Bioinformatics programming in Python: a practical course for beginners
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Weinheim
WILEY-VCH
2008
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | IX, 418 S. Ill. |
| ISBN: | 9783527320943 3527320946 |
Internformat
MARC
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| 100 | 1 | |a Flaig, Rüdiger Marcus |d 1971- |e Verfasser |0 (DE-588)123094755 |4 aut | |
| 245 | 1 | 0 | |a Bioinformatics programming in Python |b a practical course for beginners |c Ruediger-Marcus Flaig |
| 264 | 1 | |a Weinheim |b WILEY-VCH |c 2008 | |
| 300 | |a IX, 418 S. |b Ill. | ||
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| 650 | 4 | |a Python (Computer program language) | |
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Datensatz im Suchindex
| _version_ | 1804137254344458240 |
|---|---|
| adam_text | Contents
Chapter 1. Preface 1
1.1 An axe in the house is worth a carpenter: why Computers matter
in the life sciences 1
1.2 What this book is (not) about 3
1.3 A few practical hints 5
1.4 From the heart 5
1.5 Structure of the book 6
1.6 Sources 7
1.7 Author and acknowledgements 8
1.8 Somebody Special... 8
Part 1. EARTH 9
Chapter 2. A Classification of Programming Languages 11
2.1 Assembler: the language of the machine 11
2.2 Interpreter vs Compiler 15
2.3 Human, all too human... 17
2.4 Imperative languages 19
2.5 Procedural languages 21
2.6 Stack languages 21
2.7 Functional languages: the A calculus 23
2.8 Intermission: tö megä symbolon 30
2.9 Array languages 31
2.10 Object-oriented languages 32
2.11 Reflective languages 38
2.12 Declarative = logic languages: the ir calculus 39
2.13 Concurrency-oriented languages 41
2.14 Scripting languages 43
2.15 Markup languages 45
2.16 Overdose kids 47
2.17 Strong vs weak typing 48
2.18 Choose wisely... 55
2.19 Why Python? 57
Chapter 3. Propedeutics 61
Chapter 4. Getting the Materials 63
VI CONTENTS
4.1 Getting the Python interpreter 63
4.2 The editor 65
4.3 sys.argv, redirection, and pipelines: don t fear the command line 66
Chapter 5. Variables, Data Types, and Assignments 73
5.1 Relevance and purpose 73
5.2 Simple or scalar data types 74
5.3 Intermission: 0x07 - the hexcode never dies 82
5.4 Homogeneous groupings 84
5.5 Intermission: a note on assignment 93
5.6 Heterogeneous groupings 93
5.7 Strings 97
5.8 Assignments and unary Operators 98
5.9 Overview 99
5.10 Digression: orthogonality 100
Chapter 6. Flow Control 105
6.1 Comments 105
6.2 Docstrings 106
6.3 Blocks 108
6.4 The IF... THEN... ELSE... construct 109
6.5 Modifiers 114
6.6 Multiple branching: SWITCH vs ELIF 115
6.7 Applying code to piles of data: FOR, MAP, FILTER and friends 116
6.8 The REDUCE function 130
6.9 What about the locals? 130
6.10 Gimme annather try: WHILE... loops 131
6.11 Take the short cut - to be continued 134
6.12 Endless pain 135
6.13 Timer-driven loops 137
6.14 One Loop To Rule Them All... 137
6.15 Go to Statements 138
6.16 Pattern matching 140
6.17 Choosing a functional variable 141
6.18 Thou Mayst Pass 142
Chapter 7. 0 Application: Füll Impact 143
7.1 The problem 143
7.2 Approach 144
7.3 Rough and ready 145
7.4 Refinements 148
Chapter 8. Functions and Procedures
8.1 Subroutines the foundation of all higher programming i00
8.2 The importance of not getting trapped between two mirrors:
recursive programming
8.3 Iterative programming
CONTENTS VII
8.4 Digression: the joy of Stacks 164
8.5 Digression: a trick of the tail 171
8.6 The Travelling Salesman problem 173
8.7 0 Application: cytometry (I) 177
