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) 9780521720090, Cambridge University Press Paperback / softback, published 12 February 2015 711 pages, 91 b/w illus. 11 colour illus. 3 tables24.7 x 17.6 x 3.3 cm, 1.38 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]
