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High Performance In Memory Genome Data Analysis
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Book Synopsis High-Performance In-Memory Genome Data Analysis by : Hasso Plattner
Download or read book High-Performance In-Memory Genome Data Analysis written by Hasso Plattner and published by Springer Science & Business Media. This book was released on 2013-11-19 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent achievements in hardware and software developments have enabled the introduction of a revolutionary technology: in-memory data management. This technology supports the flexible and extremely fast analysis of massive amounts of data, such as diagnoses, therapies, and human genome data. This book shares the latest research results of applying in-memory data management to personalized medicine, changing it from computational possibility to clinical reality. The authors provide details on innovative approaches to enabling the processing, combination, and analysis of relevant data in real-time. The book bridges the gap between medical experts, such as physicians, clinicians, and biological researchers, and technology experts, such as software developers, database specialists, and statisticians. Topics covered in this book include - amongst others - modeling of genome data processing and analysis pipelines, high-throughput data processing, exchange of sensitive data and protection of intellectual property. Beyond that, it shares insights on research prototypes for the analysis of patient cohorts, topology analysis of biological pathways, and combined search in structured and unstructured medical data, and outlines completely new processes that have now become possible due to interactive data analyses.
Book Synopsis High-Performance In-Memory Genome Data Analysis by :
Download or read book High-Performance In-Memory Genome Data Analysis written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Methods for the Analysis of Genomic Data and Biological Processes by : Francisco A. Gómez Vela
Download or read book Computational Methods for the Analysis of Genomic Data and Biological Processes written by Francisco A. Gómez Vela and published by MDPI. This book was released on 2021-02-05 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality.
Book Synopsis Computational Methods for Next Generation Sequencing Data Analysis by : Ion Mandoiu
Download or read book Computational Methods for Next Generation Sequencing Data Analysis written by Ion Mandoiu and published by John Wiley & Sons. This book was released on 2016-09-12 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.
Book Synopsis Next-Generation Sequencing Data Analysis by : Xinkun Wang
Download or read book Next-Generation Sequencing Data Analysis written by Xinkun Wang and published by CRC Press. This book was released on 2016-04-06 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Practical Guide to the Highly Dynamic Area of Massively Parallel SequencingThe development of genome and transcriptome sequencing technologies has led to a paradigm shift in life science research and disease diagnosis and prevention. Scientists are now able to see how human diseases and phenotypic changes are connected to DNA mutation, polymorphi
Book Synopsis High Performance Computing by : Julian M. Kunkel
Download or read book High Performance Computing written by Julian M. Kunkel and published by Springer. This book was released on 2016-06-14 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 31st International Conference, ISC High Performance 2016 [formerly known as the International Supercomputing Conference] held in Frankfurt, Germany, in June 2016. The 25 revised full papers presented in this book were carefully reviewed and selected from 60 submissions. The papers cover the following topics: Autotuning and Thread Mapping; Data Locality and Decomposition; Scalable Applications; Machine Learning; Datacenters andCloud; Communication Runtime; Intel Xeon Phi; Manycore Architectures; Extreme-scale Computations; and Resilience.
Book Synopsis High Performance Computational Methods for Biological Sequence Analysis by : Tieng K. Yap
Download or read book High Performance Computational Methods for Biological Sequence Analysis written by Tieng K. Yap and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: High Performance Computational Methods for Biological Sequence Analysis presents biological sequence analysis using an interdisciplinary approach that integrates biological, mathematical and computational concepts. These concepts are presented so that computer scientists and biomedical scientists can obtain the necessary background for developing better algorithms and applying parallel computational methods. This book will enable both groups to develop the depth of knowledge needed to work in this interdisciplinary field. This work focuses on high performance computational approaches that are used to perform computationally intensive biological sequence analysis tasks: pairwise sequence comparison, multiple sequence alignment, and sequence similarity searching in large databases. These computational methods are becoming increasingly important to the molecular biology community allowing researchers to explore the increasingly large amounts of sequence data generated by the Human Genome Project and other related biological projects. The approaches presented by the authors are state-of-the-art and show how to reduce analysis times significantly, sometimes from days to minutes. High Performance Computational Methods for Biological Sequence Analysis is tremendously important to biomedical science students and researchers who are interested in applying sequence analyses to their studies, and to computational science students and researchers who are interested in applying new computational approaches to biological sequence analyses.
