Introduction to Bioinformatics and Clinical Scientific Computing

Cover
Half Title
Title Page
Copyright Page
Table of Contents
Acknowledgements
Chapter 1: Data Structures
	1.1 Introduction
	1.2 Arrays
	1.3 Stack or Heap
	1.4 Queue
	1.5 Linked List
	1.6 Binary Tree
	Notes
Chapter 2: Databases
	2.1 Introduction
	2.2 Terminology
	2.3 The Goals of Database Design
	2.4 Example
	2.5 More Terminology
	2.6 Example – Making the Design More Efficient
	2.7 Fourth and Fifth Normal Form
	2.8 Many-to-Many Relationships
	2.9 Distributed Relational Systems and Data Replication
	2.10 Columnstore and Data Warehousing
	2.11 OLAP Cubes
	2.12 Star Schema
	2.13 Database Standards and Standards for Interoperability and Integration
		2.13.1 Database Naming Conventions
		2.13.2 Data Administration Standards
		2.13.3 Database Administration Standards
		2.13.4 System Administration Standards
		2.13.5 Database Application Development Standards
		2.13.6 Database Security Standards
		2.13.7 Application Migration and Turnover Procedures
		2.13.8 Operational Support Standards
	Notes
	References
Chapter 3: SQL
	3.1 Introduction
	3.2 Common Commands: SELECT, INSERT, UPDATE and DELETE
	3.3 Some Useful Commands/Functions
	3.4 SELECT Modifiers
		3.4.1 MySQL 8.0
	3.5 Create/Alter Table
	3.6 Indexes
	3.7 Privileges
	3.8 Loading Large Data Sets
	3.9 Stored Routines
	3.10 Triggers
	3.11 Columnstore
	3.12 Concurrency Control and Transaction Management
	3.13 Database Performance Tuning
	3.14 Hints and Tips
		3.14.1 Naming Standards
		3.14.2 Data Types
		3.14.3 In Code
		3.14.4 Documentation
		3.14.5 Normalisation and Referential Integrity
		3.14.6 Maintenance: Run Periodic Scripts to Find
		3.14.7 Be Good
	Notes
	References
Chapter 4: Data Mining
	4.1 Introduction
	4.2 Pre-Processing
	4.3 Data Mining
		4.3.1 Some Data-Mining Methods
			4.3.1.1 Decision Trees and Rules
			4.3.1.2 Nonlinear Regression and Classification Methods
			4.3.1.3 Example-Based Methods
			4.3.1.4 Probabilistic Graphic Dependency Models
			4.3.1.5 Principal Component Analysis (PCA)
			4.3.1.6 Neural Networks
	4.4 Data Mining Models in Healthcare
	4.5 Results Validation
	4.6 Software
	Notes
	References
Chapter 5: Data Analysis and Presentation
	5.1 Introduction
	5.2 Appropriate Methods and Tools
	5.3 Interpretation of Results
	5.4 Presentation of Results
	5.5 Quality Indicators
	5.6 Graphical Presentation
	5.7 Standards
	5.8 Commercial Software: Excel
		5.8.1 Charts
	5.9 Blinded with Science
	Notes
	References
Chapter 6: Boolean Algebra
	6.1 Introduction
	6.2 Notation
	6.3 Truth Tables
	6.4 Algebraic Rules
	6.5 Logical Functions
		6.5.1 Functions of One Variable
		6.5.2 Functions of Two Variables
	6.6 Simplification of Logical Expressions
	6.7 A Slight Detour into NAND and NOR
	6.8 Karnaugh Maps
	6.9 Using Boolean Algebra in Forming and Validating Queries
	6.10 Binary and Masking
	Notes
	References
Chapter 7: NoSQL
	7.1 Introduction
		7.1.1 Strengths
		7.1.2 Weaknesses
	7.2 Document Storage
	7.3 GraphDB
	7.4 Conclusions
	Notes
Chapter 8: Network Architecture
	8.1 Introduction
	8.2 Networking and the Network Environment
		8.2.1 The Network Packet
		8.2.2 Hardware – Hub, Switch, Router, Firewall
		8.2.3 Network Topologies
	8.3 Cabling Infrastructure
	8.4 IP Addressing and DNS
		8.4.1 IP Mask
		8.4.2 Ports
	8.5 IP Routing Tables
