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.…mehr
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.Hinweis: Dieser Artikel kann nur an eine deutsche Lieferadresse ausgeliefert werden.
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.
Inhaltsangabe
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
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
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