation of precision medication for the individual. In addition, ongoing advancements in genomics are making it possible to identify different genetic traits that persuade people to more widespread diseases and health problems. The Emergence of Genomics Improves Disease Understanding Genomics refers to the study of the complete genetic makeup of a cell or organism. Increasing scientific research in the area substantially contributes to increasing knowledge about the human genome and assists in improving the ability to understand disease etiology, risk, diagnosis, treatment, and prevention. On account of these improvements, innovative genomic technologies and tools are being developed to enable better precision health not only for the individual but for various regional populations as well. The Way Forward With growing preference for personalized medicine and an increasing need for more accurate pathogen detection and diagnostics, genomics is gaining huge popularity across the precision health domain. Also, increasing research activities for developing novel high-precision therapeutics and rising importance of gene study in the prevention, diagnosis, and management of infectious and genetic diseases will further pave the way for genomics in the forthcoming years.

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MedTech

Immunology: A New Frontier in Medical Science

Article | July 16, 2022

Introduction Recent developments in the bioengineering of monoclonal antibodies (mAbs) have revolutionized the treatment of numerous rheumatic and immunological disorders. Currently, several immunological disorders are successfully being targeted and treated using innovative medical techniques such as immunotherapy. Leading companies are increasingly investing in research activities to expand the usage and application of immunology for the treatment of various infectious diseases, including multiple sclerosis, inflammatory bowel disorders, lupus, and psoriasis, leading companies are increasingly investing in research activities. Today, the efforts of researchers in immunology, with a long history of study and research, have borne fruit, as bioengineered mAbs are now being employed in clinical practices. Accelerating Investments: Paving the Way for Immunology The increasing prevalence of infectious diseases, cancer, and immune-mediated inflammatory disorders (IMIDs) is raising the need for more precise classification and an in-depth understanding of the pathology underlying these ailments. Numerous leaders in the biotechnology domain are thus focusing on undertaking numerous strategies, such as new facility launches and collaborations, to address the need by finding deeper inroads into immunology and its use in disease treatments. For instance, in 2022, the University of Texas MD Anderson Cancer Center announced the launch of a visionary research and innovation hub, the James P. Allison Institute, to find new roads in immunotherapy, develop new treatments, and foster groundbreaking science. These developments will result in better diagnosis through the use of selective biomarkers, and early detection of fatal diseases and their treatment, which will prevent complications from happening. Also, the identification of high-risk populations through a deeper understanding of genetic and environmental factors can assist in the prevention of disease through immunotherapy. The Way Forward Immunology has led to the development of biotechnology, making it possible to develop novel drugs and vaccines, as well as diagnostic tests, that can be used to prevent, diagnose, and treat a wide range of autoimmune, infectious, and cancerous diseases. With the rapid advancement in technology and the integration of artificial intelligence, immunology is finding its way into an array of domains and industries, encompassing several research areas including medicine, pharmaceuticals, agriculture, and space. Today, not only researchers but also leading biotech and pharmaceutical companies have recognized that conventional therapies with pharmaceutical and chemical products are being replaced by products derived from immunology. This is because they work well for health problems, are environmentally friendly, and are also emerging as a wealth-generating business in the medical field.

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Spotlight

LeanTaaS

LeanTaaS is a software company that uses lean principles, machine learning, and predictive analytics to digitally transform core operational processes in healthcare. This transformation increases patient access, decreases wait times, improves staff satisfaction, reduces healthcare delivery costs, and improves operational performance. LeanTaaS's cloud-based iQueue platform mathematically matches the demand for expensive, constrained healthcare resources – operating rooms, infusion chairs, imaging assets, inpatient beds, etc.

Related News

AI, Diagnostics

Genomic Vision Announces launch of FiberSmart

Genomic Vision | March 08, 2023

On March 7, 2023, Genomic Vision, a leading biotech company that develops products and services for the analysis and control of genome changes, launched FiberSmart®, an AI-based technology for automating the quantification and detection of fluorescent signals on combed DNA molecules. Initially available for the analysis of Replication Combing Assays (RCA), Genomic Vision's proprietary method for directly visualizing DNA replication kinetics at the single molecule level. FiberSmart uses advanced AI methods to detect, visualize, and analyze DNA replication kinetics up to 3x more accurately and up to 10x faster than Genomic Vision's existing software solutions. The technology offers a simple and user-friendly interface, facilitating quick analysis of DNA replication signals to deduce essential parameters describing replication kinetics. It is compatible with Genomic Vision's FiberVision® and FiberVision-S® scanners for the RCA assay of the company's proprietary DNA combing technology with various potential applications, including in gene and cell therapy quality control. FiberSmart has been successfully tested and validated by AstraZeneca and the Fritz Lipmann Institute in Germany. Genomic Vision's CEO Aaron Bensimon said, "The launch of FiberSmart® is an important milestone for Genomic Vision as we bring the benefits of powerful AI technology to our users, who can now perform faster and more accurate genomic analysis seamlessly. Our proprietary DNA combing technique has multiple potential applications, particularly in the cell and gene therapy space, where highly accurate genomic analysis is paramount to ensure robust quality standards are met. With the launch of this software we are making it easier for users to exploit the full potential of our proprietary advanced genomic analysis technique." (Source – Business Wire) About Genomic Vision GENOMIC VISION is a leading biotechnology company specializing in the analysis of genome modifications, with a focus on ensuring their quality and safety in genome editing technologies and biomanufacturing processes. It utilizes advanced nanotechnology for DNA analysis to develop cutting-edge diagnostic and drug discovery solutions for cancer and acute diseases at the intersection of genome dynamics and human diseases. The company's approach employs Molecular Combing Technology, a powerful technique that directly visualizes single DNA molecules to detect and quantify changes in the genome landscape and their contribution to pathology.