Chapter 9. Application: Your Most Expensive Pocket Calculator 181
Chapter 10. The Object-oriented World 187
10.1 What happened so far 187
10.2 Class and instance 188
10.3 Constructors and destructors 190
10.4 Seif vs non-self 191
10.5 The serpent and the crystal: Python vs Ruby 193
10.6 Primitive types vs objects 194
10.7 Modules and statics 195
10.8 Inheritance 196
10.9 Ram It Down! 198
10.10 Inheritance, abstractness, and privacy 199
10.11 A different point of view: a look at SMALLTALK 200
10.12 The coffee machine: a visual example 202
10.13 Tracking and banking 205
10.14 Generatio spontanea 214
10.15 The octopus and the coffee mug: C++ vs Java 217
10.16 Strings as objects 224
10.17 None and object in Python 232
10.18 Paster of Muppets 234
10.19 Meyer s Principles: a look at Eiffel 238
10.20 Application: cytometry (II) 240
10.21 And then... 241
Chapter 11. 0 Exercise: Prime Numbers 243
Chapter 12. The Cathedral and the Bazaar: Rivalling Strategies 247
12.1 The TOP-DOWN strategy 247
12.2 The BOTTOM-UP strategy 249
12.3 A few notes on style 250
12.4 Splitting a large project 250
Chapter 13. Ordo Ab Chao: Sorting and Searching 261
13.1 When is a group of data ordered? 261
13.2 Bubblesort 262
13.3 Insertsort 263
13.4 Quicksort 264
13.5 Comparison 266
13.6 Others 267
Chapter 14. Welcome to the Library 269
VIII CONTENTS
Part 2. WATER 275
Chapter 15. A A Very Short Project: Trithemizing a File 277
15.1 A brief history of coding 277
15.2 Johannes von Trittheim (Trithemius) and his method of
steganography 279
15.3 Tools of the trade 279
15.4 Your task 281
15.5 Professional cryptography now - random remarks 282
Chapter 16. Some Thoughts on Compression and Checksums 287
16.1 Introduction 287
16.2 A simple lossless compression algorithm 290
16.3 The LZW compression algorithm 301
16.4 Digression: prototyping and extending 307
16.5 Preventing unnoticed tainting of data 308
Chapter 17. Dealing with Errors 311
17.1 What are errors good for? 311
17.2 When the walls come tumbling down: errors leading to program
termination 313
17.3 Error signalling by return value 313
17.4 Error signalling by exceptions 315
17.5 Assertions 319
17.6 Crash Burn 319
Chapter 18. * A Real-life Project: Generating a Restriction Map and
Making Simple Predictions 321
18.1 Meet Micro-Willy 321
18.2 What is a restriction map? 321
18.3 Extracting data from a file 324
18.4 Finding palindromes
18.5 Naming the sites 330
18.6 Generating the protein translations 33*
18.7 Making the map 332
18.8 An artificial digest 332
18.9 Predicting problems with star activity 33
18.10 Profit motives - motive profit 333
18.11 A glance at transmembrane regions
18.12 Addressing a project 334
Chapter 19. Advanced Techniques in Python 337
19.1 Escape processing and prettyprinting
19.2 Regulär expressions
19.3 Filehandling 343
19.4 More file handling: persistent dictionaries
19.5 String handling 344
CONTENTS IX
19.6 Raising exceptions 344
19.7 Curses : the functions for advanced text Output 345
19.8 Module os : the interface to all operating Systems 346
19.9 Utile et iucundum 346
Chapter 20. * The Third Project: Python goes PCR 347
20.1 Monkey business 347
20.2 Polymerase chain reaction: the boiling hell of Dr. Mullis 348
20.3 Determining the melting point of DNA 351
20.4 ... and still my PCR doesn t work yet! 353
20.5 Is there a hairpin structure? 356
20.6 Addressing a project 358
Chapter 21. The Wizards Sabbath: A Gathering of Languages 359
21.1 Considerable considerations 359
21.2 Fortran 363