Book Synopsis Data Analysis for the Life Sciences with R by : Rafael A. Irizarry
Download or read book Data Analysis for the Life Sciences with R written by Rafael A. Irizarry and published by CRC Press. This book was released on 2016-10-04 with total page 537 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers several of the statistical concepts and data analytic skills needed to succeed in data-driven life science research. The authors proceed from relatively basic concepts related to computed p-values to advanced topics related to analyzing highthroughput data. They include the R code that performs this analysis and connect the lines of code to the statistical and mathematical concepts explained.
Book Synopsis Contemporary High Performance Computing by : Jeffrey S. Vetter
Download or read book Contemporary High Performance Computing written by Jeffrey S. Vetter and published by CRC Press. This book was released on 2017-11-23 with total page 730 pages. Available in PDF, EPUB and Kindle. Book excerpt: Contemporary High Performance Computing: From Petascale toward Exascale focuses on the ecosystems surrounding the world’s leading centers for high performance computing (HPC). It covers many of the important factors involved in each ecosystem: computer architectures, software, applications, facilities, and sponsors. The first part of the book examines significant trends in HPC systems, including computer architectures, applications, performance, and software. It discusses the growth from terascale to petascale computing and the influence of the TOP500 and Green500 lists. The second part of the book provides a comprehensive overview of 18 HPC ecosystems from around the world. Each chapter in this section describes programmatic motivation for HPC and their important applications; a flagship HPC system overview covering computer architecture, system software, programming systems, storage, visualization, and analytics support; and an overview of their data center/facility. The last part of the book addresses the role of clouds and grids in HPC, including chapters on the Magellan, FutureGrid, and LLGrid projects. With contributions from top researchers directly involved in designing, deploying, and using these supercomputing systems, this book captures a global picture of the state of the art in HPC.
Book Synopsis Bringing Large-scale Multiple Genome Analysis One Step Closer by :
Download or read book Bringing Large-scale Multiple Genome Analysis One Step Closer written by and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome sequence comparisons of exponentially growing data sets form the foundation for the comparative analysis tools provided by community biological data resources such as the Integrated Microbial Genome (IMG) system at the Joint Genome Institute (JGI). We present an example of how ScalaBLAST, a high-throughput sequence analysis program harnesses increasingly critical high-performance computing to perform sequence analysis which is a critical component of maintaining a state-of-the-art sequence data repository. The Integrated Microbial Genomes (IMG) system1 is a data management and analysis platform for microbial genomes hosted at the JGI. IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for interactive analysis of genomes, genes and functions, individually or in a comparative context. Most of these tools are based on pre-computed pairwise sequence similarities involving millions of genes. These computations are becoming prohibitively time consuming with the rapid increase in the number of newly sequenced genomes incorporated into IMG and the need to refresh regularly the content of IMG in order to reflect changes in the annotations of existing genomes. Thus, building IMG 2.0 (released on December 1st 2006) entailed reloading from NCBI's RefSeq all the genomes in the previous version of IMG (IMG 1.6, as of September 1st, 2006) together with 1,541 new public microbial, viral and eukaryal genomes, bringing the total of IMG genomes to 2,301. A critical part of building IMG 2.0 involved using PNNL ScalaBLAST software for computing pairwise similarities for over 2.2 million genes in under 26 hours on 1,000 processors, thus illustrating the impact that new generation bioinformatics tools are poised to make in biology. The BLAST algorithm2, 3 is a familiar bioinformatics application for computing sequence similarity, and has become a workhorse in large-scale genomics projects. The rapid growth of genome resources such as IMG cannot be sustained without more powerful tools such as ScalaBLAST that use more effectively large scale computing resources to perform the core BLAST calculations. ScalaBLAST is a high performance computing algorithm designed to give high throughput BLAST results on high-end supercomputers. Other parallel sequence comparison applications have been developed4-6. However problems with scaling generally prevent these applications from being used for very large searches. ScalaBLAST7 is the first BLAST application to be both highly scaleable against the size of the database as well as the number of computer processors on high-end hardware and on commodity clusters. ScalaBLAST achieves high throughput by parsing a large collection of query sequences into independent subgroups. These smaller tasks are assigned to independent process groups. Efficient scaling is achieved by (transparently to the user) sharing only one copy of the target database across all processors using the Global Array toolkit 8, 9, which provides software implementation of shared memory interface. ScalaBLAST was initially deployed on the 1,960 processor MPP2 cluster in the Wiliam R. Wiley Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory, and has since been ported to a variety of linux-based clusters and shared memory architectures, including SGI Altix, AMD opteron, and Intel Xeon-based clusters. Future targets include IBM BlueGene, Cray, and SGI Altix XE architectures. The importance of performing high-throughput calculations rapidly lies in