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Medical

Spotlight Therapeutics Raises $36.5 Million Series B to Advance a Pipeline of Cell-Targeted In Vivo CRISPR Gene Editing Biologics

Spotlight Therapeutics | March 22, 2022

Spotlight Therapeutics, Inc. (“Spotlight”), a biotechnology company applying new insights to develop cell-targeted in vivo CRISPR gene editing biologics, today announced a $36.5M Series B financing to fuel a drive toward the clinic. The financing round was co-led by new investors GordonMD Global Investments and EPIQ Capital Group, with participation from Magnetic Ventures, as well as existing investors GV (formerly Google Ventures) and Emerson Collective and other investors. Craig Gordon, M.D., Founder, CEO and CIO of GordonMD Global Investments, joins the Company’s Board of Directors. Spotlight's proprietary technology platform, TAGE (Targeted Active Gene Editors), is a new class of biologics; highly engineered, modular programmable CRISPR effectors designed to target and edit selected cell types in vivo. This approach circumvents the complexity of packaged viral, viral-like, and nanoparticle delivery systems, opens the door to expanded applications, and holds the promise of increasing patient access. We are excited to help Spotlight advance its pioneering work, which shows promise for cell-targeted delivery of CRISPR effectors in vivo. Spotlight’s TAGE platform could enable significant expansion of CRISPR medicines to a wide range of diseases." Dr. Gordon. This Series B funding is a crucial milestone as we advance our lead first-in-class immuno-oncology (IO) program and progress our pipeline of programs in IO, ophthalmic diseases and hemoglobinopathies,It will enable us to execute our development plan, leveraging Spotlight’s unique cell-targeted in vivo delivery approach, as we aspire to unlock the full potential of gene editing and enable effective one-and-done medicines for patients.” Mary Haak-Frendscho, Ph.D., President and CEO of Spotlight Therapeutics. About Spotlight Therapeutics Established in mid-2018, Spotlight Therapeutics is a privately held biotechnology company advancing a pipeline of cell-targeted in vivo CRISPR gene editing therapies. Spotlight's proprietary technology platform TAGE (Targeted Active Gene Editors) is a new class of biologics, CRISPR effectors engineered for direct delivery in vivo, to achieve cell-selective therapeutic genome editing. Spotlight's pipeline is advancing its modular programmable CRISPR effectors towards clinical studies in immuno-oncology, ophthalmic diseases and hemoglobinopathies. The company is headquartered in Hayward, California.

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Medical

TGen Selects MemVerge to Accelerate Idiopathic Pulmonary Fibrosis Research Discovery with Big Memory Technology

