Managing Your Biological Data with Python
eBook - PDF

Managing Your Biological Data with Python

Allegra Via, Kristian Rother, Anna Tramontano

  1. 560 pages
  2. English
  3. PDF
  4. Available on iOS & Android
eBook - PDF

Managing Your Biological Data with Python

Allegra Via, Kristian Rother, Anna Tramontano

Book details
Table of contents
Citations

About This Book

Take Control of Your Data and Use Python with ConfidenceRequiring no prior programming experience, Managing Your Biological Data with Python empowers biologists and other life scientists to work with biological data on their own using the Python language. The book teaches them not only how to program but also how to manage their data. It shows how

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Information

Publisher
Chapman and Hall/CRC
Year
2014
ISBN
9781439880944
Edition
1
Topic
Computer Science
Subtopic
Programming Games
Index
Computer Science

Table of contents

  1. Front Cover
  2. Table of Contents
  3. Preface
  4. Acknowledgements
  5. Chapter 1: The Python Shell
  6. Chapter 2: Your First Python Program
  7. Chapter 3: Analyzing a Data Column
  8. Chapter 4: Parsing Data Records
  9. Chapter 5: Searching Data
  10. Chapter 6: Filtering Data
  11. Chapter 7: Managing Tabular Data
  12. Chapter 8: Sorting Data
  13. Chapter 9: Pattern Matching and Text Mining
  14. Chapter 10: Divide a Program into Functions
  15. Chapter 11: Managing Complexity with Classes
  16. Chapter 12: Debugging
  17. Chapter 13: Using External Modules: The Python Interface to R
  18. Chapter 14: Building Program Pipelines
  19. Chapter 15: Writing Good Programs
  20. Chapter 16: Creating Scientific Diagrams
  21. Chapter 17: Creating Molecule Images with PyMOL
  22. Chapter 18: Manipulating Images
  23. Chapter 19: Working with Sequence Data
  24. Chapter 20: Retrieving Data from Web Resources
  25. Chapter 21: Working with 3D Structure Data
  26. Recipe 1: The PyCogent Library
  27. Recipe 2: Reversing and Randomizing a Sequence
  28. Recipe 3: Creating a Random Sequence with Probabilities
  29. Recipe 4: Parsing Multiple Sequence Alignments Using Biopython
  30. Recipe 5: Calculating a Consensus Sequence from a Multiple Sequence Alignment
  31. Recipe 6: Calculating the Distance between Phylogenetic Tree Nodes
  32. Recipe 7: Codon Frequencies in a Nucleotide Sequence
  33. Recipe 8: Parsing RNA 2D Structures in the Vienna Format
  34. Recipe 9: Parsing BLAST XML Output
  35. Recipe 10: Parsing SBML Files
  36. Recipe 11: Running BLAST
  37. Recipe 12: Accessing, Downloading, and Reading Web Pages
  38. Recipe 13: Parsing HTML Files
  39. Recipe 14: Splitting a PDB File into PDB Chain Files
  40. Recipe 15: Finding the Two Closest Cα Atoms in a PDB Structure
  41. Recipe 16: Extracting the Interface between Two PDB Chains
  42. Recipe 17: Building Homology Models Using Modeller
  43. Recipe 18: RNA 3D Homology Modeling with ModeRNA
  44. Recipe 19: Calculating RNA Base Pairs from a 3D Structure
  45. Recipe 20: A Real Case of Structural Superimposition: The Serine Protease Catalytic Triad
  46. Appendix A: Command Overview
  47. Appendix B: Python Resources
  48. Appendix C: Record Samples
  49. Appendix D: Handling Directories and Programs with UNIX
  50. Back Cover