		8.5.1 IP Routing Table Entry Types
		8.5.2 Route Determination Process
		8.5.3 Example Routing Table for Windows 2000
		8.5.4 Static, Dynamic and Reserved IPs
			8.5.4.1 Two Devices with the Same IP Address
		8.5.5 Where Is Your Data?
	8.6 Connecting Medical Devices to the Hospital Network
		8.6.1 Firewalls
		8.6.2 Bandwidth
	8.7 Infrastructure
	8.8 The OSI 7-Layer Model
	8.9 Scalability
		8.9.1 RIP
		8.9.2 OSPF
		8.9.3 Intermediate System to Intermediate System (IS-IS)
		8.9.4 EIGRP
	8.10 Web Services: Introduction
	8.11 Web Services: Representational State Transfer (REST)
		8.11.1 Client-Server Architecture
		8.11.2 Statelessness
		8.11.3 Cacheability
		8.11.4 Layered System
		8.11.5 Code on Demand
		8.11.6 Uniform Interface
			8.11.6.1 Resource Identification in Requests
			8.11.6.2 Resource Manipulation Through Representations
			8.11.6.3 Self-Descriptive Messages
			8.11.6.4 Hypermedia As the Engine of Application State (HATEOAS)
		8.11.7 Relationship between URL and HTTP Methods
	8.12 Web Services: Simple Object Access Protocol (SOAP)
	8.13 Web Services and the Service Web
	8.14 SOAP Messages
	Notes
	References
Chapter 9: Storage Services
	9.1 Introduction
	9.2 Virtual Environments
	9.3 Cloud Computing
	9.4 Security and Governance for Cloud Services
	Notes
	References
Chapter 10: Encryption
	10.1 Introduction
	10.2 Encryption
		10.2.1 Ciphers and Cryptography
		10.2.2 RSA and PGP Encryption
		10.2.3 Steganography, Checksums and Digital Signatures
	Notes
	References
Chapter 11: Web Programming
	11.1 Introduction
	11.2 Strategies for Web Development
		11.2.1 Design Style
	11.3 HTML
		11.3.1 Static HTML
	11.4 Style Sheets – CSS
		11.4.1 The Class Selector
		11.4.2 Applying a Style Sheet
		11.4.3 Multiple Style Sheets
	11.5 Dynamic HTML – Forms
	11.6 Dynamic HTML – JavaScript
	11.7 Dynamic HTML – CGI
	11.8 Server- and Client-Side Architecture
	11.9 Server Files
	11.10 Limiting Access
	11.11 Interfacing with a Database
	11.12 Privacy and Security
		11.12.1 Web Sessions
		11.12.2 Cookies
	Notes
	References
Chapter 12: Data Exchange
	12.1 Introduction
	12.2 Parity and Hamming Codes
		12.2.1 Decide on the Number of Bits in the Codeword
		12.2.2 Determine the Bit Positions of the Check Bits
		12.2.3 Determine which Parity Bits Check which Positions
		12.2.4 Calculate the Values of the Parity Bits
		12.2.5 Using the Codeword to Correct an Error
	12.3 JSON and XML
	12.4 DICOM
		12.4.1 Images as Data
		12.4.2 Information Entities
		12.4.3 Information Object Definitions
		12.4.4 Attributes
			12.4.4.1 Value Representations
			12.4.4.2 Sequence Attributes
			12.4.4.3 Private Attributes
			12.4.4.4 Unique Identifiers
			12.4.4.5 Attribute Example: Orientation
		12.4.5 Standard Orientations
		12.4.6 DICOM Associations
		12.4.7 DICOM-RT
	12.5 HL7 (Health Level Seven)
	12.6 Fast Healthcare Interoperability Resources (FHIR)
	Notes
	References
Chapter 13: Hospital Information Systems and Interfaces
	13.1 Introduction
	13.2 Data Retention
	13.3 Hospital Information Systems and Interfaces
	13.4 Equipment Management Database Systems
	13.5 Device Tracking Systems
	13.6 Interfaces
	Notes
	References
Chapter 14: Backup
	14.1 Introduction
	14.2 Replication
	14.3 Archiving
	14.4 Resilience using RAID
	14.5 Business Continuity
	Notes
	Reference
Chapter 15: Software Engineering
