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E-raamat: Introduction to Bioinformatics and Clinical Scientific Computing

  • Formaat: 404 pages
  • Ilmumisaeg: 19-Dec-2022
  • Kirjastus: CRC Press
  • Keel: eng
  • ISBN-13: 9781000809664
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Introduction to Bioinformatics and Clinical Scientific ComputingSuurem pilt
  • Formaat: 404 pages
  • Ilmumisaeg: 19-Dec-2022
  • Kirjastus: CRC Press
  • Keel: eng
  • ISBN-13: 9781000809664
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This textbook provides an introduction to computer science theory, informatics best practice, and the standards and legislation that apply to computing in a healthcare environment.

It delivers an accessible discussion of databases (construction, interrogation and maintenance); networking (design and low-level application); programming (best practice rather than the specifics of any one language design, maintenance, safety).

It can be used to accompany the NHS Modernising Scientific Careers syllabus. It is also targeted towards those creating software rather than those using it, particularly computer scientists working in healthcare, specifically those in or close to the Physical Sciences, including radiotherapy, nuclear medicine, and equipment management and those working with genomics and health informatics.

Features











Combines all topics into one comprehensive introduction.





Explores practical applications of theory to healthcare.





Can be used to accompany the NHS Modernising Scientific Careers syllabus.
Acknowledgements xiv
Chapter 1 Data Structures
1(20)
1.1 Introduction
1(1)
1.2 Arrays
1(7)
1.3 Stack or Heap
8(3)
1.4 Queue
11(2)
1.5 Linked List
13(5)
1.6 Binary Tree
18(3)
Notes
19(2)
Chapter 2 Databases
21(28)
2.1 Introduction
21(1)
2.2 Terminology
22(1)
2.3 The Goals of Database Design
23(1)
2.4 Example
24(1)
2.5 More Terminology
24(2)
2.6 Example - Making the Design More Efficient
26(3)
2.7 Fourth and Fifth Normal Form
29(4)
2.8 Many-to-Many Relationships
33(1)
2.9 Distributed Relational Systems and Data Replication
33(2)
2.10 Columnstore and Data Warehousing
35(3)
2.11 OLAP Cubes
38(2)
2.12 Star Schema
40(1)
2.13 Database Standards and Standards for Interoperability and Integration
41(8)
2.13.1 Database Naming Conventions
42(1)
2.13.2 Data Administration Standards
43(1)
2.13.3 Database Administration Standards
44(1)
2.13.4 System Administration Standards
44(1)
2.13.5 Database Application Development Standards
44(1)
2.13.6 Database Security Standards
45(1)
2.13.7 Application Migration and Turnover Procedures
45(1)
2.13.8 Operational Support Standards
46(1)
Notes
46(1)
References
47(2)
Chapter 3 SQL
49(54)
3.1 Introduction
49(1)
3.2 Common Commands: SELECT, INSERT, UPDATE and DELETE
49(4)
3.3 Some Useful Commands/Functions
53(1)
3.4 SELECT Modifiers
53(21)
3.4.1 MySQL 8.0
74(1)
3.5 Create/Alter Table
74(4)
3.6 Indexes
78(2)
3.7 Privileges
80(4)
3.8 Loading Large Data Sets
84(1)
3.9 Stored Routines
85(3)
3.10 Triggers
88(2)
3.11 Columnstore
90(1)
3.12 Concurrency Control and Transaction Management
91(4)
3.13 Database Performance Tuning
95(3)
3.14 Hints and Tips
98(5)
3.14.1 Naming Standards
98(1)
3.14.2 Data Types
98(1)
3.14.3 In Code
98(1)
3.14.4 Documentation
98(1)
3.14.5 Normalization and Referential Integrity
99(1)
3.14.6 Maintenance: Run Periodic Scripts to Find
99(1)
3.14.7 Be Good
99(1)
Notes
99(2)
