search for books and compare prices
Tables of Contents for Developing Bioinformatics Computer Skills
Chapter/Section Title
Page #
Page Count
Preface
ix
I. Introduction
1
44
Biology in the Computer Age
3
19
How Is Computing Changing Biology?
4
4
Isn't Bioinformatics Just About Building Databases?
8
4
What Does Informatics Mean to Biologists?
12
1
What Challenges Does Biology Offer Computer Scientists?
13
1
What Skills Should a Bioinformatician Have?
13
1
Why Should Biologists Use Computers?
14
2
How Can I Configure a PC to Do Bioinformatics Research?
16
2
What Information and Software Are Available?
18
1
Can I Learn a Programming Language Without Classes?
18
1
How Can I Use Web Information?
19
1
How Do I Understand Sequence Alignment Data?
20
1
How Do I Write a Program to Align Two Biological Sequences?
20
1
How Do I Predict Protein Structure from Sequence?
21
1
What Questions Can Bioinformatics Answer?
21
1
Computational Approaches to Biological Questions
22
23
Molecular Biology's Central Dogma
22
5
What Biologists Model
27
4
Why Biologists Model
31
1
Computational Methods Covered in This Book
32
6
A Computational Biology Experiment
38
7
II. The Bioinformatics Workstation
45
86
Setting Up Your Workstation
47
17
Working on a Unix System
47
3
Setting Up a Linux Workstation
50
6
How to Get Software Working
56
6
What Software Is Needed?
62
2
Files and Directories in Unix
64
23
Filesystem Basics
64
7
Commands for Working with Directories and Files
71
8
Working in a Multiuser Environment
79
8
Working on a Unix System
87
44
The Unix Shell
87
2
Issuing Commands on a Unix System
89
5
Viewing and Editing Files
94
7
Transformations and Filters
101
7
File Statistics and Comparisons
108
2
The Language of Regular Expressions
110
3
Unix Shell Scripts
113
1
Communicating with Other Computers
114
5
Playing Nicely with Others in a Shared Environment
119
12
III. Tools for Bioinformatics
131
198
Biological Research on the Web
133
26
Using Search Engines
134
2
Finding Scientific Articles
136
4
The Public Biological Databases
140
7
Searching Biological Databases
147
8
Depositing Data into the Public Databases
155
1
Finding Software
155
1
Judging the Quality of Information
156
3
Sequence Analysis, Pairwise Alignment, and Database Searching
159
32
Chemical Composition of Biomolecules
160
1
Composition of DNA and RNA
161
1
Watson and Crick Solve the Structure of DNA
161
3
Development of DNA Sequencing Methods
164
5
Genefinders and Feature Detection in DNA
169
2
DNA Translation
171
1
Pairwise Sequence Comparison
172
10
Sequence Queries Against Biological Databases
182
6
Multifunctional Tools for Sequence Analysis
188
3
Multiple Sequence Alignments, Trees, and Profiles
191
24
The Morphological to the Molecular
191
2
Multiple Sequence Alignment
193
6
Phylogenetic Analysis
199
6
Profiles and Motifs
205
10
Visualizing Protein Structures and Computing Structural Properties
215
53
A Word About Protein Structure Data
216
1
The Chemistry of Proteins
217
12
Web-Based Protein Structure Tools
229
2
Structure Visualization
231
10
Structure Classification
241
5
Structural Alignment
246
4
Structure Analysis
250
4
Solvent Accessibility and Interactions
254
4
Computing Physicochemical Properties
258
2
Structure Optimization
260
3
Protein Resource Databases
263
2
Putting It All Together
265
3
Predicting Protein Structure and Function from Sequence
268
26
Determining the Structures of Proteins
269
4
Predicting the Structures of Proteins
273
2
From 3D to 1D
275
1
Feature Detection in Protein Sequences
276
1
Secondary Structure Prediction
277
6
Predicting 3D Structure
283
4
Putting It All Together: A Protein Modeling Project
287
6
Summary
293
1
Tools for Genomics and Proteomics
294
35
From Sequencing Genes to Sequencing Genomes
296
5
Sequence Assembly
301
2
Accessing Genome Information the Web
303
4
Annotating and Analyzing Whole Genome Sequences
307
3
Functional Genomics: New Data Analysis Challenges
310
7
Proteomics
317
4
Biochemical Pathway Databases
321
4
Modeling Kinetics and Physiology
325
2
Summary
327
2
IV. Databases and Visualization
329
74
Automating Data Analysis with Perl
331
19
Why Perl?
331
1
Perl Basics
332
7
Pattern Matching and Regular Expressions
339
1
Parsing BLAST Output Using Perl
340
5
Applying Perl to Bioinformatics
345
5
Building Biological Databases
350
33
Types of Databases
351
8
Database Software
359
2
Introduction to SQL
361
5
Installing the MySQL DBMS
366
5
Database Design
371
4
Developing Web-Based Software That Interacts with Databases
375
8
Visualization and Data Mining
383
20
Preparing Your Data
384
1
Viewing Graphics
385
1
Sequence Data Visualization
386
2
Networks and Pathway Visualization
388
2
Working with Numerical Data
390
6
Visualization: Summary
396
1
Data Mining and Biological Information
397
6
Bibliography
403
6
Index
409