Developing Bioinformatics Computer Skills

ISBN-10: 1565926641

ISBN-13: 9781565926646

Edition: 2001

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Description: 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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Book details

List price: $44.99
Copyright year: 2001
Publisher: O'Reilly Media, Incorporated
Publication date: 5/3/2001
Binding: Paperback
Pages: 424
Size: 7.00" wide x 9.00" long x 1.00" tall
Weight: 1.584
Language: English

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.

Introduction
Biology in the Computer Age
How Is Computing Changing Biology?
Isn't Bioinformatics Just About Building Databases?
What Does Informatics Mean to Biologists?
What Challenges Does Biology Offer Computer Scientists?
What Skills Should a Bioinformatician Have?
Why Should Biologists Use Computers?
How Can I Configure a PC to Do Bioinformatics Research?
What Information and Software Are Available?
Can I Learn a Programming Language Without Classes?
How Can I Use Web Information?
How Do I Understand Sequence Alignment Data?
How Do I Write a Program to Align Two Biological Sequences?
How Do I Predict Protein Structure from Sequence?
What Questions Can Bioinformatics Answer?
Computational Approaches to Biological Questions
Molecular Biology's Central Dogma
What Biologists Model
Why Biologists Model
Computational Methods Covered in This Book
A Computational Biology Experiment
The Bioinformatics Workstation
Setting Up Your Workstation
Working on a Unix system
Setting Up a Linux Workstation
How to Get Software Working
What Software Is Needed?
Files and Directories in Unix
Filesystem Basics
Commands for Working with Directories and Files
Working in a Multiuser Environment
Working on a Unix System
The Unix Shell
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
Finding Software
Judging the Quality of Information
Sequence Analysis, Pairwise Alignment, and Database Searching
Chemical Composition of Biomolecules
Composition of DNA and RNA
Watson and Crick Solve the Structure of DNA
Development of DNA Sequencing Methods
Genefinders and Feature Detection in DNA
DNA Translation
Pairwise Sequence Comparison
Sequence Queries Against Biological Databases
Multifunctional Tools for Sequence Analysis
Multiple Sequence Alignments, Trees, and Profiles
The Morphological to the Molecular
Multiple Sequence Alignment
Phylogenetic Analysis
Profiles and Motifs
Visualizing Protein Structures and Computing Structural Properties
A Word About Protein Structure Data
The Chemistry of Proteins
Web-Based Protein Structure Tools
Structure Visualization
Structure Classification
Structural Alignment
Structure Analysis
Solvent Accessibility and Interactions
Computing Physicochemical Properties
Structure Optimization
Protein Resource Databa
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