Introduction to Bioinformatics and Clinical Scientific Computing

405 Pages·2022·19.067 MB·English

by  Paul S. Ganney

Introduction to Bioinformatics and
Clinical Scientific Computing
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 and
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 man-
agement and those working with genomics and health informatics.
There is an accompanying website (https://www.routledge.com/9781032324135)
from which one can download some of the code referred to in the text, as well as
colour versions of some of the images in colour.
Paul S. 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) and has lec-
tured at Liverpool University, Hull University and Kings College London. Now
mostly retired, he still writes articles and software as required.

Introduction to
Bioinformatics and Clinical
Scientific Computing
Paul S. Ganney
Cover image: spainter_vfx/Shutterstock
First edition published 2023
by CRC Press
6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742
and by CRC Press
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© 2023 Paul S. Ganney
CRC Press is an imprint of Informa UK Limited
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ISBN: 978-1-032-32413-5 (hbk)
ISBN: 978-1-032-32693-1 (pbk)
ISBN: 978-1-003-31624-4 (ebk)
DOI: 10.1201/9781003316244
Typeset in Times
by SPi Technologies India Pvt Ltd (Straive)
Access the companion website: https://www.routledge.com/9781032324135
Contents
Acknowledgements .................................................................................................xiv
Chapter 1 Data Structures .....................................................................................1
1.1 Introduction ...............................................................................1
1.2 Arrays ........................................................................................1
1.3 Stack or Heap ............................................................................8
1.4 Queue .......................................................................................11
1.5 Linked List ...............................................................................13
1.6 Binary Tree ..............................................................................18
Notes ...................................................................................................19
Chapter 2 Databases ............................................................................................21
2.1 Introduction .............................................................................21
2.2 Terminology.............................................................................22
2.3 The Goals of Database Design ................................................23
2.4 Example ...................................................................................24
2.5 More Terminology ...................................................................24
2.6 Example – Making the Design More Efficient ........................26
2.7 Fourth and Fifth Normal Form ................................................29
2.8 Many-to-Many Relationships ..................................................33
2.9 Distributed Relational Systems and Data Replication .............33
2.10 Columnstore and Data Warehousing .......................................35
2.11 OLAP Cubes ............................................................................38
2.12 Star Schema .............................................................................40
2.13 Database Standards and Standards for Interoperability
and Integration .........................................................................41
2.13.1 Database Naming Conventions ..................................42
2.13.2 Data Administration Standards ...................................43
2.13.3 Database Administration Standards............................44
2.13.4 System Administration Standards ..............................44
2.13.5 Database Application Development Standards ..........44
2.13.6 Database Security Standards ......................................45
2.13.7 Application Migration and Turnover Procedures .......45
2.13.8 Operational Support Standards ...................................46
Notes ...................................................................................................46
References ..........................................................................................47
Chapter 3 SQL ....................................................................................................49
3.1 Introduction .............................................................................49
3.2 Common Commands: SELECT, INSERT, UPDATE and
DELETE ..................................................................................49
v
vi Contents
3.3 Some Useful Commands/Functions ........................................53
3.4 SELECT Modifiers ..................................................................53
3.4.1 MySQL 8.0 .................................................................74
3.5 Create/Alter Table ....................................................................74
3.6 Indexes .....................................................................................78
3.7 Privileges .................................................................................80
3.8 Loading Large Data Sets .........................................................84
3.9 Stored Routines .......................................................................85
3.10 Triggers ....................................................................................88
3.11 Columnstore ............................................................................90
3.12 Concurrency Control and Transaction Management ...............91
3.13 Database Performance Tuning .................................................95
3.14 Hints and Tips ..........................................................................98
3.14.1 Naming Standards ......................................................98
3.14.2 Data Types ..................................................................98
3.14.3 In Code .......................................................................98
3.14.4 Documentation ...........................................................98
3.14.5 Normalization and Referential Integrity .....................99
3.14.6 Maintenance: Run Periodic Scripts to Find ................99
3.14.7 Be Good ......................................................................99
Notes ...................................................................................................99
References ........................................................................................101
Chapter 4 Data Mining ......................................................................................103
4.1 Introduction ...........................................................................103
4.2 Pre-Processing .......................................................................105
4.3 Data Mining ...........................................................................105
4.3.1 Some Data-Mining Methods ....................................109
4.3.1.1 Decision Trees and Rules ..........................109
4.3.1.2 Nonlinear Regression and
Classification Methods ..............................110
4.3.1.3 Example-Based Methods ..........................111
4.3.1.4 Probabilistic Graphic Dependency
Models ......................................................112
4.3.1.5 Principal Component Analysis (PCA) ......113
4.3.1.6 Neural Networks .......................................116
4.4 Data Mining Models in Healthcare .......................................118
4.5 Results Validation ..................................................................118
4.6 Software .................................................................................119
Notes .................................................................................................119
References ........................................................................................119
Chapter 5 Data Analysis and Presentation ........................................................121
5.1 Introduction ...........................................................................121
5.2 Appropriate Methods and Tools ............................................121
Contents vii
5.3 Interpretation of Results ........................................................122
5.4 Presentation of Results ..........................................................123
5.5 Quality Indicators ..................................................................123
5.6 Graphical Presentation ...........................................................124
5.7 Standards ...............................................................................127
5.8 Commercial Software: Excel .................................................127
5.8.1 Charts .......................................................................127
5.9 Blinded with Science .............................................................138
Notes .................................................................................................140
References ........................................................................................141