the rate of growth of sequence data. For a genome sequencing center to provide multiple-genome comparison capabilities, it must keep pace with exponentially growing collection of protein data, both from its own genomes, and from the public genome information as well. As sequence data continues to grow exponentially, this challenge will only increase with time. Solving the BLAST throughput challenge for centralized data resources like IMG has the potential to unlock the power of emerging analysis methods which, until recently, were limited by the availability of multiple genome comparison data. Fig. 1 illustrates how the run-time achieved by efficient scaling in ScalaBLAST enabled the IMG all vs. all BLAST calculations to complete in roughly 1 day. Note that to keep pace with growing IMG database, we will have to double the number of processors used in these calculations during the upcoming year. Grid-based solutions for improving throughput for BLAST searches has become a popular and attractive option for some centers. The Institute for Genome Research (http://www.tigr.org/), for instance, has implemented a grid-based BLAST tool allowing users to submit requests to be farmed out to available computers on an on-demand basis.
Book Synopsis EHealth - For Continuity of Care by : C. Lovis
Download or read book EHealth - For Continuity of Care written by C. Lovis and published by IOS Press. This book was released on 2014-09-30 with total page 1328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Information technology and the information sciences have been part of our lives for some time now. They have revolutionized the healthcare system, changing the whole health landscape, as well as health culture. New devices, sources of data and roles for all those involved in healthcare are being developed as a result. This book presents the proceedings of the 25th European Medical Informatics Conference, held in Istanbul, Turkey in August/September 2014. The conference aims to present the most recent developments in biomedical informatics. The book is divided into 15 sections, which include: decision support systems and clinical practice guidelines; improved healthcare through informatics; data analysis; mobile health; technology and system evaluation; and text mining. The final two sections present posters from the conference. The book will be of interest to all those in the healthcare sector, researchers and practitioners alike, who develop, evaluate or work with information technology.
Book Synopsis Cloud Computing by : Nick Antonopoulos
Download or read book Cloud Computing written by Nick Antonopoulos and published by Springer. This book was released on 2017-06-02 with total page 418 pages. Available in PDF, EPUB and Kindle. Book excerpt: This practically-focused reference presents a comprehensive overview of the state of the art in Cloud Computing, and examines the potential for future Cloud and Cloud-related technologies to address specific industrial and research challenges. This new edition explores both established and emergent principles, techniques, protocols and algorithms involved with the design, development, and management of Cloud-based systems. The text reviews a range of applications and methods for linking Clouds, undertaking data management and scientific data analysis, and addressing requirements both of data analysis and of management of large scale and complex systems. This new edition also extends into the emergent next generation of mobile telecommunications, relating network function virtualization and mobile edge Cloud Computing, as supports Smart Grids and Smart Cities. As with the first edition, emphasis is placed on the four quality-of-service cornerstones of efficiency, scalability, robustness, and security.
Book Synopsis A Course in In-Memory Data Management by : Hasso Plattner
Download or read book A Course in In-Memory Data Management written by Hasso Plattner and published by Springer. This book was released on 2014-05-28 with total page 315 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent achievements in hardware and software development, such as multi-core CPUs and DRAM capacities of multiple terabytes per server, enabled the introduction of a revolutionary technology: in-memory data management. This technology supports the flexible and extremely fast analysis of massive amounts of enterprise data. Professor Hasso Plattner and his research group at the Hasso Plattner Institute in Potsdam, Germany, have been investigating and teaching the corresponding concepts and their adoption in the software industry for years. This book is based on an online course that was first launched in autumn 2012 with more than 13,000 enrolled students and marked the successful starting point of the openHPI e-learning platform. The course is mainly designed for students of computer science, software engineering, and IT related subjects, but addresses business experts, software developers, technology experts, and IT analysts alike. Plattner and his group focus on exploring the inner mechanics of a column-oriented dictionary-encoded in-memory database. Covered topics include - amongst others - physical data storage and access, basic database operators, compression mechanisms, and parallel join algorithms. Beyond that, implications for future enterprise applications and their development are discussed. Step by step, readers will understand the radical differences and advantages of the new technology over traditional row-oriented, disk-based databases. In this completely revised 2nd edition, we incorporate the feedback of thousands of course participants on openHPI and take into account latest advancements in hard- and software. Improved figures, explanations, and examples further ease the understanding of the concepts presented. We introduce advanced data management techniques such as transparent aggregate caches and provide new showcases that demonstrate the potential of in-memory databases for two diverse industries: retail and life sciences.
