Genomics in the AWS Cloud

Genomics in the AWS Cloud

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 ...

Author: David Wall

Publisher: Sybex

ISBN: 1119573378

Category: Computers

Page: 360

View: 104

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.
Categories: Computers

Bioinformatics and Human Genomics Research

Bioinformatics and Human Genomics Research

a community and enterprise solutions based on the same concept of cloudworkbenching supporting AWS, GCP and Azure cloud platforms as well as onpremises installs. Table 12 Advanced bioinformatic solutions for WGS workflows Tool ...

Author: Diego A. Forero

Publisher: CRC Press

ISBN: 9781000405682

Category: Science

Page: 374

View: 130

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.
Categories: Science

Genomics in the Cloud

Genomics in the Cloud

... biomedical research would clearly benefit from having mechanisms in place to run federated analyses seamlessly across infrastructure platforms; for example, cloud to cloud (Google Cloud and AWS), cloud to on-premises (Google Cloud ...

Author: Geraldine A. Van der Auwera

Publisher: "O'Reilly Media, Inc."

ISBN: 9781491975145

Category: Computers

Page: 496

View: 394

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
Categories: Computers

Delivery and Adoption of Cloud Computing Services in Contemporary Organizations

Delivery and Adoption of Cloud Computing Services in Contemporary Organizations

The case for cloud computing in genome informatics. Genome Biology, 11(5), ... Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. ... 1000 genomes on Amazon's cloud.

Author: Chang, Victor

Publisher: IGI Global

ISBN: 9781466682115

Category: Computers

Page: 519

View: 924

The ubiquity of technology has not only brought the need for computer knowledge to every aspect of the modern business world; it has also increased our need to safely store the data we are now creating at a rate never experienced before. Delivery and Adoption of Cloud Computing Services in Contemporary Organizations brings together the best practices for storing massive amounts of data. Highlighting ways cloud services can work effectively in production and in real time, this book is an essential reference source for professionals and academics of various disciplines, such as computer science, consulting, information technology, information and communication sciences, healthcare, and finance.
Categories: Computers

Cancer Genomics

Cancer Genomics

A number of services like Amazon Elastic Compute Cloud (EC2) or Windows Azure allow access to whole servers or “virtual machines” that can be customized based on the user's computing requirements. Like the cloud for storing personal ...

Author: Matthew Parker

Publisher: Elsevier Inc. Chapters

ISBN: 9780128061077

Category: Medical

Page: 510

View: 527

The vast amount of genomic data being produced by the research community is becoming readily accessible to biomedical researchers and clinicians to apply to their cancer(s) of interest. The major cancer genome projects, among others, The Cancer Genome Atlas (TCGA), the International Cancer Genome Consortium (ICGC) and the Pediatric Cancer Genome Project (PCGP) are contributing to this genomic data goldmine by sequencing hundreds to thousands of cancer genomes and supplementing these data with analyses such as gene expression and methylation. In addition to the raw data that are being made available through large data warehouses, “Data Portals” are becoming the norm for accessing and analyzing these data by third parties. We describe key features of some of these portals and other tools for the analysis of next-generation sequencing and other genomic data.
Categories: Medical

Cloud Computing

Cloud Computing

Bioinformatics platforms CloudBioLinux [56] is a publicly accessible virtual machine (VM) that is based on an Ubuntu Linux distribution and is available to all Amazon EC2 users for free. It comes with a userfriendly graphical user ...

Author: Jaydip Sen

Publisher: BoD – Books on Demand

ISBN: 9789535132431

Category: Computers

Page: 140

View: 927

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.
Categories: Computers

Cancer Genomics

Cancer Genomics

Like the cloud for storing personal data, these services are offered on a pay-as-you-go basis. Amazon EC2 ... The 1000 Genomes Project has also uploaded all current data (1700 genomes) to the Amazon cloud as a free public dataset.

Author: Graham Dellaire

Publisher: Academic Press

ISBN: 9780123972743

Category: Medical

Page: 510

View: 894

Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics. Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.
Categories: Medical

Predictive Computing and Information Security

Predictive Computing and Information Security

TCGA on AWS: Raw and processed genomic, transcriptomic and epigenomic data from The Cancer Genome Atlas (TCGA) available to qualified researchers via the Cancer Genomics Cloud. • ICGC on AWS: Whole genome sequence data available to ...

Author: P.K. Gupta

Publisher: Springer

ISBN: 9789811051074

Category: Computers

Page: 162

View: 956

This book describes various methods and recent advances in predictive computing and information security. It highlights various predictive application scenarios to discuss these breakthroughs in real-world settings. Further, it addresses state-of-art techniques and the design, development and innovative use of technologies for enhancing predictive computing and information security. Coverage also includes the frameworks for eTransportation and eHealth, security techniques, and algorithms for predictive computing and information security based on Internet-of-Things and Cloud computing. As such, the book offers a valuable resource for graduate students and researchers interested in exploring predictive modeling techniques and architectures to solve information security, privacy and protection issues in future communication.
Categories: Computers

Machine Learning and Systems Biology in Genomics and Health

Machine Learning and Systems Biology in Genomics and Health

This cloud-based AI technology was first used for lung cancer patients to provide the correct treatment. ... 9.8.3.4 Amazon Web Services AWS in short is a subsidiary of Amazon that provides cloud computing services and application ...

Author: Shailza Singh

Publisher: Springer Nature

ISBN: 9789811659935

Category: Bioinformatics

Page:

View: 234

This book discusses the application of machine learning in genomics. Machine Learning offers ample opportunities for Big Data to be assimilated and comprehended effectively using different frameworks. Stratification, diagnosis, classification and survival predictions encompass the different health care regimes representing unique challenges for data pre-processing, model training, refinement of the systems with clinical implications. The book discusses different models for in-depth analysis of different conditions. Machine Learning techniques have revolutionized genomic analysis. Different chapters of the book describe the role of Artificial Intelligence in clinical and genomic diagnostics. It discusses how systems biology is exploited in identifying the genetic markers for drug discovery and disease identification. Myriad number of diseases whether be infectious, metabolic, cancer can be dealt in effectively which combines the different omics data for precision medicine. Major breakthroughs in the field would help reflect more new innovations which are at their pinnacle stage. This book is useful for researchers in the fields of genomics, genetics, computational biology and bioinformatics.
Categories: Bioinformatics

Public Private Partnerships as Drivers of Innovation in Healthcare 2nd Edition

Public Private Partnerships as Drivers of Innovation in Healthcare  2nd Edition

... TCGA are also stored and released through AWS. The ICGC and TCGA have collected, stored, analyzed, and released data from 10,000 genomes. ... The CGC is the academic partner, and AWS is the commercial partner in this hybrid cloud.

Author: Hilde Stevens

Publisher: Frontiers Media SA

ISBN: 9782889639458

Category:

Page: 107

View: 557

Multi-stakeholder collaborations involving partners from public and private sectors are essential to address global health challenges and to move precision medicine forward. This eBook assembles a collection of papers which either illustrate recent achievements or discuss new perspectives offered by public-private partnerships in healthcare. Publisher’s note: In this 2nd edition, the following article has been added: Laverty H and Meulien P (2019) The Innovative Medicines Initiative −10 Years of Public-Private Collaboration. Front. Med. 6:275. doi: 10.3389/fmed.2019.00275
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