II. The Bioinformatics Workstation
by Cynthia Gibas, Per Jambeck
Developing Bioinformatics Computer Skills
- Copyright
- Preface
- I. Introduction
- 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?
- 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
- 2.5.1. Identifying the Problem
- 2.5.2. Separating the Problem into Simpler Components
- 2.5.3. Evaluating Your Needs
- 2.5.4. Selecting the Appropriate Data Set
- 2.5.5. Identifying the Criteria for Success
- 2.5.6. Performing and Documenting a Computational Experiment
- 2.5.6.1. Documentation issues in computational biology
- 2.5.6.2. Electronic notebooks
- II. The Bioinformatics Workstation
- 3. Setting Up Your Workstation
- 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
- 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
- 5.9.1. Processes and Process Management
- 5.9.2. Scheduling Recurring Activities with cron
- 5.9.3. Monitoring Space Usage and File Sizes
- 5.9.4. Creating Archives of Your Data
- 5.9.4.1. tar: Hold the feathers
- 5.9.4.2. compress
- 5.9.4.3. gzip
- III. Tools for Bioinformatics
- 6. Biological Research on the Web
- 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
- 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
- 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
- 10. Predicting Protein Structure and Function from Sequence
- 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
- IV. Databases and Visualization
- 12. Automating Data Analysis with Perl
- 13. Building Biological Databases
- 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
- 1. Biology in the Computer Age
-
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