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UNIX and Perl to the Rescue!
A Field Guide for the Life Sciences (and Other Data-rich Pursuits)

  • Date Published: August 2012
  • availability: Available
  • format: Paperback
  • isbn: 9780521169820

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About the Authors
  • Your research has generated gigabytes of data and now you need to analyse it. You hate using spreadsheets but it is all you know, so what else can you do? This book will transform how you work with large and complex data sets, teaching you powerful programming tools for slicing and dicing data to suit your needs. Written in a fun and accessible style, this step-by-step guide will inspire and inform non-programmers about the essential aspects of Unix and Perl. It shows how, with just a little programming knowledge, you can write programs that could save you hours, or even days. No prior experience is required and new concepts are introduced using numerous code examples that you can try out for yourself. Going beyond the basics, the authors touch upon many broader topics that will help those new to programming, including debugging and how to write in a good programming style. Follow the book on Twitter at: @unixandperl.

    • A step-by-step guide that really is step-by-step – makes programming accessible to non-programmers
    • Written in a fun, lively and engaging style – more approachable than typical books on programming
    • Includes many code examples – modifying existing programs is a very effective way to learn
    Read more

    Reviews & endorsements

    "My chief regret about this book is that it wasn’t available last year, when I was working with a group of life-science researchers. I could have persuaded them all to purchase a copy, thereby saving myself a great deal of the time I spent assisting with their data analysis tasks!"
    G. K. Jenkins, Computing Reviews

    "With their book on UNIX and Perl, scientists Bradnam and Korf have come to the aid of laboratory or field researchers floundering helplessly under overwhelming gigabytes of unstructured raw data. With a characteristic charming and chipper cheerfulness, the book quickly guides the readers through finding/installing a UNIX system of any variety... Highly recommended."
    F.E.J. Linton, emeritus, Wesleyan University, Choice Magazine

    "Unix and Perl to the Rescue! is a book I highly recommend for all those students, post-docs, and academics who are scared of programming but can benefit immensely from the power of Unix and scripting languages. It’s time to come out of your shell."
    Dr MD Sharma, Genetics Society News

    "Bradnam and Korf provide an intuitive and enjoyable volume that shows how to make the terminal window useful to scientists looking to build automation into data queries using UNIX and Perl scripting.
    With a thorough treatment of more than just the basics, this book fills a missing niche in the Perl and UNIX world with a focus on data processing. The authors have crafted a brilliant treatment of pattern searching with regular expressions to help the reader unleash some of the most powerful parts of the Perl programming language. For scientists looking to parse data files and extract the essential pieces this is a thorough and well explained complete with sprinkles of humor and biologically motivated examples."
    Jason Stajich, University of California, Riverside

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    Product details

    • Date Published: August 2012
    • format: Paperback
    • isbn: 9780521169820
    • length: 428 pages
    • dimensions: 244 x 170 x 22 mm
    • weight: 0.7kg
    • contains: 5 b/w illus.
    • availability: Available
  • Table of Contents

    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 @ARGV 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.

  • Instructors have used or reviewed this title for the following courses

    • Introduction to Biocomputing
  • Authors

    Keith Bradnam, University of California, Davis
    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.

    Ian Korf, University of California, Davis
    Ian Korf is an Associate Professor in Molecular and Cellular Biology at the University of California, Davis. His research seeks to understand structure and function in genomic DNA. He has developed new tools for gene prediction, co-authored the only book devoted to BLAST and helped in the development of BioPerl.

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