References
101(2)
Chapter 4 Data Mining
103(18)
4.1 Introduction
103(2)
4.2 Pre-Processing
105(1)
4.3 Data Mining
105(13)
4.3.1 Some Data-Mining Methods
109(1)
4.3.1.1 Decision Trees and Rules
109(1)
4.3.1.2 Nonlinear Regression and Classification Methods
110(1)
4.3.1.3 Example-Based Methods
111(1)
4.3.1.4 Probabilistic Graphic Dependency Models
112(1)
4.3.1.5 Principal Component Analysis (PCA)
113(3)
4.3.1.6 Neural Networks
116(2)
4.4 Data Mining Models in Healthcare
118(1)
4.5 Results Validation
118(1)
4.6 Software
119(2)
Notes
119(1)
References
119(2)
Chapter 5 Data Analysis and Presentation
121(22)
5.1 Introduction
121(1)
5.2 Appropriate Methods and Tools
121(1)
5.3 Interpretation of Results
122(1)
5.4 Presentation of Results
123(1)
5.5 Quality Indicators
123(1)
5.6 Graphical Presentation
124(3)
5.7 Standards
127(1)
5.8 Commercial Software: Excel
127(11)
5.8.1 Charts
127(11)
5.9 Blinded with Science
138(5)
Notes
140(1)
References
141(2)
Chapter 6 Boolean Algebra
143(10)
6.1 Introduction
143(1)
6.2 Notation
143(1)
6.3 Truth Tables
143(1)
6.4 Algebraic Rules
144(2)
6.5 Logical Functions
146(1)
6.5.1 Functions of One Variable
146(1)
6.5.2 Functions of Two Variables
146(1)
6.6 Simplification of Logical Expressions
147(1)
6.7 A Slight Detour into NAND and NOR
148(1)
6.8 Karnaugh Maps
149(2)
6.9 Using Boolean Algebra in Forming and Validating Queries
151(1)
6.10 Binary and Masking
151(2)
Notes
152(1)
References
152(1)
Chapter 7 NoSQL
153(10)
7.1 Introduction
153(2)
7.1.1 Strengths
155(1)
7.1.2 Weaknesses
155(1)
7.2 Document Storage
155(3)
7.3 GraphDB
158(3)
7.4 Conclusions
161(2)
Notes
161(2)
Chapter 8 Network Architecture
163(42)
8.1 Introduction
163(1)
8.2 Networking and the Network Environment
163(7)
8.2.1 The Network Packet
163(1)
8.2.2 Hardware - Hub, Switch, Router, Firewall
164(2)
8.2.3 Network Topologies
166(4)
8.3 Cabling Infrastructure
170(3)
8.4 IP Addressing and DNS
173(3)
8.4.1 IP Mask
173(2)
8.4.2 Ports
175(1)
8.5 IP Routing Tables
176(5)
8.5.1 IP Routing Table Entry Types
176(1)
8.5.2 Route Determination Process
177(1)
8.5.3 Example Routing Table for Windows 2000
178(1)
8.5.4 Static, Dynamic and Reserved IPs
179(1)
8.5.4.1 Two Devices with the Same IP Address
180(1)
8.5.5 Where Is Your Data?
180(1)
8.6 Connecting Medical Devices to the Hospital Network
181(3)
8.6.1 Firewalls
182(1)
8.6.2 Bandwidth
183(1)
8.7 Infrastructure
184(1)
8.8 The OSI 7-layer Model
184(2)
8.9 Scalability
186(3)
8.9.1 RIP
187(1)
8.9.2 OSPF
187(1)
8.9.3 Intermediate System to Intermediate System (IS-IS)
188(1)
8.9.4 EIGRP
188(1)
8.10 Web Services: Introduction
189(1)
8.11 Web Services: Representational State Transfer (REST)
190(4)
8.11.1 Client-Server Architecture
191(1)
8.11.2 Statelessness
191(1)
8.11.3 Cacheability
191(1)
8.11.4 Layered System
191(1)
8.11.5 Code on Demand
191(1)
8.11.6 Uniform Interface
191(1)
8.11.6.1 Resource Identification in Requests
192(1)
8.11.6.2 Resource Manipulation through Representations
192(1)
8.11.6.3 Self-Descriptive Messages
192(1)
8.11.6.4 Hypermedia as the Engine of Application State (HATEOAS)
192(1)
8.11.7 Relationship between URL and HTTP Methods
193(1)
8.12 Web Services: Simple Object Access Protocol (SOAP)
194(3)
8.13 Web Services and the Service Web
197(1)
8.14 SOAP Messages
198(7)
Notes
200(3)
References
203(2)
Chapter 9 Storage Services
205(6)
9.1 Introduction
205(1)
9.2 Virtual Environments
205(2)
9.3 Cloud Computing
207(1)