21.3 Oberon 364
21.4 Lisp 366
21.5 Erlang 368
21.6 Ruby 369
21.7 Lua 370
21.8 C++ 371
21.9 Java 374
Chapter 22. Facing up to Python-3000 377
22.1 Functional print 377
22.2 Standardized unicode support 380
22.3 Goodbye A, it was nice to know you 381
22.4 Number representations, arithmetics, c. 383
22.5 Function annotations 383
22.6 String formatting and I/O 383
22.7 Classes - as you ve never seen them before 388
22.8 Class and function decorators 390
22.9 Miscellaneous 391
Chapter 23. Anna will Return 395
Glossary 401
Index 407
|
| adam_txt |
Contents
Chapter 1. Preface 1
1.1 An axe in the house is worth a carpenter: why Computers matter
in the life sciences 1
1.2 What this book is (not) about 3
1.3 A few practical hints 5
1.4 From the heart 5
1.5 Structure of the book 6
1.6 Sources 7
1.7 Author and acknowledgements 8
1.8 Somebody Special. 8
Part 1. EARTH 9
Chapter 2. A Classification of Programming Languages 11
2.1 Assembler: the language of the machine 11
2.2 Interpreter vs Compiler 15
2.3 Human, all too human. 17
2.4 Imperative languages 19
2.5 Procedural languages 21
2.6 Stack languages 21
2.7 Functional languages: the A calculus 23
2.8 Intermission: tö megä symbolon 30
2.9 Array languages 31
2.10 Object-oriented languages 32
2.11 Reflective languages 38
2.12 Declarative = logic languages: the ir calculus 39
2.13 Concurrency-oriented languages 41
2.14 Scripting languages 43
2.15 Markup languages 45
2.16 Overdose kids 47
2.17 Strong vs weak typing 48
2.18 Choose wisely. 55
2.19 Why Python? 57
Chapter 3. Propedeutics 61
Chapter 4. Getting the Materials 63
VI CONTENTS
4.1 Getting the Python interpreter 63
4.2 The editor 65
4.3 sys.argv, redirection, and pipelines: don't fear the command line 66
Chapter 5. Variables, Data Types, and Assignments 73
5.1 Relevance and purpose 73
5.2 Simple or "scalar" data types 74
5.3 Intermission: 0x07 - the hexcode never dies 82
5.4 Homogeneous groupings 84
5.5 Intermission: a note on assignment 93
5.6 Heterogeneous groupings 93
5.7 Strings 97
5.8 Assignments and unary Operators 98
5.9 Overview 99
5.10 Digression: orthogonality 100
Chapter 6. Flow Control 105
6.1 Comments 105
6.2 Docstrings 106
6.3 Blocks 108
6.4 The IF. THEN. ELSE. construct 109
6.5 Modifiers 114
6.6 Multiple branching: SWITCH vs ELIF 115
6.7 Applying code to piles of data: FOR, MAP, FILTER and friends 116
6.8 The REDUCE function 130
6.9 What about the locals? 130
6.10 Gimme annather try: WHILE. loops 131
6.11 Take the short cut - to be continued 134
6.12 Endless pain 135
6.13 Timer-driven loops 137
6.14 One Loop To Rule Them All. 137
6.15 "Go to" Statements 138
6.16 Pattern matching 140
6.17 Choosing a functional variable 141
6.18 Thou Mayst Pass 142
Chapter 7. 0 Application: Füll Impact 143
7.1 The problem 143
7.2 Approach 144
7.3 Rough and ready 145
7.4 Refinements 148
Chapter 8. Functions and Procedures
8.1 Subroutines the foundation of all higher programming i00
8.2 The importance of not getting trapped between two mirrors:
recursive programming
8.3 Iterative programming
CONTENTS VII
8.4 Digression: the joy of Stacks 164
8.5 Digression: a trick of the tail 171
8.6 The Travelling Salesman problem 173
8.7 0 Application: cytometry (I) 177
Chapter 9. Application: Your Most Expensive Pocket Calculator 181
Chapter 10. The Object-oriented World 187
10.1 What happened so far 187
10.2 Class and instance 188
10.3 Constructors and destructors 190
10.4 Seif vs non-self 191
10.5 The serpent and the crystal: Python vs Ruby 193
10.6 Primitive types vs objects 194
