Genomics in the Cloud PDF Download

Author: Geraldine A. Van der Auwera
Publisher: O'Reilly Media
ISBN: 1491975164
Category : Computers
Languages : en
Pages : 496

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Book Description
Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytes—or over 50 million gigabytes—of genomic data, and they’re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian O’Connor of the UC Santa Cruz Genomics Institute, guide you through the process. You’ll learn by working with real data and genomics algorithms from the field. This book covers: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK, plus three major GATK Best Practices pipelines Automating analysis with scripted workflows using WDL and Cromwell Scaling up workflow execution in the cloud, including parallelization and cost optimization Interactive analysis in the cloud using Jupyter notebooks Secure collaboration and computational reproducibility using Terra

Author: Geraldine A. Van der Auwera
Publisher: "O'Reilly Media, Inc."
ISBN: 1491975148
Category : Science
Languages : en
Pages : 570

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Book Description
Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytesâ??or over 50 million gigabytesâ??of genomic data, and theyâ??re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian Oâ??Connor of the UC Santa Cruz Genomics Institute, guide you through the process. Youâ??ll learn by working with real data and genomics algorithms from the field. This book covers: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK, plus three major GATK Best Practices pipelines Automating analysis with scripted workflows using WDL and Cromwell Scaling up workflow execution in the cloud, including parallelization and cost optimization Interactive analysis in the cloud using Jupyter notebooks Secure collaboration and computational reproducibility using Terra

Author: Catherine Vacher
Publisher: Wiley
ISBN: 9781119573371
Category : Computers
Languages : en
Pages : 0

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Book Description
Perform genome analysis and sequencing of data with Amazon Web Services Genomics in the AWS Cloud: Analyzing Genetic Code Using Amazon Web Services enables a person who has moderate familiarity with AWS Cloud to perform full genome analysis and research. Using the information in this book, you’ll be able to take a FASTQ file containing raw data from a lab or a BAM file from a service provider and perform genome analysis on it. You’ll also be able to identify potentially pathogenic gene sequences. • Get an introduction to Whole Genome Sequencing (WGS) • Make sense of WGS on AWS • Master AWS services for genome analysis Some key advantages of using AWS for genomic analysis is to help researchers utilize a wide choice of compute services that can process diverse datasets in analysis pipelines. Genomic sequencers that generate raw data files are located in labs on premises and AWS provides solutions to make it easy for customers to transfer these files to AWS reliably and securely. Storing Genomics and Medical (e.g., imaging) data at different stages requires enormous storage in a cost-effective manner. Amazon Simple Storage Service (Amazon S3), Amazon Glacier, and Amazon Elastics Block Store (Amazon EBS) provide the necessary solutions to securely store, manage, and scale genomic file storage. Moreover, the storage services can interface with various compute services from AWS to process these files. Whether you’re just getting started or have already been analyzing genomics data using the AWS Cloud, this book provides you with the information you need in order to use AWS services and features in the ways that will make the most sense for your genomic research.

Author: Ian Foster
Publisher: MIT Press
ISBN: 0262037246
Category : Computers
Languages : en
Pages : 391

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Book Description
A guide to cloud computing for students, scientists, and engineers, with advice and many hands-on examples. The emergence of powerful, always-on cloud utilities has transformed how consumers interact with information technology, enabling video streaming, intelligent personal assistants, and the sharing of content. Businesses, too, have benefited from the cloud, outsourcing much of their information technology to cloud services. Science, however, has not fully exploited the advantages of the cloud. Could scientific discovery be accelerated if mundane chores were automated and outsourced to the cloud? Leading computer scientists Ian Foster and Dennis Gannon argue that it can, and in this book offer a guide to cloud computing for students, scientists, and engineers, with advice and many hands-on examples. The book surveys the technology that underpins the cloud, new approaches to technical problems enabled by the cloud, and the concepts required to integrate cloud services into scientific work. It covers managing data in the cloud, and how to program these services; computing in the cloud, from deploying single virtual machines or containers to supporting basic interactive science experiments to gathering clusters of machines to do data analytics; using the cloud as a platform for automating analysis procedures, machine learning, and analyzing streaming data; building your own cloud with open source software; and cloud security. The book is accompanied by a website, Cloud4SciEng.org, that provides a variety of supplementary material, including exercises, lecture slides, and other resources helpful to readers and instructors.

Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
ISBN: 0309676738
Category : Science
Languages : en
Pages : 201

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Book Description
One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from "-omics" screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.

