Developing Bioinformatics Computer Skills
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.
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Biology in the Computer Age
How Is Computing Changing Biology?
Isnt Bioinformatics Just About Building Databases?
What Does Informatics Mean to Biologists?
What Challenges Does Biology Offer Computer Scientists?
Why Should Biologists Use Computers?
How Can I Configure a PC to Do Bioinformatics Research?
What Information and Software Are Available?
The Chemistry of Proteins
WebBased Protein Structure Tools
Solvent Accessibility and Interactions
Computing Physicochemical Properties
How Can I Use Web Information?
How Do I Understand Sequence Alignment Data?
How Do I Predict Protein Structure from Sequence?
Computational Approaches to Biological Questions
What Biologists Model
Why Biologists Model
Computational Methods Covered in This Book
A Computational Biology Experiment
The Bioinformatics Workstation
Setting Up Your Workstation
Setting Up a Linux Workstation
How to Get Software Working
What Software Is Needed?
Files and Directories in Unix
Working in a Multiuser Environment
Working on a Unix System
Issuing Commands on a Unix System
Viewing and Editing Files
Transformations and Filters
File Statistics and Comparisons
The Language of Regular Expressions
Unix Shell Scripts
Communicating with Other Computers
Playing Nicely with Others in a Shared Environment
Tools for Bioinformatics
Biological Research on the Web
Using Search Engines
Finding Scientific Articles
The Public Biological Databases
Searching Biological Databases
Depositing Data into the Public Databases
Judging the Quality of Information
Sequence Analysis Pairwise Alignment and Database Searching
Chemical Composition of Biomolecules
Composition of DNA and RNA
Development of DNA Sequencing Methods
Genefinders and Feature Detection in DNA
Pairwise Sequence Comparison
Sequence Queries Against Biological Databases
Multifunctional Tools for Sequence Analysis
Multiple Sequence Alignments Trees and Profiles
Multiple Sequence Alignment
Profiles and Motifs
Visualizing Protein Structures and Computing Structural Properties
A Word About Protein Structure Data
Protein Resource Databases
Putting It All Together
Predicting Protein Structure and Function from Sequence
Determining the Structures of Proteins
Predicting the Structures of Proteins
From 3D to ID
Feature Detection in Protein Sequences
Secondary Structure Prediction
Predicting 3D Structure
A Protein Modeling Project
Tools for Genomics and Proteomics
From Sequencing Genes to Sequencing Genomes
Accessing Genome Information on the Web
Annotating and Analyzing Whole Genome Sequences
New Data Analysis Challenges
Biochemical Pathway Databases
Modeling Kinetics and Physiology
Databases and Visualization
Automating Data Analysis with Perl
Pattern Matching and Regular Expressions
Parsing BLAST Output Using Perl
Applying Perl to Bioinformatics
Building Biological Databases
Types of Databases
Introduction to SQL
Installing the MySQL DBMS
Developing WebBased Software That Interacts with Databases
Visualization and Data Mining
Preparing Your Data
Sequence Data Visualization
Networks and Pathway Visualization
Working with Numerical Data
Data Mining and Biological Information