10.7 Modules and statics 195
10.8 Inheritance 196
10.9 Ram It Down! 198
10.10 Inheritance, abstractness, and privacy 199
10.11 A different point of view: a look at SMALLTALK 200
10.12 The coffee machine: a visual example 202
10.13 Tracking and banking 205
10.14 Generatio spontanea 214
10.15 The octopus and the coffee mug: C++ vs Java 217
10.16 Strings as objects 224
10.17 None and object in Python 232
10.18 Paster of Muppets 234
10.19 Meyer's Principles: a look at Eiffel 238
10.20 Application: cytometry (II) 240
10.21 And then. 241
Chapter 11. 0 Exercise: Prime Numbers 243
Chapter 12. The Cathedral and the Bazaar: Rivalling Strategies 247
12.1 The TOP-DOWN strategy 247
12.2 The BOTTOM-UP strategy 249
12.3 A few notes on style 250
12.4 Splitting a large project 250
Chapter 13. Ordo Ab Chao: Sorting and Searching 261
13.1 When is a group of data ordered? 261
13.2 Bubblesort 262
13.3 Insertsort 263
13.4 Quicksort 264
13.5 Comparison 266
13.6 Others 267
Chapter 14. Welcome to the Library 269
VIII CONTENTS
Part 2. WATER 275
Chapter 15. A A Very Short Project: Trithemizing a File 277
15.1 A brief history of coding 277
15.2 Johannes von Trittheim (Trithemius) and his method of
steganography 279
15.3 Tools of the trade 279
15.4 Your task 281
15.5 Professional cryptography now - random remarks 282
Chapter 16. Some Thoughts on Compression and Checksums 287
16.1 Introduction 287
16.2 A simple lossless compression algorithm 290
16.3 The LZW compression algorithm 301
16.4 Digression: prototyping and extending 307
16.5 Preventing unnoticed tainting of data 308
Chapter 17. Dealing with Errors 311
17.1 What are errors good for? 311
17.2 When the walls come tumbling down: errors leading to program
termination 313
17.3 Error signalling by return value 313
17.4 Error signalling by exceptions 315
17.5 Assertions 319
17.6 Crash Burn 319
Chapter 18. * A Real-life Project: Generating a Restriction Map and
Making Simple Predictions 321
18.1 Meet Micro-Willy 321
18.2 What is a restriction map? 321
18.3 Extracting data from a file 324
18.4 Finding palindromes
18.5 Naming the sites 330
18.6 Generating the protein translations 33*
18.7 Making the map 332
18.8 An artificial digest 332
18.9 Predicting problems with star activity 33
18.10 Profit motives - motive profit 333
18.11 A glance at transmembrane regions
18.12 Addressing a project 334
Chapter 19. Advanced Techniques in Python 337
19.1 Escape processing and prettyprinting
19.2 Regulär expressions
19.3 Filehandling 343
19.4 More file handling: persistent dictionaries
19.5 String handling 344
CONTENTS IX
19.6 Raising exceptions 344
19.7 "Curses": the functions for advanced text Output 345
19.8 Module "os": the interface to all operating Systems 346
19.9 Utile et iucundum 346
Chapter 20. * The Third Project: Python goes PCR 347
20.1 Monkey business 347
20.2 Polymerase chain reaction: the boiling hell of Dr. Mullis 348
20.3 Determining the melting point of DNA 351
20.4 . and still my PCR doesn't work yet! 353
20.5 Is there a hairpin structure? 356
20.6 Addressing a project 358
Chapter 21. The Wizards' Sabbath: A Gathering of Languages 359
21.1 Considerable considerations 359
21.2 Fortran 363
21.3 Oberon 364
21.4 Lisp 366
21.5 Erlang 368
21.6 Ruby 369
21.7 Lua 370
21.8 C++ 371
21.9 Java 374
Chapter 22. Facing up to Python-3000 377
22.1 Functional "print" 377
22.2 Standardized unicode support 380
22.3 Goodbye A, it was nice to know you 381
22.4 Number representations, arithmetics, c. 383
22.5 Function annotations 383