Chapter 6 Boolean Algebra ...............................................................................143
6.1 Introduction ...........................................................................143
6.2 Notation .................................................................................143
6.3 Truth Tables ...........................................................................143
6.4 Algebraic Rules .....................................................................144
6.5 Logical Functions ..................................................................146
6.5.1 Functions of One Variable ........................................146
6.5.2 Functions of Two Variables ......................................146
6.6 Simplification of Logical Expressions ...................................147
6.7 A Slight Detour into NAND and NOR ..................................148
6.8 Karnaugh Maps .....................................................................149
6.9 Using Boolean Algebra in Forming and
Validating Queries .................................................................151
6.10 Binary and Masking ..............................................................151
Notes .................................................................................................152
References ........................................................................................152
Chapter 7 NoSQL .............................................................................................153
7.1 Introduction ...........................................................................153
7.1.1 Strengths ...................................................................155
7.1.2 Weaknesses ...............................................................155
7.2 Document Storage .................................................................155
7.3 GraphDB ................................................................................158
7.4 Conclusions ...........................................................................161
Notes .................................................................................................161
Chapter 8 Network Architecture .......................................................................163
8.1 Introduction ...........................................................................163
8.2 Networking and the Network Environment ...........................163
8.2.1 The Network Packet .................................................163
8.2.2 Hardware – Hub, Switch, Router, Firewall ..............164
8.2.3 Network Topologies .................................................166
viii Contents
8.3 Cabling Infrastructure ............................................................170
8.4 IP Addressing and DNS .........................................................173
8.4.1 IP Mask ....................................................................173
8.4.2 Ports ..........................................................................175
8.5 IP Routing Tables ..................................................................176
8.5.1 IP Routing Table Entry Types...................................176
8.5.2 Route Determination Process ...................................177
8.5.3 Example Routing Table for Windows 2000 .............178
8.5.4 Static, Dynamic and Reserved IPs ...........................179
8.5.4.1 Two Devices with the Same
IP Address .................................................180
8.5.5 Where Is Your Data? .................................................180
8.6 Connecting Medical Devices to the Hospital Network .........181
8.6.1 Firewalls ...................................................................182
8.6.2 Bandwidth ................................................................183
8.7 Infrastructure .........................................................................184
8.8 The OSI 7-layer Model ..........................................................184
8.9 Scalability ..............................................................................186
8.9.1 RIP ............................................................................187
8.9.2 OSPF ........................................................................187
8.9.3 Intermediate System to Intermediate
System (IS-IS) ..........................................................188
8.9.4 EIGRP ......................................................................188
8.10 Web Services: Introduction ...................................................189
8.11 Web Services: Representational State Transfer (REST) ........190
8.11.1 Client-Server Architecture ........................................191
8.11.2 Statelessness .............................................................191
8.11.3 Cacheability ..............................................................191
8.11.4 Layered System ........................................................191
8.11.5 Code on Demand ......................................................191
8.11.6 Uniform Interface .....................................................191
8.11.6.1 Resource Identification in Requests ........192
8.11.6.2 Resource Manipulation through
Representations .......................................192
8.11.6.3 Self-Descriptive Messages ......................192
8.11.6.4 Hypermedia as the Engine of
Application State (HATEOAS) ...............192
8.11.7 Relationship between URL and HTTP Methods ......193
8.12 Web Services: Simple Object Access Protocol (SOAP) ........194
8.13 Web Services and the Service Web ........................................197
8.14 SOAP Messages.....................................................................198
Notes .................................................................................................200
References ........................................................................................203
Contents ix
Chapter 9 Storage Services ...............................................................................205
9.1 Introduction ...........................................................................205
9.2 Virtual Environments .............................................................205
9.3 Cloud Computing ..................................................................207
9.4 Security and Governance for Cloud Services ........................208
Notes .................................................................................................209
References ........................................................................................209
Chapter 10 Encryption ........................................................................................211
10.1 Introduction ...........................................................................211
10.2 Encryption .............................................................................211
10.2.1 Ciphers and Cryptography........................................211
10.2.2 RSA and PGP Encryption ........................................212
10.2.3 Steganography, Checksums and
Digital Signatures .....................................................213
Notes .................................................................................................214
References ........................................................................................215
Chapter 11 Web Programming ............................................................................217
11.1 Introduction ...........................................................................217
11.2 Strategies for Web Development ...........................................217
11.2.1 Design Style .............................................................218
11.3 HTML ....................................................................................218
11.3.1 Static HTML ............................................................219
11.4 Style Sheets – CSS ................................................................222
11.4.1 The Class Selector ....................................................224
11.4.2 Applying a Style Sheet .............................................225
11.4.3 Multiple Style Sheets ...............................................226
11.5 Dynamic HTML – Forms ......................................................226
11.6 Dynamic HTML – JavaScript ................................................227
11.7 Dynamic HTML – CGI .........................................................230
11.8 Server- and Client-Side Architecture .....................................231
11.9 Server Files ............................................................................232
11.10 Limiting Access .....................................................................233
11.11 Interfacing with a Database ...................................................234
11.12 Privacy and Security ..............................................................235
11.12.1 Web Sessions ............................................................237
11.12.2 Cookies .....................................................................238
Notes .................................................................................................239
References ........................................................................................240