9.4 Security and Governance for Cloud Services
208(3)
Notes
209(1)
References
209(2)
Chapter 10 Encryption
211(6)
10.1 Introduction
211(1)
10.2 Encryption
211(6)
10.2.1 Ciphers and Cryptography
211(1)
10.2.2 RSA and PGP Encryption
212(1)
10.2.3 Steganography, Checksums and Digital Signatures
213(1)
Notes
214(1)
References
215(2)
Chapter 11 Web Programming
217(24)
11.1 Introduction
217(1)
11.2 Strategies for Web Development
217(1)
11.2.1 Design Style
218(1)
11.3 HTML
218(4)
11.3.1 Static HTML
219(3)
11.4 Style Sheets - CSS
222(4)
11.4.1 The Class Selector
224(1)
11.4.2 Applying a Style Sheet
225(1)
11.4.3 Multiple Style Sheets
226(1)
11.5 Dynamic HTML - Forms
226(1)
11.6 Dynamic HTML - JavaScript
227(3)
11.7 Dynamic HTML - CGI
230(1)
11.8 Server- and Client-Side Architecture
231(1)
11.9 Server Files
232(1)
11.10 Limiting Access
233(1)
11.11 Interfacing with a Database
234(1)
11.12 Privacy and Security
235(6)
11.12.1 Web Sessions
237(1)
11.12.2 Cookies
238(1)
Notes
239(1)
References
240(1)
Chapter 12 Data Exchange
241(30)
12.1 Introduction
241(1)
12.2 Parity and Hamming Codes
241(3)
12.2.1 Decide on the Number of Bits in the Codeword
242(1)
12.2.2 Determine the Bit Positions of the Check Bits
242(1)
12.2.3 Determine Which Parity Bits Check Which Positions
242(1)
12.2.4 Calculate the Values of the Parity Bits
243(1)
12.2.5 Using the Codeword to Correct an Error
243(1)
12.3 JSON and XML
244(2)
12.4 DICOM
246(15)
12.4.1 Images as Data
247(1)
12.4.2 Information Entities
248(1)
12.4.3 Information Object Definitions
249(2)
12.4.4 Attributes
251(1)
12.4.4.1 Value Representations
252(1)
12.4.4.2 Sequence Attributes
252(2)
12.4.4.3 Private Attributes
254(1)
12.4.4.4 Unique Identifiers
255(1)
12.4.4.5 Attribute Example: Orientation
256(2)
12.4.5 Standard Orientations
258(1)
12.4.6 DICOM Associations
259(1)
12.4.7 DICOM-RT
259(2)
12.5 HL7 (Health Level Seven)
261(5)
12.6 Fast Healthcare Interoperability Resources (FHIR)
266(5)
Notes
267(2)
References
269(2)
Chapter 13 Hospital Information Systems and Interfaces
271(6)
13.1 Introduction
271(1)
13.2 Data Retention
271(1)
13.3 Hospital Information Systems and Interfaces
271(1)
13.4 Equipment Management Database Systems
272(1)
13.5 Device Tracking Systems
273(2)
13.6 Interfaces
275(2)
Notes
275(1)
References
275(2)
Chapter 14 Backup
277(4)
14.1 Introduction
277(1)
14.2 Replication
277(1)
14.3 Archiving
278(1)
14.4 Resilience Using RAID
278(2)
14.5 Business Continuity
280(1)
Notes
280(1)
Reference
280(1)
Chapter 15 Software Engineering
281(34)
15.1 Introduction
281(1)
15.2 Software
282(5)
15.2.1 Operating Systems
282(1)
15.2.1.1 Microsoft Windows
282(1)
15.2.1.2 Unix
283(1)
15.2.1.3 Linux
283(1)
15.2.1.4 iOS/macOS
284(1)
15.2.1.5 General
284(1)
15.2.1.6 Paradigms
285(2)
15.3 The Software Lifecycle
287(15)
15.3.1 Requirements Specification: Gathering and Analysing User Requirements
288(3)
15.3.2 Software Design
291(1)
15.3.3 Coding
292(2)
15.3.4 Testing
294(6)
15.3.4.1 Acceptance Testing
300(1)
15.3.5 Installation and Maintenance
301(1)
15.4 Software Lifecycle Models
302(4)
15.4.1 Waterfall Model
302(1)
15.4.2 Incremental Model/Prototyping Model
302(2)
15.4.3 Spiral Model
304(1)
15.4.4 Agile Methodology
304(2)
15.5 Overview of Process Models and Their Importance
306(3)
15.5.1 Comparison of Process Models
307(1)
15.5.1.1 Joint Application Development
307(1)
15.5.1.2 Assembling Reusable Components
308(1)
15.5.1.3 Application Generation
309(1)
15.6 Systems Design Methods
