Synopses & Reviews
Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. Genome sequencing projects are producing vast amounts of biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological literature. It's impossible for even the most zealous researcher to stay on top of necessary information in the field without the aid of computer-based tools. Bioinformatics is all about building these tools.Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, as well as for experienced biology researchers who are just starting to use computers to handle their data. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, and data visualization.Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data.
The application of computational and analytical methods to biological problems is a rapidly evolving scientific discipline. This book is designed to help any biologist develop a structured approach to data, as well as provide the tools they'll need to analyze it.
This practical, hands-on guide shows how to develop a structured approach to biological data and the tools needed to analyze it. It's aimed at scientists and students learning computational approaches to biological data, as well as experienced biology researchers starting to use computers to handle data.
About the Author
Cynthia Gibas is an assistant professor of biology at Virginia Tech, in Blacksburg, Virginia. She's been a computational biologist since before computational biology was cool, and is currently learning to drive her spankin' new home-built Linux cluster. Her research interests include the structure and evolution of genomes, the properties of protein surfaces and interfaces, and prediction of protein structure. She teaches introductory courses in bioinformatics methods for biologists and is looking forward to her next real vacation, sometime in 2006.
Per Jambeck is a Ph.D. student in the bioengineering department at the University of California, San Diego. He has worked on computational biology problems since 1994, concentrating on machine learning applications in understanding multidimensional biological data. Per smiles wistfully at the mention of free time, but he manages to host shows at community and student-run radio stations anyway.
Table of Contents
Preface; Audience for This Book; Structure of This Book; Our Approach to Bioinformatics; URLs Referenced in This Book; Conventions Used in This Book; Comments and Questions; Acknowledgments; Introduction; Chapter 1: Biology in the Computer Age; 1.1 How Is Computing Changing Biology?; 1.2 Isn't Bioinformatics Just About Building Databases?; 1.3 What Does Informatics Mean to Biologists?; 1.4 What Challenges Does Biology Offer Computer Scientists?; 1.5 What Skills Should a Bioinformatician Have?; 1.6 Why Should Biologists Use Computers?; 1.7 How Can I Configure a PC to Do Bioinformatics Research?; 1.8 What Information and Software Are Available?; 1.9 Can I Learn a Programming Language Without Classes?; 1.10 How Can I Use Web Information?; 1.11 How Do I Understand Sequence Alignment Data?; 1.12 How Do I Write a Program to Align Two Biological Sequences?; 1.13 How Do I Predict Protein Structure from Sequence?; 1.14 What Questions Can Bioinformatics Answer?; Chapter 2: Computational Approaches to Biological Questions; 2.1 Molecular Biology's Central Dogma; 2.2 What Biologists Model; 2.3 Why Biologists Model; 2.4 Computational Methods Covered in This Book; 2.5 A Computational Biology Experiment; The Bioinformatics Workstation; Chapter 3: Setting Up Your Workstation; 3.1 Working on a Unix System; 3.2 Setting Up a Linux Workstation; 3.3 How to Get Software Working; 3.4 What Software Is Needed?; Chapter 4: Files and Directories in Unix; 4.1 Filesystem Basics; 4.2 Commands for Working with Directories and Files; 4.3 Working in a Multiuser Environment; Chapter 5: Working on a Unix System; 5.1 The Unix Shell; 5.2 Issuing Commands on a Unix System; 5.3 Viewing and Editing Files; 5.4 Transformations and Filters; 5.5 File Statistics and Comparisons; 5.6 The Language of Regular Expressions; 5.7 Unix Shell Scripts; 5.8 Communicating with Other Computers; 5.9 Playing Nicely with Others in a Shared Environment; Tools for Bioinformatics; Chapter 6: Biological Research on the Web; 6.1 Using Search Engines; 6.2 Finding Scientific Articles; 6.3 The Public Biological Databases; 6.4 Searching Biological Databases; 6.5 Depositing Data into the Public Databases; 6.6 Finding Software; 6.7 Judging the Quality of Information; Chapter 7: Sequence Analysis, Pairwise Alignment, and Database Searching; 7.1 Chemical Composition of Biomolecules; 7.2 Composition of DNA and RNA; 7.3 Watson and Crick Solve the Structure of DNA; 7.4 Development of DNA Sequencing Methods; 7.5 Genefinders and Feature Detection in DNA; 7.6 DNA Translation; 7.7 Pairwise Sequence Comparison; 7.8 Sequence Queries Against Biological Databases; 7.9 Multifunctional Tools for Sequence Analysis; Chapter 8: Multiple Sequence Alignments, Trees, and Profiles; 8.1 The Morphological to the Molecular; 8.2 Multiple Sequence Alignment; 8.3 Phylogenetic Analysis; 8.4 Profiles and Motifs; Chapter 9: Visualizing Protein Structures and Computing Structural Properties; 9.1 A Word About Protein Structure Data; 9.2 The Chemistry of Proteins; 9.3 Web-Based Protein Structure Tools; 9.4 Structure Visualization; 9.5 Structure Classification; 9.6 Structural Alignment; 9.7 Structure Analysis; 9.8 Solvent Accessibility and Interactions; 9.9 Computing Physicochemical Properties; 9.10 Structure Optimization; 9.11 Protein Resource Databases; 9.12 Putting It All Together; Chapter 10: Predicting Protein Structure and Function from Sequence; 10.1 Determining the Structures of Proteins; 10.2 Predicting the Structures of Proteins; 10.3 From 3D to 1D; 10.4 Feature Detection in Protein Sequences; 10.5 Secondary Structure Prediction; 10.6 Predicting 3D Structure; 10.7 Putting It All Together: A Protein Modeling Project; 10.8 Summary; Chapter 11: Tools for Genomics and Proteomics; 11.1 From Sequencing Genes to Sequencing Genomes; 11.2 Sequence Assembly; 11.3 Accessing Genome Informationon the Web; 11.4 Annotating and Analyzing Whole Genome Sequences; 11.5 Functional Genomics: New Data Analysis Challenges; 11.6 Proteomics; 11.7 Biochemical Pathway Databases; 11.8 Modeling Kinetics and Physiology; 11.9 Summary; Databases and Visualization; Chapter 12: Automating Data Analysis with Perl; 12.1 Why Perl?; 12.2 Perl Basics; 12.3 Pattern Matching and Regular Expressions; 12.4 Parsing BLAST Output Using Perl; 12.5 Applying Perl to Bioinformatics; Chapter 13: Building Biological Databases; 13.1 Types of Databases; 13.2 Database Software; 13.3 Introduction to SQL; 13.4 Installing the MySQL DBMS; 13.5 Database Design; 13.6 Developing Web-Based Software That Interacts with Databases; Chapter 14: Visualization and Data Mining; 14.1 Preparing Your Data; 14.2 Viewing Graphics; 14.3 Sequence Data Visualization; 14.4 Networks and Pathway Visualization; 14.5 Working with Numerical Data; 14.6 Visualization: Summary; 14.7 Data Mining and Biological Information; Bibliography; Colophon;