MemVerge | March 21, 2022

MemVerge™, the pioneers of Big Memory software, today announced that TGen, the Translational Genomics Research Institute, an affiliate of City of Hope, has selected MemVerge Memory Machine Big Memory virtualization software to accelerate time to discovery for Idiopathic Pulmonary Fibrosis (IPF), a disease which affects 100,000 people annually in the U.S. Using MemVerge technology, TGen is able to dramatically speed analytical processing by nearly 36% for single-cell RNA sequencing. As a nonprofit medical research institute, TGen researchers process single-cell RNA sequences to characterize cell transcriptomic profiles. The process can take up to six and a half hours to analyze a matrix of 30,000 genes by 114,000 cells. With consistently growing datasets, this processing time was preventing a desired time to discovery. The data required for analysis was simply too large to retain in traditional memory, and scaling capacity with dynamic random-access memory (DRAM) was too costly. TGen has instead deployed memory virtualization technology from MemVerge which virtualizes both DRAM and PMem (persistent memory) memory technologies, to increase the memory pool available for processing without requiring more high-cost DRAM. The solution further speeds TGen's genomics sequencing analysis with Memory Machine ZeroIO in-memory snapshots which capture multi-terabyte data sets at any point for rapid reloads at each stage of processing. The ZeroIO snapshot service is 1,000 times faster than the fastest storage snapshot to SSD and enables TGen to run processing workflows in parallel. This ensures that in the event of a system crash, in-memory snapshots are available to instantly re-start long running jobs without lengthy reloading. By utilizing the snapshotting and cloning capabilities of Memory Machine, we were able to parallelize the processing workflow, As a result, we can now save nearly 36% of computational time while also taking advantage of the big memory nodes. This will save a lot of time in downstream analysis." Glen Otero, Ph.D., Vice President of Scientific Computing at TGen. MemVerge Memory Machine has quickly resulted in research value for TGen, We have removed performance barriers from their research process so that they are able to perform vital, life-saving, research faster than ever possible. Now TGen is expanding the use of Big Memory technology across other research use cases where results and discoveries can produce findings for a healthier tomorrow." Jonathan Jiang, COO of MemVerge. MemVerge Memory Machine makes 100% use of available memory capacity while providing new operational capabilities to memory-centric workloads. Memory Machine answers the need for a modern in-memory computing model to support emerging applications that require real-time analytics, true in-memory computing, and fault-tolerant memory persistence to speed massive processing workloads. About MemVerge MemVerge is pioneering Big Memory Computing and Big Memory Cloud technology for the memory-centric and multi-cloud future. MemVerge® Memory Machine™ is the industry's first software to virtualize memory hardware for fine-grained provisioning of capacity, performance, availability, and mobility. On top of the transparent memory service, Memory Machine provides another industry first, ZeroIO™ in-memory snapshots which can encapsulate terabytes of application state within seconds and enable data management at the speed of memory. The breakthrough capabilities of Big Memory Computing and Big Memory Cloud Technology are opening the door to cloud agility and flexibility for thousands of Big Memory applications.

Read More

AI, Diagnostics

Genomic Vision Announces launch of FiberSmart

Genomic Vision | March 08, 2023

On March 7, 2023, Genomic Vision, a leading biotech company that develops products and services for the analysis and control of genome changes, launched FiberSmart®, an AI-based technology for automating the quantification and detection of fluorescent signals on combed DNA molecules. Initially available for the analysis of Replication Combing Assays (RCA), Genomic Vision's proprietary method for directly visualizing DNA replication kinetics at the single molecule level. FiberSmart uses advanced AI methods to detect, visualize, and analyze DNA replication kinetics up to 3x more accurately and up to 10x faster than Genomic Vision's existing software solutions. The technology offers a simple and user-friendly interface, facilitating quick analysis of DNA replication signals to deduce essential parameters describing replication kinetics. It is compatible with Genomic Vision's FiberVision® and FiberVision-S® scanners for the RCA assay of the company's proprietary DNA combing technology with various potential applications, including in gene and cell therapy quality control. FiberSmart has been successfully tested and validated by AstraZeneca and the Fritz Lipmann Institute in Germany. Genomic Vision's CEO Aaron Bensimon said, "The launch of FiberSmart® is an important milestone for Genomic Vision as we bring the benefits of powerful AI technology to our users, who can now perform faster and more accurate genomic analysis seamlessly. Our proprietary DNA combing technique has multiple potential applications, particularly in the cell and gene therapy space, where highly accurate genomic analysis is paramount to ensure robust quality standards are met. With the launch of this software we are making it easier for users to exploit the full potential of our proprietary advanced genomic analysis technique." (Source – Business Wire) About Genomic Vision GENOMIC VISION is a leading biotechnology company specializing in the analysis of genome modifications, with a focus on ensuring their quality and safety in genome editing technologies and biomanufacturing processes. It utilizes advanced nanotechnology for DNA analysis to develop cutting-edge diagnostic and drug discovery solutions for cancer and acute diseases at the intersection of genome dynamics and human diseases. The company's approach employs Molecular Combing Technology, a powerful technique that directly visualizes single DNA molecules to detect and quantify changes in the genome landscape and their contribution to pathology.

Read More

Medical

Spotlight Therapeutics Raises $36.5 Million Series B to Advance a Pipeline of Cell-Targeted In Vivo CRISPR Gene Editing Biologics

