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Book Description

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.

Table of Contents

  1. Front cover
  2. Notices
    1. Trademarks
  3. Preface
    1. Authors
    2. Now you can become a published author, too
      1. Comments welcome
      2. Stay connected to IBM Redbooks
  4. Chapter 1. Trends and challenges for precision medicine
    1. 1.1 New trend: The era of precision medicine
    2. 1.2 Challenges
      1. 1.2.1 Data management challenges
      2. 1.2.2 Other data challenges
  5. Chapter 2. The journey of the reference architecture
    1. 2.1 The history of IBM Reference Architecture
      1. 2.1.1 First-generation reference architecture
      2. 2.1.2 Second-generation reference architecture
    2. 2.2 Overview of IBM Reference Architecture for High Performance Data and AI
      1. 2.2.1 Challenges
      2. 2.2.2 The solution
      3. 2.2.3 Key values
    3. 2.3 Datahub for High-Performance Data Analytics
      1. 2.3.1 Datahub functions
      2. 2.3.2 Datahub solution and use cases
    4. 2.4 Orchestrator of High-Performance Data Analytics
      1. 2.4.1 Orchestrator functions
      2. 2.4.2 Orchestrator solution and use cases
  6. Chapter 3. Deployment model
    1. 3.1 Composable genomics blueprint
    2. 3.2 IBM Software-Defined Infrastructure
    3. 3.3 Multicloud deployment model
      1. 3.3.1 Clouds over the ocean
  7. Chapter 4. Building blocks
    1. 4.1 IBM Spectrum Storage
      1. 4.1.1 IBM Spectrum Scale
      2. 4.1.2 IBM Spectrum Archive
      3. 4.1.3 IBM Cloud Object Storage
      4. 4.1.4 IBM Spectrum Discover
    2. 4.2 IBM Spectrum Computing
      1. 4.2.1 IBM Spectrum LSF Suite
      2. 4.2.2 IBM Spectrum Conductor
    3. 4.3 IBM Power System AC922 for HPC
      1. 4.3.1 Accelerated computing with IBM POWER9 processor-based systems
      2. 4.3.2 OpenPOWER Foundation
      3. 4.3.3 OpenPOWER processors
      4. 4.3.4 Recent advancements
      5. 4.3.5 Applications
  8. Chapter 5. Use cases
    1. 5.1 The Broad Institute Genome Analysis Toolkit (GATK)
    2. 5.2 Expanding IBM Reference Architecture for High-Performance Data Analytics into medical imaging
      1. 5.2.1 Harnessing AI to transform diagnosis and treatment of brain cancer
      2. 5.2.2 Pushing the boundaries of traditional medicine
      3. 5.2.3 Diving into deep learning
      4. 5.2.4 Giving physicians the tools to excel
  9. Chapter 6. Case studies
    1. 6.1 Sidra Medicine
      1. 6.1.1 About Sidra
      2. 6.1.2 The Qatar Genome Project focuses on population health and better treatments
      3. 6.1.3 Personalized medical advances depend on having a unified view
      4. 6.1.4 Converging high-performance computing, big data, and cognitive computing
      5. 6.1.5 Why cognitive computing and IBM
      6. 6.1.6 A collaboration
      7. 6.1.7 Software-defined infrastructure for all data and workloads
      8. 6.1.8 Faster results with scalability, reliability, and speed
      9. 6.1.9 Adding big data and cognitive computing to high-performance computing
      10. 6.1.10 Future
    2. 6.2 Amsterdam UMC
      1. 6.2.1 Customer background
      2. 6.2.2 Business challenge
      3. 6.2.3 Transformation
      4. 6.2.4 Business benefits
      5. 6.2.5 Solution components
    3. 6.3 L7 Informatics
      1. 6.3.1 Customer background
      2. 6.3.2 Business challenge
      3. 6.3.3 Transformation
      4. 6.3.4 Business benefits
      5. 6.3.5 Solution components
    4. 6.4 University of Birmingham
      1. 6.4.1 Customer background
      2. 6.4.2 Business challenge
      3. 6.4.3 Transformation
      4. 6.4.4 Business benefits
      5. 6.4.5 Solution components
    5. 6.5 Thomas Jefferson University
      1. 6.5.1 Customer background
      2. 6.5.2 Business challenge
      3. 6.5.3 Transformation
      4. 6.5.4 Business benefits
      5. 6.5.5 Solution components
    6. 6.6 Biotechnology and Biomedicine Center of the Czech Academy of Sciences and Charles University: BIOCEV
      1. 6.6.1 Customer background
      2. 6.6.2 Business challenge
      3. 6.6.3 Transformation
      4. 6.6.4 Business benefits
      5. 6.6.5 Solution components
    7. 6.7 Washington University St. Louis and Vanderbilt University
      1. 6.7.1 Customer background
      2. 6.7.2 Business challenge
      3. 6.7.3 Transformation
      4. 6.7.4 Business benefits
      5. 6.7.5 Solution components
  10. Appendix A. Profiling GATK
  11. Related publications
    1. IBM Redbooks
    2. Online resources
    3. Help from IBM
  12. Back cover
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