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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
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
Advances in high-throughput biological methods have led to the publication of a large number of genome-wide studies in human and animal models. In this context, recent tools from bioinformatics and computational biology have been fundamental for the analysis of these genomic studies. The book Bioinformatics and Human Genomics Research provides updated and comprehensive information about multiple approaches of the application of bioinformatic tools to research in human genomics. It covers strategies analysis of genome-wide association studies, genome-wide expression studies and genome-wide DNA methylation, among other topics. It provides interesting strategies for data mining in human genomics, network analysis, prediction of binding sites for miRNAs and transcription factors, among other themes. Experts from all around the world in bioinformatics and human genomics have contributed chapters in this book. Readers will find this book as quite useful for their in silico explorations, which would contribute to a better and deeper understanding of multiple biological processes and of pathophysiology of many human diseases.
If you’re like most R users, you have deep knowledge and love for statistics. But as your organization continues to collect huge amounts of data, adding tools such as Apache Spark makes a lot of sense. With this practical book, data scientists and professionals working with large-scale data applications will learn how to use Spark from R to tackle big data and big compute problems. Authors Javier Luraschi, Kevin Kuo, and Edgar Ruiz show you how to use R with Spark to solve different data analysis problems. This book covers relevant data science topics, cluster computing, and issues that should interest even the most advanced users. Analyze, explore, transform, and visualize data in Apache Spark with R Create statistical models to extract information and predict outcomes; automate the process in production-ready workflows Perform analysis and modeling across many machines using distributed computing techniques Use large-scale data from multiple sources and different formats with ease from within Spark Learn about alternative modeling frameworks for graph processing, geospatial analysis, and genomics at scale Dive into advanced topics including custom transformations, real-time data processing, and creating custom Spark extensions
This practical guide bridges the gap between general cloud computing architecture in Microsoft Azure and scientific computing for bioinformatics and genomics. You'll get a solid understanding of the architecture patterns and services that are offered in Azure and how they might be used in your bioinformatics practice. You'll get code examples that you can reuse for your specific needs. And you'll get plenty of concrete examples to illustrate how a given service is used in a bioinformatics context. You'll also get valuable advice on how to: Use enterprise platform services to easily scale your bioinformatics workloads Organize, query, and analyze genomic data at scale Build a genomics data lake and accompanying data warehouse Use Azure Machine Learning to scale your model training, track model performance, and deploy winning models Orchestrate and automate processing pipelines using Azure Data Factory and Databricks Cloudify your organization's existing bioinformatics pipelines by moving your workflows to Azure high-performance compute services And more
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.
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
This edited volume is devoted to Big Data Analysis from a Machine Learning standpoint as presented by some of the most eminent researchers in this area. It demonstrates that Big Data Analysis opens up new research problems which were either never considered before, or were only considered within a limited range. In addition to providing methodological discussions on the principles of mining Big Data and the difference between traditional statistical data analysis and newer computing frameworks, this book presents recently developed algorithms affecting such areas as business, financial forecasting, human mobility, the Internet of Things, information networks, bioinformatics, medical systems and life science. It explores, through a number of specific examples, how the study of Big Data Analysis has evolved and how it has started and will most likely continue to affect society. While the benefits brought upon by Big Data Analysis are underlined, the book also discusses some of the warnings that have been issued concerning the potential dangers of Big Data Analysis along with its pitfalls and challenges.
This IBM® Redpaper publication provides an update to the original description of IBM Reference Architecture for Genomics. This paper expands the reference architecture to cover all of the major vertical areas of healthcare and life sciences industries, such as genomics, imaging, and clinical and translational research. The architecture was renamed IBM Reference Architecture for High Performance Data and AI in Healthcare and Life Sciences to reflect the fact that it incorporates key building blocks for high-performance computing (HPC) and software-defined storage, and that it supports an expanding infrastructure of leading industry partners, platforms, and frameworks. The reference architecture defines a highly flexible, scalable, and cost-effective platform for accessing, managing, storing, sharing, integrating, and analyzing big data, which can be deployed on-premises, in the cloud, or as a hybrid of the two. IT organizations can use the reference architecture as a high-level guide for overcoming data management challenges and processing bottlenecks that are frequently encountered in personalized healthcare initiatives, and in compute-intensive and data-intensive biomedical workloads. This reference architecture also provides a framework and context for modern healthcare and life sciences institutions to adopt cutting-edge technologies, such as cognitive life sciences solutions, machine learning and deep learning, Spark for analytics, and cloud computing. To illustrate these points, this paper includes case studies describing how clients and IBM Business Partners alike used the reference architecture in the deployments of demanding infrastructures for precision medicine. This publication targets technical professionals (consultants, technical support staff, IT Architects, and IT Specialists) who are responsible for providing life sciences solutions and support.
This IBM® Redbooks® publication introduces the IBM Reference Architecture for Genomics, IBM Power SystemsTM edition on IBM POWER8®. It addresses topics such as why you would implement Life Sciences workloads on IBM POWER8, and shows how to use such solution to run Life Sciences workloads using IBM PlatformTM Computing software to help set up the workloads. It also provides technical content to introduce the IBM POWER8 clustered solution for Life Sciences workloads. This book customizes and tests Life Sciences workloads with a combination of an IBM Platform Computing software solution stack, Open Stack, and third party applications. All of these applications use IBM POWER8, and IBM Spectrum ScaleTM for a high performance file system. This book helps strengthen IBM Life Sciences solutions on IBM POWER8 with a well-defined and documented deployment model within an IBM Platform Computing and an IBM POWER8 clustered environment. This system provides clients in need of a modular, cost-effective, and robust solution with a planned foundation for future growth. This book highlights IBM POWER8 as a flexible infrastructure for clients looking to deploy life sciences workloads, and at the same time reduce capital expenditures, operational expenditures, and optimization of resources. This book helps answer clients' workload challenges in particular with Life Sciences applications, and provides expert-level documentation and how-to-skills to worldwide teams that provide Life Sciences solutions and support to give a broad understanding of a new architecture.