Python Programming for Biology
Bioinformatics and Beyond

This book introduces Python as a powerful tool for the investigation of problems in computational biology, for novices and experienced programmers alike.

Tim J. Stevens (Author), Wayne Boucher (Author)

9780521895835, Cambridge University Press

Hardback, published 12 February 2015

711 pages, 91 b/w illus. 11 colour illus. 3 tables
25.3 x 18.2 x 3.5 cm, 1.55 kg

'[Stevens and Boucher's] understanding of the needs of the target audience for this book (primarily bench scientists with minimal programming experience) is complete. They have accurately customized the book, to meet those specific requirements which are so distinct from those of students aspiring to be specialist programmers. They have achieved this difficult objective without 'dumbing down' the content or omitting any relevant aspect of Python. The book provides an easy and comprehensive introduction for the complete novice as well as offering plenty to engage the more experienced reader. This work is exactly what is required for us to build new training events upon.' David Judge, University of Cambridge

Do you have a biological question that could be readily answered by computational techniques, but little experience in programming? Do you want to learn more about the core techniques used in computational biology and bioinformatics? Written in an accessible style, this guide provides a foundation for both newcomers to computer programming and those interested in learning more about computational biology. The chapters guide the reader through: a complete beginners' course to programming in Python, with an introduction to computing jargon; descriptions of core bioinformatics methods with working Python examples; scientific computing techniques, including image analysis, statistics and machine learning. This book also functions as a language reference written in straightforward English, covering the most common Python language elements and a glossary of computing and biological terms. This title will teach undergraduates, postgraduates and professionals working in the life sciences how to program with Python, a powerful, flexible and easy-to-use language.

Preface
Acknowledgements
1. Prologue
2. Beginners' guide
3. Python basics
4. Program control and logic
5. Functions
6. Files
7. Object orientation
8. Object data modelling
9. Mathematics
10. Coding tips
11. Biological sequences
12. Pairwise sequence alignments
13. Multiple sequence alignments
14. Sequence variation and evolution
15. Macromolecular structures
16. Array data
17. High-throughput sequence analyses
18. Images
19. Signal processing
20. Databases
21. Probability
22. Statistics
23. Clustering and discrimination
24. Machine learning
25. Hard problems
26. Graphical interfaces
27. Improving speed
Appendix 1: simplified language reference
Appendix 2: selected standard type methods and operations
Appendix 3: standard module highlights
Appendix 4: string formatting
Appendix 5: regular expressions
Appendix 6: further statistics
Glossary
Index.

Subject Areas: Life sciences: general issues [PSA], Biology, life sciences [PS], Science: general issues [PD], Mathematics & science [P]