Book Synopsis Encyclopedia of Bioinformatics and Computational Biology by :
Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Book Synopsis Transactions on Large-Scale Data- and Knowledge-Centered Systems XLVI by : Abdelkader Hameurlain
Download or read book Transactions on Large-Scale Data- and Knowledge-Centered Systems XLVI written by Abdelkader Hameurlain and published by Springer Nature. This book was released on 2020-11-20 with total page 197 pages. Available in PDF, EPUB and Kindle. Book excerpt: The LNCS journal Transactions on Large-Scale Data- and Knowledge-Centered Systems focuses on data management, knowledge discovery, and knowledge processing, which are core and hot topics in computer science. Since the 1990s, the Internet has become the main driving force behind application development in all domains. An increase in the demand for resource sharing (e.g., computing resources, services, metadata, data sources) across different sites connected through networks has led to an evolution of data- and knowledge-management systems from centralized systems to decentralized systems enabling large-scale distributed applications providing high scalability. This, the 46th issue of Transactions on Large-Scale Data- and Knowledge-Centered Systems, contains six fully revised selected regular papers. Topics covered include an elastic framework for genomic data management, medical data cloud federations, temporal pattern mining, scalable schema discovery, load shedding, and selectivity estimation using linked Bayesian networks.
Book Synopsis Big Data – BigData 2020 by : Surya Nepal
Download or read book Big Data – BigData 2020 written by Surya Nepal and published by Springer Nature. This book was released on 2020-09-17 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 9th International Conference on Big Data, BigData 2020, held as part of SCF 2020, during September 18-20, 2020. The conference was planned to take place in Honolulu, HI, USA and was changed to a virtual format due to the COVID-19 pandemic. The 16 full and 3 short papers presented were carefully reviewed and selected from 52 submissions. The topics covered are Big Data Architecture, Big Data Modeling, Big Data As A Service, Big Data for Vertical Industries (Government, Healthcare, etc.), Big Data Analytics, Big Data Toolkits, Big Data Open Platforms, Economic Analysis, Big Data for Enterprise Transformation, Big Data in Business Performance Management, Big Data for Business Model Innovations and Analytics, Big Data in Enterprise Management Models and Practices, Big Data in Government Management Models and Practices, and Big Data in Smart Planet Solutions.
Book Synopsis High Performance Computing by : Ponnuswamy Sadayappan
Download or read book High Performance Computing written by Ponnuswamy Sadayappan and published by Springer Nature. This book was released on 2020-06-15 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 35th International Conference on High Performance Computing, ISC High Performance 2020, held in Frankfurt/Main, Germany, in June 2020.* The 27 revised full papers presented were carefully reviewed and selected from 87 submissions. The papers cover a broad range of topics such as architectures, networks & infrastructure; artificial intelligence and machine learning; data, storage & visualization; emerging technologies; HPC algorithms; HPC applications; performance modeling & measurement; programming models & systems software. *The conference was held virtually due to the COVID-19 pandemic. Chapters "Scalable Hierarchical Aggregation and Reduction Protocol (SHARP) Streaming-Aggregation Hardware Design and Evaluation", "Solving Acoustic Boundary Integral Equations Using High Performance Tile Low-Rank LU Factorization", "Scaling Genomics Data Processing with Memory-Driven Computing to Accelerate Computational Biology", "Footprint-Aware Power Capping for Hybrid Memory Based Systems", and "Pattern-Aware Staging for Hybrid Memory Systems" are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