Spotlight Therapeutics | March 22, 2022

Spotlight Therapeutics, Inc. (“Spotlight”), a biotechnology company applying new insights to develop cell-targeted in vivo CRISPR gene editing biologics, today announced a $36.5M Series B financing to fuel a drive toward the clinic. The financing round was co-led by new investors GordonMD Global Investments and EPIQ Capital Group, with participation from Magnetic Ventures, as well as existing investors GV (formerly Google Ventures) and Emerson Collective and other investors. Craig Gordon, M.D., Founder, CEO and CIO of GordonMD Global Investments, joins the Company’s Board of Directors. Spotlight's proprietary technology platform, TAGE (Targeted Active Gene Editors), is a new class of biologics; highly engineered, modular programmable CRISPR effectors designed to target and edit selected cell types in vivo. This approach circumvents the complexity of packaged viral, viral-like, and nanoparticle delivery systems, opens the door to expanded applications, and holds the promise of increasing patient access. We are excited to help Spotlight advance its pioneering work, which shows promise for cell-targeted delivery of CRISPR effectors in vivo. Spotlight’s TAGE platform could enable significant expansion of CRISPR medicines to a wide range of diseases." Dr. Gordon. This Series B funding is a crucial milestone as we advance our lead first-in-class immuno-oncology (IO) program and progress our pipeline of programs in IO, ophthalmic diseases and hemoglobinopathies,It will enable us to execute our development plan, leveraging Spotlight’s unique cell-targeted in vivo delivery approach, as we aspire to unlock the full potential of gene editing and enable effective one-and-done medicines for patients.” Mary Haak-Frendscho, Ph.D., President and CEO of Spotlight Therapeutics. About Spotlight Therapeutics Established in mid-2018, Spotlight Therapeutics is a privately held biotechnology company advancing a pipeline of cell-targeted in vivo CRISPR gene editing therapies. Spotlight's proprietary technology platform TAGE (Targeted Active Gene Editors) is a new class of biologics, CRISPR effectors engineered for direct delivery in vivo, to achieve cell-selective therapeutic genome editing. Spotlight's pipeline is advancing its modular programmable CRISPR effectors towards clinical studies in immuno-oncology, ophthalmic diseases and hemoglobinopathies. The company is headquartered in Hayward, California.

Read More

Medical

TGen Selects MemVerge to Accelerate Idiopathic Pulmonary Fibrosis Research Discovery with Big Memory Technology

MemVerge | March 21, 2022

MemVerge™, the pioneers of Big Memory software, today announced that TGen, the Translational Genomics Research Institute, an affiliate of City of Hope, has selected MemVerge Memory Machine Big Memory virtualization software to accelerate time to discovery for Idiopathic Pulmonary Fibrosis (IPF), a disease which affects 100,000 people annually in the U.S. Using MemVerge technology, TGen is able to dramatically speed analytical processing by nearly 36% for single-cell RNA sequencing. As a nonprofit medical research institute, TGen researchers process single-cell RNA sequences to characterize cell transcriptomic profiles. The process can take up to six and a half hours to analyze a matrix of 30,000 genes by 114,000 cells. With consistently growing datasets, this processing time was preventing a desired time to discovery. The data required for analysis was simply too large to retain in traditional memory, and scaling capacity with dynamic random-access memory (DRAM) was too costly. TGen has instead deployed memory virtualization technology from MemVerge which virtualizes both DRAM and PMem (persistent memory) memory technologies, to increase the memory pool available for processing without requiring more high-cost DRAM. The solution further speeds TGen's genomics sequencing analysis with Memory Machine ZeroIO in-memory snapshots which capture multi-terabyte data sets at any point for rapid reloads at each stage of processing. The ZeroIO snapshot service is 1,000 times faster than the fastest storage snapshot to SSD and enables TGen to run processing workflows in parallel. This ensures that in the event of a system crash, in-memory snapshots are available to instantly re-start long running jobs without lengthy reloading. By utilizing the snapshotting and cloning capabilities of Memory Machine, we were able to parallelize the processing workflow, As a result, we can now save nearly 36% of computational time while also taking advantage of the big memory nodes. This will save a lot of time in downstream analysis." Glen Otero, Ph.D., Vice President of Scientific Computing at TGen. MemVerge Memory Machine has quickly resulted in research value for TGen, We have removed performance barriers from their research process so that they are able to perform vital, life-saving, research faster than ever possible. Now TGen is expanding the use of Big Memory technology across other research use cases where results and discoveries can produce findings for a healthier tomorrow." Jonathan Jiang, COO of MemVerge. MemVerge Memory Machine makes 100% use of available memory capacity while providing new operational capabilities to memory-centric workloads. Memory Machine answers the need for a modern in-memory computing model to support emerging applications that require real-time analytics, true in-memory computing, and fault-tolerant memory persistence to speed massive processing workloads. About MemVerge MemVerge is pioneering Big Memory Computing and Big Memory Cloud technology for the memory-centric and multi-cloud future. MemVerge® Memory Machine™ is the industry's first software to virtualize memory hardware for fine-grained provisioning of capacity, performance, availability, and mobility. On top of the transparent memory service, Memory Machine provides another industry first, ZeroIO™ in-memory snapshots which can encapsulate terabytes of application state within seconds and enable data management at the speed of memory. The breakthrough capabilities of Big Memory Computing and Big Memory Cloud Technology are opening the door to cloud agility and flexibility for thousands of Big Memory applications.

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