From the reviews of the second edition:
“This book aims to guide an astute pupil on the path to acquiring a practical familiarity with the UNIX command line. … I found the book entertainingly written and well edited--increasingly rare attributes in current books on computing. … The book is a spirited introduction to data processing on Unix, and will also be useful to driven data wranglers who are not necessarily in the biology field.” (A. Squassabia, Computing Reviews, November, 2013)
“This work will be valuable to new computational biology/bioinformatics students who want to learn programming. … Students can follow each chapter by working out the code on their own computers, and they can sharpen their programming skills by trying out the exercise at the end. … The book will be a good starting point for many newcomers who have no or little idea of programming as well as a concise reference guide for students and scientists. Summing Up: Highly recommended. All academic and professional audiences.” (V. Mathura, Choice, Vol. 51 (3), November, 2013)
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.