22.6 String formatting and I/O 383
22.7 Classes - as you've never seen them before 388
22.8 Class and function decorators 390
22.9 Miscellaneous 391
Chapter 23. Anna will Return 395
Glossary 401
Index 407 |
| any_adam_object | 1 |
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| author | Flaig, Rüdiger Marcus 1971- |
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| author_facet | Flaig, Rüdiger Marcus 1971- |
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| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 570 - Biology |
| dewey-raw | 570.2855133 |
| dewey-search | 570.2855133 |
| dewey-sort | 3570.2855133 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Informatik |
| discipline_str_mv | Biologie Informatik |
| format | Book |
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| id | DE-604.BV023030212 |
| illustrated | Illustrated |
| index_date | 2024-07-02T19:16:41Z |
| indexdate | 2024-07-09T21:09:22Z |
| institution | BVB |
| isbn | 9783527320943 3527320946 |
| language | English |
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| open_access_boolean | |
| owner | DE-706 DE-20 DE-M49 DE-BY-TUM DE-11 |
| owner_facet | DE-706 DE-20 DE-M49 DE-BY-TUM DE-11 |
| physical | IX, 418 S. Ill. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | WILEY-VCH |
| record_format | marc |
| spelling | Flaig, Rüdiger Marcus 1971- Verfasser (DE-588)123094755 aut Bioinformatics programming in Python a practical course for beginners Ruediger-Marcus Flaig Weinheim WILEY-VCH 2008 IX, 418 S. Ill. txt rdacontent n rdamedia nc rdacarrier Bioinformatics Python (Computer program language) Bioinformatik (DE-588)4611085-9 gnd rswk-swf Python Programmiersprache (DE-588)4434275-5 gnd rswk-swf Bioinformatik (DE-588)4611085-9 s Python Programmiersprache (DE-588)4434275-5 s DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016234113&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Flaig, Rüdiger Marcus 1971- Bioinformatics programming in Python a practical course for beginners Bioinformatics Python (Computer program language) Bioinformatik (DE-588)4611085-9 gnd Python Programmiersprache (DE-588)4434275-5 gnd |
| subject_GND | (DE-588)4611085-9 (DE-588)4434275-5 |
| title | Bioinformatics programming in Python a practical course for beginners |
| title_auth | Bioinformatics programming in Python a practical course for beginners |
| title_exact_search | Bioinformatics programming in Python a practical course for beginners |
| title_exact_search_txtP | Bioinformatics programming in Python a practical course for beginners |
| title_full | Bioinformatics programming in Python a practical course for beginners Ruediger-Marcus Flaig |
| title_fullStr | Bioinformatics programming in Python a practical course for beginners Ruediger-Marcus Flaig |
| title_full_unstemmed | Bioinformatics programming in Python a practical course for beginners Ruediger-Marcus Flaig |
| title_short | Bioinformatics programming in Python |
| title_sort | bioinformatics programming in python a practical course for beginners |
| title_sub | a practical course for beginners |
| topic | Bioinformatics Python (Computer program language) Bioinformatik (DE-588)4611085-9 gnd Python Programmiersprache (DE-588)4434275-5 gnd |
| topic_facet | Bioinformatics Python (Computer program language) Bioinformatik Python Programmiersprache |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016234113&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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