Author: Geraldine Van der Auwera
Publisher:
ISBN: 9781491975183
Category :
Languages : en
Pages : 300

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Book Description
Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytes-or 52.4 million gigabytes-of genomic data, and they're turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Brian O'Connor of the UC Santa Cruz Genomics Institute and Geraldine Van der Auwera, longtime custodian of the GATK user community, guide you through the process. You'll learn by working with real data and genomics algorithms from the field. This book takes you through: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK Three major GATK best practices for variant discovery pipelines Automating analysis with scripted workflows using WDL and Cromwell Scaling up workflow execution in the cloud, including parallelization and cost optimization Interactive analysis in the cloud using Jupyter notebooks Secure collaboration and computational reproducibility using Terra.

Author: Assad Abbas
Publisher: John Wiley & Sons
ISBN: 1119551692
Category : Technology & Engineering
Languages : en
Pages : 616

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Book Description
Summarizes the current state and upcoming trends within the area of fog computing Written by some of the leading experts in the field, Fog Computing: Theory and Practice focuses on the technological aspects of employing fog computing in various application domains, such as smart healthcare, industrial process control and improvement, smart cities, and virtual learning environments. In addition, the Machine-to-Machine (M2M) communication methods for fog computing environments are covered in depth. Presented in two parts—Fog Computing Systems and Architectures, and Fog Computing Techniques and Application—this book covers such important topics as energy efficiency and Quality of Service (QoS) issues, reliability and fault tolerance, load balancing, and scheduling in fog computing systems. It also devotes special attention to emerging trends and the industry needs associated with utilizing the mobile edge computing, Internet of Things (IoT), resource and pricing estimation, and virtualization in the fog environments. Includes chapters on deep learning, mobile edge computing, smart grid, and intelligent transportation systems beyond the theoretical and foundational concepts Explores real-time traffic surveillance from video streams and interoperability of fog computing architectures Presents the latest research on data quality in the IoT, privacy, security, and trust issues in fog computing Fog Computing: Theory and Practice provides a platform for researchers, practitioners, and graduate students from computer science, computer engineering, and various other disciplines to gain a deep understanding of fog computing.

Author: Kelly E. Happe
Publisher: NYU Press
ISBN: 0814790690
Category : Social Science
Languages : en
Pages : 305

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Book Description
Winner of the 2014 Diamond Anniversary Book Award Finalist for the 2014 National Communications Association Critical and Cultural Studies Division Book of the Year Award In 2000, the National Human Genome Research Institute announced the completion of a “draft” of the human genome, the sequence information of nearly all 3 billion base pairs of DNA. Since then, interest in the hereditary basis of disease has increased considerably. In The Material Gene, Kelly E. Happe considers the broad implications of this development by treating “heredity” as both a scientific and political concept. Beginning with the argument that eugenics was an ideological project that recast the problems of industrialization as pathologies of gender, race, and class, the book traces the legacy of this ideology in contemporary practices of genomics. Delving into the discrete and often obscure epistemologies and discursive practices of genomic scientists, Happe maps the ways in which the hereditarian body, one that is also normatively gendered and racialized, is the new site whereby economic injustice, environmental pollution, racism, and sexism are implicitly reinterpreted as pathologies of genes and by extension, the bodies they inhabit. Comparing genomic approaches to medicine and public health with discourses of epidemiology, social movements, and humanistic theories of the body and society, The Material Gene reworks our common assumption of what might count as effective, just, and socially transformative notions of health and disease.

Author: Jaydip Sen
Publisher: BoD – Books on Demand
ISBN: 9535132431
Category : Computers
Languages : en
Pages : 142

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Book Description
In the era of Internet of Things and with the explosive worldwide growth of electronic data volume, and associated need of processing, analysis, and storage of such humongous volume of data, it has now become mandatory to exploit the power of massively parallel architecture for fast computation. Cloud computing provides a cheap source of such computing framework for large volume of data for real-time applications. It is, therefore, not surprising to see that cloud computing has become a buzzword in the computing fraternity over the last decade. This book presents some critical applications in cloud frameworks along with some innovation design of algorithms and architecture for deployment in cloud environment. It is a valuable source of knowledge for researchers, engineers, practitioners, and graduate and doctoral students working in the field of cloud computing. It will also be useful for faculty members of graduate schools and universities.

Author: David J. Balding
Publisher: John Wiley & Sons
ISBN: 1119429250
Category : Science
Languages : en
Pages : 1828

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Book Description
A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.