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Computational Biology

Unix/Linux, Data Processing and Programming

  • Textbook
  • © 2004

Overview

Authors:
  1. Röbbe Wünschiers

    1. Institute for Genetics, University of Cologne, Köln, Germany

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  • A practical approach with examples from biological data analysis
  • Includes supplementary material: sn.pub/extras

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Table of contents (12 chapters)

  1. Front Matter

    Pages I-XVII
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  2. Whetting Your Appetite

    1. Front Matter

      Pages 1-1
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    2. Introduction

      • Röbbe Wünschiers
      Pages 3-6

  3. Computer and Operating Systems

    1. Front Matter

      Pages 7-7
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    2. Unix/Linux

      • Röbbe Wünschiers
      Pages 9-23

  4. Working with Unix/Linux

    1. Front Matter

      Pages 25-25
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    2. The First Touch

      • Röbbe Wünschiers
      Pages 27-34

    3. Working with Files

      • Röbbe Wünschiers
      Pages 35-52

    4. Installing BLAST and ClustalW

      • Röbbe Wünschiers
      Pages 53-61

    5. Working with Text

      • Röbbe Wünschiers
      Pages 63-79

    6. Using the Shell

      • Röbbe Wünschiers
      Pages 81-96

    7. Shell Programming

      • Röbbe Wünschiers
      Pages 97-125

    8. Regular Expressions

      • Röbbe Wünschiers
      Pages 127-140

    9. Sed

      • Röbbe Wünschiers
      Pages 141-160

  5. Programming

    1. Front Matter

      Pages 161-161
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    2. Awk

      • Röbbe Wünschiers
      Pages 163-220

    3. Perl

      • Röbbe Wünschiers
      Pages 221-263

  6. Back Matter

    Pages 265-284
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Keywords

About this book

A shift in culture Only a decade ago, the ?rst thing a molecular biologist would have had to learn when he or she started the lab work was how to handle pipettes, extract DNA, useenzymesandcloneagene. Now,the?rstthing thatheorsheshould learn is how to handle databases and to extract all the information that is already known about the gene that he or she wants to study. In all likelihood, he or she will ?nd that the gene has already been sequenced from several organisms, that it was recovered in a variety of EST projects, that expression data are available from microarray and SAGE studies, that it was included in linkage studies, that proteomics data are rapidly accumulating, that lists of interacting proteins are being compiled, that domain structure data are available and that it is part of a network of genetic interactions which is intensively modelled. He or she will discover that all this information resides in many di?erent databases with di?erent data formats and with di?erent levels of analyses and linking. Starting to work on this gene will make sense only, if all this information is put together in a project-speci?c manner and set into the context of what is known about related genes and processes. At this point he or she may decide to walk up to the bioinformatics group in house and ask for help with arranging the data in a useful manner.

Reviews

From the reviews:

"This book is a practical introduction to Unix/Linux and programming for biologists … . The goal is to learn about the power of … . It is written for beginners with no computational knowledge. Basic programming constructs are introduced and applied. With this book, the reader will be able to work in the Unix … and to write programs in order to format and analyse large data files. This book was written for graduate students, professional, researchers as well as libraries." (Bio World, Issue no. 6, 2004)

Authors and Affiliations

  • Institute for Genetics, University of Cologne, Köln, Germany

    Röbbe Wünschiers

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