Genomics in the Cloud: Using Docker, GATK, and WDL in Terra

Author by : Geraldine A. Van der Auwera
Languange Used : en
Release Date : 2020-04-02
Publisher by : O'Reilly Media

ISBN :

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 by : Geraldine Van der Auwera
Languange Used : en
Release Date : 2020
Publisher by :

ISBN :

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 by : Food and Agriculture Organization of the United Nations
Languange Used : en
Release Date : 2023-01-12
Publisher by : Food & Agriculture Org.

ISBN :

Description : Molecular biotechnologies have developed rapidly and substantially since the release of these previous guidelines. The livestock sector has been an active participant in the so-called “genomic revolution.” Advancements in the sequencing of genomes and related genotyping methods have created opportunities for gathering much more information on the molecular level than ever possible, at a faster rate, and for exponentially decreased costs. Scientists and other livestock stakeholders in countries with highly developed economies have been among the main beneficiaries of this revolution. However, the greatly decreased costs of genomic applications have also created opportunities in countries with developing and transitional economies. In many instances, the lack of awareness of these opportunities and in the technical capacity for the full application of genomic tools may represent a greater obstacle to their utilization than the expenses involved.The development of these guidelines and the subsequent application of the information contained herein may help to bridge this gap, bringing new opportunities to light and transferring knowledge that can be used to increase the genetic characterization of AnGR and subsequently improve the sustainable use and conservation of livestock genetic diversity....

Author by : J. Mantas
Languange Used : en
Release Date : 2022-02-25
Publisher by : IOS Press

ISBN :

Description : Data, informatics, and technology are now among the most important aspects inspiring health professionals and informaticians to improve healthcare for the benefit of patients. This book presents the proceedings of the 19th annual International Conference on Informatics, Management, and Technology in Healthcare (ICIMTH 2021), held as a virtual event due to COVID-19 pandemic restrictions on 16 and 17 October 2021 in Athens, Greece. The ICIMTH conferences are a series of scientific events which bring together scientists working in the field of biomedical and health informatics from around the world. The 2021 conference examined the field of biomedical and health informatics in a very broad framework, presenting the research and application outcomes of informatics from cell to populations, and including a number of technologies such as imaging, sensors and biomedical equipment, as well as management and organizational aspects, including legal and social issues and the setting of research priorities in health informatics. A significant number of the papers included here relate to the COVID-19 pandemic. Providing an insight into the latest developments in biomedical and health informatics, the book will be of interest to all those working in the field....

Author by : Arthur M. Lesk
Languange Used : de
Release Date : 2002-11-07
Publisher by : Spektrum Akademischer Verlag

ISBN :

Description : Bioinformatik ist eine Wissenschaftsdisziplin und ein Methodenfeld, das in der heutigen Forschung und klinischen Anwendung zu einem der wichtigsten Werkzeuge der Informationssammlung, Dateninterpretation und Wissensschaffung geworden ist. Das vorliegende Lehrbuch kommt zur rechten Zeit und erfüllt den großen Bedarf nach einer grundlegenden und sorgfältig konzipierten Einführung in diesen fundamentalen Zweig der modernen Lebenswissenschaften. Als ein Pionier der Nutzung von Bioinformatikverfahren in der Forschung bringt Arthur Lesk seine ganze Erfahrung und Fachkenntnis in diese Darstellung ein. Das Buch zielt darauf ab, ein Verständnis des biologischen Hintergrunds der Bioinformatik mit der Entwicklung der nötigen Computerfertigkeiten zu kombinieren. Ohne auf komplizierte computerwissenschaftliche Methoden oder Programmierkenntnisse angewiesen zu sein, unterstützt und ermutigt das anregend geschriebene Buch den Leser bei der adäquaten Anwendung der vielen Bioinformatikwerkzeuge. Zahlreiche Übungen und Aufgaben sowie innovative webbasierte Problemstellungen ("Webleme"/"WWW-Fragen") fordern den Studenten zur aktiven Teilnahme statt und erlauben dem Dozenten oder Kursleiter, das Material auf die spezifischen Bedürfnisse der Lernenden zuzuschneiden. Die begleitende (englischsprachige) Website des Originalverlags führt von den im Buch präsentierten Aufgaben und Programmen zu interaktiven Links und ermöglicht es dem Leser somit, ein praktisches Verständnis und Wertschätzung der Macht der Bioinformatik als Forschungswerkzeug zu entwickeln. Unter der URL www.oup.com/uk/lesk/bioinf/ sind folgende Angebote abzurufen: - Links zu allen im Buch erwähnten Websites - Grafiken in hoher Qualität einschließlich farbiger Animationen von Strukturschemata - Material aus dem Buch, das sinnvollerweise in computerlesbarer Form zur Verfügung steht, etwa Daten für die Aufgaben und Übungen sowie alle Programme...

Author by : Alexey Moskalev
Languange Used : en
Release Date : 2023-07-07
Publisher by : Springer Nature

ISBN :

Description : This book reviews the state-of-the-art efforts to apply machine learning and AI methods for healthy aging and longevity research, diagnosis, and therapy development. The book examines the methods of machine learning and their application in the analysis of big medical data, medical images, the creation of algorithms for assessing biological age, and effectiveness of geroprotective medications. The promises and challenges of using AI to help achieve healthy longevity for the population are manifold. This volume, written by world-leading experts working at the intersection of AI and aging, provides a unique synergy of these two highly prominent fields and aims to create a balanced and comprehensive overview of the application methodology that can help achieve healthy longevity for the population. The book is accessible and valuable for specialists in AI and longevity research, as well as a wide readership, including gerontologists, geriatricians, medical specialists, and students from diverse fields, basic scientists, public and private research entities, and policy makers interested in potential intervention in degenerative aging processes using advanced computational tools....

Author by : R. Röhrig
Languange Used : en
Release Date : 2023-10-19
Publisher by : IOS Press

ISBN :

Description : The Covid-19 pandemic affected the daily lives of all of us on many levels. Epidemiology suddenly became a personal matter and general interest in many aspects of medical data science became much more widespread. And physical distance became the new normal. This book presents the full paper part of the proceedings of GMDS 2023, the 68th annual meeting of the German Association for Medical Informatics, Biometry and Epidemiology, held from 17 to 21 September 2023 in Heilbronn, Germany. The theme of the conference was, Science. Close to People, a particularly appropriate theme for the first of these annual conferences to be held face-to-face since 2019. A total of 227 scientific contributions were submitted to GMDS 2023, including 41 full papers for this volume in Studies in HTI. Of these, 30 papers are included here, following a rigorous two-stage review process, which represents an acceptance rate of 73%. The 30 papers in this book are grouped under 8 headings: FAIRification; research software engineering for research infrastructure & study data management; human factors; data quality; clinical decision support & artificial intelligence; evaluation of healthcare IT; biosignals; and interoperability. Providing a broad overview of current developments in the disciplines of medical informatics, biometry and epidemiology, the book will be of interest to all those working in these fields....