Keith Bradnam is a project scientist in the Genome Center at the University of California, Davis. He has extensive experience working with model organism databases and spent four years as a project leader at WormBase, helping to develop this important bioinformatics resource.

Part I. Introduction and Background: 1. Introduction; 2. How to use this book; Part II. Installing Unix and Perl: 3. What do I need in order to learn Unix and Perl?; 4. Installing Linux on a PC; 5. Installing a code editor; Part III. Essential Unix: 6. Introduction to Unix; 7. The Unix terminal; 8. The Unix command prompt; 9. Your first Unix command; 10. The hierarchy of a Unix file system; 11. Finding out where you are in the filesystem; 12. How to navigate a Unix filesystem; 13. Absolute and relative paths; 14. Working with your home directory; 15. The Unix shell; 16. Environment variables; 17. Introduction to command-line options; 18. Main pages; 19. Working with directories; 20. The importance of saving keystrokes; 21. Moving and renaming files; 22. Moving and renaming directories; 23. How to remove files; 24. How to copy files and directories; 25. Working with text files; 26. Introduction to aliases; 27. Editing text files; 28. Automating Unix commands; 29. How to hide files and find hidden files; 30. Creating a configuration file; 31. Programming with Unix; 32. Unix file permissions; 33. How to specify which directories contain programs; 34. Creating useful shell scripts; 35. Unix summary; Part IV. Essential Perl: 36. Hello world; 37. Scalar variables; 38. Use warnings; 39. Maths and functions; 40. Perl vs perl; 41. Conditional statements; 42. Use strict; 43. Stopping programs; 44. Working with strings; 45. Dealing with special characters; 46. Matching operators; 47. The transliteration operator; 48. List context; 49. Introduction to arrays; 50. Array manipulation; 51. The [...] array; 52. Defined and undefined variables; 53. Sorting; 54. Introduction to loops; 55. More loops; 56. Loop control; 57. Data input and output; 58. Reading and writing files; 59. Introduction to hashes; 60. Working with hashes; 61. Introduction to regular expressions; 62. Regular expression metacharacters; 63. Working with regular expressions; 64. Interacting with other programs; 65. Using functions and subroutines; 66. Returning data from a subroutine; 67. Part IV summary; Part V. Advanced Unix: 68. Introduction to advanced Unix; 69. Introduction to process control; 70. The grep command; 71. Viewing, and controlling, program output; 72. Redirecting input and output; 73. Standard error; 74. Connecting commands with pipelines; 75. Advanced text manipulation; Part VI. Advanced Perl: 76. Regular expressions revisited; 77. Function libraries; 78. References and 2-dimensional arrays; 79. Records and other hash references; 80. Using references with subroutines; 81. Complex data structures; 82. Adding command-line options; 83. OOP basics; 84. CPAN; Part VII. Programming Topics: 85. Debugging strategies; 86. Common error messages; 87. Code beautification; 88. Abstraction; 89. Data management; 90. Documentation; 91. Revision control; 92. Working with other peoples' data; 93. Getting help; Appendix; Index.