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Table of Contents
Intro; Foreword; Preface; Scope of the Book; Chapter Overview; Summary; Acknowledgements; Contents; Acronyms; Part I Background; 1 Formal Model of 3D Protein Structures for Functional Genomics, Comparative Bioinformatics, and Molecular Modeling; 1.1 Introduction; 1.2 General Definition of Protein Spatial Structure; 1.3 A Reference to Representation Levels; 1.3.1 Primary Structure; 1.3.2 Secondary Structure; 1.3.3 Tertiary Structure; 1.3.4 Quaternary Structure; 1.4 Relative Coordinates of Protein Structures; 1.5 Energy Properties of Protein Structures; 1.6 Summary; References.
2 Technological Roadmap2.1 Cloud Computing; 2.1.1 Cloud Service Models; 2.1.2 Cloud Deployment Models; 2.2 Big Data Challenge; 2.2.1 The 5V Model of Big Data; 2.2.2 Hadoop Platform; 2.3 Multi-threading and Multi-threaded Applications; 2.4 Graphics Processing Units and the CUDA; 2.4.1 Graphics Processing Units; 2.4.2 CUDA Architecture and Threads; 2.5 Relational Databases and SQL; 2.5.1 Relational Database Management Systems; 2.5.2 SQL For Manipulating Relational Data; 2.6 Scalability; 2.7 Summary; References; Part II Cloud Services for Scalable Computations; 3 Azure Cloud Services.
3.1 Microsoft Azure3.2 Virtual Machines, Series, and Sizes; 3.3 Cloud Services in Action; 3.4 Summary; References; 4 Scaling 3D Protein Structure Similarity Searching with Azure Cloud Services; 4.1 Introduction; 4.1.1 Why We Need Cloud Computing in Protein Structure Similarity Searching; 4.1.2 Algorithms for Protein Structure Similarity Searching; 4.1.3 Other Cloud-Based Solutions for Bioinformatics; 4.2 Cloud4PSi for 3D Protein Structure Alignment; 4.2.1 Use Case: Interaction with the Cloud4PSi; 4.2.2 Architecture and Processing Model of the Cloud4PSi; 4.2.3 Scaling Cloud4PSi.
4.3 Scalability of the Cloud4PSi4.3.1 Horizontal Scalability; 4.3.2 Vertical Scalability; 4.3.3 Influence of the Package Size; 4.3.4 Scaling Up or Scaling Out?; 4.4 Discussion; 4.5 Summary; References; 5 Cloud Services for Efficient Ab Initio Predictions of 3D Protein Structures; 5.1 Introduction; 5.1.1 Computational Approaches for 3D Protein Structure Prediction; 5.1.2 Cloud and Grid Computing in Protein Structure Determination; 5.2 Cloud4PSP for 3D Protein Structure Prediction; 5.2.1 Prediction Method; 5.2.2 Cloud4PSP Architecture; 5.2.3 Cloud4PSP Processing Model; 5.2.4 Extending Cloud4PSP.
5.2.5 Scaling the Cloud4PSP5.3 Performance of the Cloud4PSP; 5.3.1 Vertical Scalability; 5.3.2 Horizontal Scalability; 5.3.3 Influence of the Task Size; 5.3.4 Scale Up, Scale Out, or Combine?; 5.4 Discussion; 5.5 Summary; 5.6 Availability; References; Part III Big Data Analytics in Protein Bioinformatics; 6 Foundations of the Hadoop Ecosystem; 6.1 Big Data; 6.2 Hadoop; 6.2.1 Hadoop Distributed File System; 6.2.2 MapReduce Processing Model; 6.2.3 MapReduce 1.0 (MRv1); 6.2.4 MapReduce 2.0 (MRv2); 6.3 Apache Spark; 6.4 Hadoop Ecosystem; 6.5 Summary; References.
2 Technological Roadmap2.1 Cloud Computing; 2.1.1 Cloud Service Models; 2.1.2 Cloud Deployment Models; 2.2 Big Data Challenge; 2.2.1 The 5V Model of Big Data; 2.2.2 Hadoop Platform; 2.3 Multi-threading and Multi-threaded Applications; 2.4 Graphics Processing Units and the CUDA; 2.4.1 Graphics Processing Units; 2.4.2 CUDA Architecture and Threads; 2.5 Relational Databases and SQL; 2.5.1 Relational Database Management Systems; 2.5.2 SQL For Manipulating Relational Data; 2.6 Scalability; 2.7 Summary; References; Part II Cloud Services for Scalable Computations; 3 Azure Cloud Services.
3.1 Microsoft Azure3.2 Virtual Machines, Series, and Sizes; 3.3 Cloud Services in Action; 3.4 Summary; References; 4 Scaling 3D Protein Structure Similarity Searching with Azure Cloud Services; 4.1 Introduction; 4.1.1 Why We Need Cloud Computing in Protein Structure Similarity Searching; 4.1.2 Algorithms for Protein Structure Similarity Searching; 4.1.3 Other Cloud-Based Solutions for Bioinformatics; 4.2 Cloud4PSi for 3D Protein Structure Alignment; 4.2.1 Use Case: Interaction with the Cloud4PSi; 4.2.2 Architecture and Processing Model of the Cloud4PSi; 4.2.3 Scaling Cloud4PSi.
4.3 Scalability of the Cloud4PSi4.3.1 Horizontal Scalability; 4.3.2 Vertical Scalability; 4.3.3 Influence of the Package Size; 4.3.4 Scaling Up or Scaling Out?; 4.4 Discussion; 4.5 Summary; References; 5 Cloud Services for Efficient Ab Initio Predictions of 3D Protein Structures; 5.1 Introduction; 5.1.1 Computational Approaches for 3D Protein Structure Prediction; 5.1.2 Cloud and Grid Computing in Protein Structure Determination; 5.2 Cloud4PSP for 3D Protein Structure Prediction; 5.2.1 Prediction Method; 5.2.2 Cloud4PSP Architecture; 5.2.3 Cloud4PSP Processing Model; 5.2.4 Extending Cloud4PSP.
5.2.5 Scaling the Cloud4PSP5.3 Performance of the Cloud4PSP; 5.3.1 Vertical Scalability; 5.3.2 Horizontal Scalability; 5.3.3 Influence of the Task Size; 5.3.4 Scale Up, Scale Out, or Combine?; 5.4 Discussion; 5.5 Summary; 5.6 Availability; References; Part III Big Data Analytics in Protein Bioinformatics; 6 Foundations of the Hadoop Ecosystem; 6.1 Big Data; 6.2 Hadoop; 6.2.1 Hadoop Distributed File System; 6.2.2 MapReduce Processing Model; 6.2.3 MapReduce 1.0 (MRv1); 6.2.4 MapReduce 2.0 (MRv2); 6.3 Apache Spark; 6.4 Hadoop Ecosystem; 6.5 Summary; References.