Practical Computing for Biologists [1 ed.] 9780878933914

Increasingly, scientists find themselves facing exponentially larger data sets and analyses without suitable tools to de

285 72 1011KB

English Pages 538 [562] Year 2011

Table of contents :
Before YouBegin 1
PART I: Text Files 7
Chapter 1: Getting Set Up 9
Chapter 2: Regular Expressions: Powerful Search and Replace 17
Chapter 3: Exploring the Flexibility of Regular Expression 31

PART II: The Shell 45
Chapter 4: Command-line Operations: The Shell 47
Chapter 5: Handling Text in the Shell 67
Chapter 6: Scripting with the Shell 83

PART III: Programming 103
Chapter 7: Components of Programming 105
Chapter 8: Beginning Python Programming 125
Chapter 9: Decisions and Loops 141
Chapter 10: Reading and Writing Files 173
Chapter 11: Merging Files 201
Chapter 12: Modules and Libraries 215
Chapter 13: Debugging Strategies 231

PART IV: Combining Methods 243
Chapter 14: Selecting and Combining Tools 245
Chapter 15: Relational Databases 255
Chapter 16: Advanced Shell and Pipelines 299

PART V: Graphics 321
Chapter 17: Graphical Concepts 323
Chapter 18: Working with Vector Art 345
Chapter 19: Working with Pixel Images 363

PART VI: Advanced Topics 381
Chapter 20: Working on Remote Computers 383
Chapter 21: Installing Software 411
Chapter 22: Electronics: Interacting with the Physical World 425

Appendices 449

Practical Computing for Biologists [1 ed.]
9780878933914

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Steven H. D. Haddock
Casey W. Dunn

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