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Computational Biology

A Practical Introduction to BioData Processing and Analysis with Linux, MySQL, and R

  • Röbbe Wünschiers

Table of contents

  1. Front Matter
    Pages i-xxix
  2. Whetting Your Appetite

    1. Front Matter
      Pages 1-1
    2. Röbbe Wünschiers
      Pages 3-9
    3. Röbbe Wünschiers
      Pages 11-17
  3. Computer & Operating Systems

    1. Front Matter
      Pages 19-19
    2. Röbbe Wünschiers
      Pages 21-35
  4. Working with Linux

    1. Front Matter
      Pages 37-37
    2. Röbbe Wünschiers
      Pages 39-51
    3. Röbbe Wünschiers
      Pages 53-70
    4. Röbbe Wünschiers
      Pages 71-75
    5. Röbbe Wünschiers
      Pages 77-96
    6. Röbbe Wünschiers
      Pages 97-114
    7. Röbbe Wünschiers
      Pages 115-123
    8. Röbbe Wünschiers
      Pages 125-155
    9. Röbbe Wünschiers
      Pages 157-174
    10. Röbbe Wünschiers
      Pages 175-193
  5. Programming

    1. Front Matter
      Pages 195-195
    2. AWK
      Röbbe Wünschiers
      Pages 197-254
    3. Röbbe Wünschiers
      Pages 255-290
    4. Röbbe Wünschiers
      Pages 291-292
  6. Advanced Data Analysis

    1. Front Matter
      Pages 293-293
    2. Röbbe Wünschiers
      Pages 295-315
    3. Röbbe Wünschiers
      Pages 317-341
  7. Worked Examples

    1. Front Matter
      Pages 343-343
    2. Röbbe Wünschiers
      Pages 375-391
    3. Röbbe Wünschiers
      Pages 393-407
    4. Röbbe Wünschiers
      Pages 409-423
  8. Back Matter
    Pages 425-449

About this book

Introduction

This greatly expanded 2nd edition provides a practical introduction to

- data processing with Linux tools and the programming languages AWK and Perl

- data management with the relational database system MySQL, and

- data analysis and visualization with the statistical computing environment R

for students and practitioners in the life sciences. Although written for beginners, experienced researchers in areas involving bioinformatics and computational biology may benefit from numerous tips and tricks that help to process, filter and format large datasets. Learning by doing is the basic concept of this book. Worked examples illustrate how to employ data processing and analysis techniques, e.g. for

- finding proteins potentially causing pathogenicity in bacteria,

- supporting the significance of BLAST with homology modeling, or

- detecting candidate proteins that may be redox-regulated, on the basis of their structure.

All the software tools and datasets used are freely available. One section is devoted to explaining setup and maintenance of Linux as an operating system independent virtual machine. The author's experiences and knowledge gained from working and teaching in both academia and industry constitute the foundation for this practical approach.

Keywords

Bioinformatics Computational Biology Linux MySQL Programming Unix

Authors and affiliations

  • Röbbe Wünschiers
    • 1
  1. 1.University of Applied SciencesBiotechnology / Computational Biology University of Applied SciencesMittweidaGermany

Bibliographic information