309(6)
15.6.1 Top-Down Example
311(2)
Notes
313(1)
References
314(1)
Chapter 16 Software Quality Assurance
315(34)
16.1 Introduction
315(4)
16.1.1 Attributes
315(1)
16.1.2 Configuration Management and Change Control
316(1)
16.1.3 Documentation
316(1)
16.1.4 Hungarian Notation
317(1)
16.1.5 Comments
318(1)
16.2 Version Control
319(1)
16.3 Software Tools and Automation for Testing
320(6)
16.3.1 Record and Playback
322(1)
16.3.2 Web Testing
322(1)
16.3.3 Database Tests
322(1)
16.3.4 Data Functions
323(1)
16.3.5 Object Mapping
323(1)
16.3.6 Image Testing
324(1)
16.3.7 Test/Error Recovery
324(1)
16.3.8 Object Name Map
324(1)
16.3.9 Object Identity Tool
324(1)
16.3.10 Extensible Language
325(1)
16.3.11 Environment Support
325(1)
16.3.12 Integration
325(1)
16.4 Standards
326(17)
16.4.1 IEC601
326(1)
16.4.2 The Medical Devices Directive
327(3)
16.4.3 The Medical Devices Regulations
330(5)
16.4.3.1 Scripts
335(1)
16.4.3.2 Brexit
336(1)
16.4.4 CE Marking
337(1)
16.4.5 Other Standards
338(1)
16.4.6 Process Standards
339(2)
16.4.6.1 ISO/IEC 62366-1: 2015 Medical Devices - Part 1: Application of Usability Engineering to Medical Devices
341(1)
16.4.6.2 ISO 14971:2012 Application of Risk Management to Medical Devices
341(1)
16.4.6.3 IEC 62304:2006/Al:2015 Medical Device Software - Lifecycle Processes
341(1)
16.4.6.4 ISO 13485: 2016 Medical Devices - Quality Management Systems - Requirements for Regulatory Purposes
342(1)
16.4.7 Coding Standards
342(1)
16.4.8 Standards and Guidelines Issued by Professional Bodies
343(1)
16.5 Market
343(6)
Notes
344(2)
References
346(3)
Chapter 17 Project Management
349(16)
17.1 Introduction
349(1)
17.2 Starting Off
350(2)
17.3 Keeping It Going - Managing the Project
352(1)
17.4 Stopping (The Hard Bit)
352(4)
17.5 Risk Management
356(1)
17.6 Team Management (Personnel and Technical)
356(1)
17.7 Project Planning (Resource and Technical)
357(3)
17.7.1 Quantifying the Resource Requirements: Labour
359(1)
17.7.2 Constructing a Resource Schedule
360(1)
17.8 Education and Training
360(1)
17.9 Cost Estimation
361(4)
17.9.1 Tactical versus Strategic Purchasing Decisions
362(1)
Notes
362(1)
References
363(2)
Chapter 18 Safety Cases
365(10)
18.1 Introduction
365(1)
18.2 The Purpose of a Safety Case
365(1)
18.3 The Structure of a Safety Case
366(3)
18.3.1 Claims
366(1)
18.3.2 Evidence
366(1)
18.3.3 Argument
366(1)
18.3.4 Inference
367(1)
18.3.5 The GSN Diagram
368(1)
18.4 Implementation of a Safety Case
369(1)
18.5 Design for Assessment
370(1)
18.6 The Safety Case Lifecycle
370(1)
18.7 The Contents of a Safety Case
370(1)
18.8 Hazard Log
371(4)
18.8.1 The Therac-25 Incident
372(2)
Notes
374(1)
References
374(1)
Chapter 19 Critical Path Analysis
375(6)
19.1 Introduction
375(1)
19.2 Planning Stage
375(2)
19.3 Analysis Stage
377(1)
19.3.1 The Forward Pass
377(1)
19.3.2 The Backward Pass
377(1)
19.3.3 Float
378(1)
19.4 Scheduling
378(1)
19.5 Control Stage
379(2)
Note
379(2)
Appendix 381(1)
List of Abbreviations 381(6)
Index 387
Paul Ganney has had a long career in the world of Medical Physics, always with Scientific Computing at its heart. He has been Head of Scientific Computing at two NHS Trusts (Hull and East Yorkshire and University College London), has lectured at Liverpool University, Hull University and Kings College London. Now mostly retired, he still writes articles and software as required.
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