	15.1 Introduction
	15.2 Software
		15.2.1 Operating Systems
			15.2.1.1 Microsoft Windows
			15.2.1.2 Unix
			15.2.1.3 Linux
			15.2.1.4 iOS/macOS
			15.2.1.5 General
			15.2.1.6 Paradigms
	15.3 The Software Lifecycle
		15.3.1 Requirements Specification: Gathering and Analysing User Requirements
		15.3.2 Software Design
		15.3.3 Coding
		15.3.4 Testing
			15.3.4.1 Acceptance Testing
		15.3.5 Installation and Maintenance
	15.4 Software Lifecycle Models
		15.4.1 Waterfall Model
		15.4.2 Incremental Model/Prototyping Model
		15.4.3 Spiral Model
		15.4.4 Agile Methodology
	15.5 Overview of Process Models and Their Importance
		15.5.1 Comparison of Process Models
			15.5.1.1 Joint Application Development
			15.5.1.2 Assembling Reusable Components
			15.5.1.3 Application Generation
	15.6 Systems Design Methods
		15.6.1 Top-Down Example
	Notes
	References
Chapter 16: Software Quality Assurance
	16.1 Introduction
		16.1.1 Attributes
		16.1.2 Configuration Management and Change Control
		16.1.3 Documentation
		16.1.4 Hungarian Notation
		16.1.5 Comments
	16.2 Version Control
	16.3 Software Tools and Automation for Testing
		16.3.1 Record and Playback
		16.3.2 Web Testing
		16.3.3 Database Tests
		16.3.4 Data Functions
		16.3.5 Object Mapping
		16.3.6 Image Testing
		16.3.7 Test/Error Recovery
		16.3.8 Object Name Map
		16.3.9 Object Identity Tool
		16.3.10 Extensible Language
		16.3.11 Environment Support
		16.3.12 Integration
	16.4 Standards
		16.4.1 IEC 601
		16.4.2 The Medical Devices Directive
		16.4.3 The Medical Devices Regulations
			16.4.3.1 Scripts
			16.4.3.2 Brexit
		16.4.4 CE Marking
		16.4.5 Other Standards
		16.4.6 Process Standards
			16.4.6.1 ISO/IEC 62366-1: 2015 Medical Devices – Part 1: Application of Usability Engineering to Medical Devices
			16.4.6.2 ISO 14971:2012 Application of Risk Management to Medical Devices
			16.4.6.3 IEC 62304:2006/A1:2015 Medical Device Software – Lifecycle Processes
			16.4.6.4 ISO 13485: 2016 Medical Devices – Quality Management Systems – Requirements for Regulatory Purposes
		16.4.7 Coding Standards
		16.4.8 Standards and Guidelines Issued by Professional Bodies
	16.5 Market
	Notes
	References
Chapter 17: Project Management
	17.1 Introduction
	17.2 Starting Off
	17.3 Keeping It Going – Managing the Project
	17.4 Stopping (The Hard Bit)
	17.5 Risk Management
	17.6 Team Management (Personnel and Technical)
	17.7 Project Planning (Resource and Technical)
		17.7.1 Quantifying the Resource Requirements: Labour
		17.7.2 Constructing A Resource Schedule
	17.8 Education and Training
	17.9 Cost Estimation
		17.9.1 Tactical versus Strategic Purchasing Decisions
	Notes
	References
Chapter 18: Safety Cases
	18.1 Introduction
	18.2 The Purpose of a Safety Case
	18.3 The Structure of a Safety Case
		18.3.1 Claims
		18.3.2 Evidence
		18.3.3 Argument
		18.3.4 Inference
		18.3.5 The GSN Diagram
	18.4 Implementation of a Safety Case
	18.5 Design for Assessment
	18.6 The Safety Case Lifecycle
	18.7 The Contents of a Safety Case
	18.8 Hazard Log
		18.8.1 The Therac-25 Incident
	Notes
	References
Chapter 19: Critical Path Analysis
	19.1 Introduction
	19.2 Planning Stage
	19.3 Analysis Stage
		19.3.1 The Forward Pass
		19.3.2 The Backward Pass
		19.3.3 Float
	19.4 Scheduling
	19.5 Control Stage
	Note
Appendix
Index