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Mastering Perl for bioinformatics /
Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capa...
| Clasificación: | Libro Electrónico |
|---|---|
| Autor principal: | |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
Sebastopol, Calif. ; Farnham :
O'Reilly,
2003.
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| Temas: | |
| Acceso en línea: | Texto completo (Requiere registro previo con correo institucional) |
Tabla de Contenidos:
- Machine derived contents note: Copyright; Foreword; Preface; About This Book; What You Need to Know to Use This Book; Organization of This Book; Conventions Used in This Book; Comments and Questions; Acknowledgments; Part I: Object-Oriented Programming in Perl; Chapter 1: Modular Programming with Perl; 1.1 What Is a Module?; 1.2 Why Perl Modules?; 1.3 Namespaces; 1.4 Packages; 1.5 Defining Modules; 1.6 Storing Modules; 1.7 Writing Your First Perl Module; 1.8 Using Modules; 1.9 CPAN Modules; 1.10 Exercises; Chapter 2: Data Structures and String Algorithms; 2.1 Basic Perl Data Types; 2.2 References; 2.3 Matrices; 2.4 Complex Data Structures; 2.5 Printing Complex Data Structures; 2.6 Data Structures in Action; 2.7 Dynamic Programming; 2.8 Approximate String Matching; 2.9 Resources; 2.10 Exercises; Chapter 3: Object-Oriented Programming in Perl; 3.1 What Is Object-Oriented Programming?; 3.2 Using Perl Classes (Without Writing Them); 3.3 Objects, Methods, and Classes in Perl; 3.4 Arrow Notation ( ->); 3.5 Gene1: An Example of a Perl Class; 3.6 Details of the Gene1 Class; 3.7 Gene2.pm: A Second Example of a Perl Class; 3.8 Gene3.pm: A Third Example of a Perl Class; 3.9 How AUTOLOAD Works; 3.10 Cleaning Up Unused Objects with DESTROY; 3.11 Gene.pm: A Fourth Example of a Perl Class; 3.12 How to Document a Perl Class with POD; 3.13 Additional Topics; 3.14 Resources; 3.15 Exercises; Chapter 4: Sequence Formats and Inheritance; 4.1 Inheritance; 4.2 FileIO.pm: A Class to Read and Write Files; 4.3 SeqFileIO.pm: Sequence File Formats; 4.4 Resources; 4.5 Exercises; Chapter 5: A Class for Restriction Enzymes; 5.1 Envisioning an Object; 5.2 Rebase.pm: A Class Module; 5.3 Restriction.pm: Finding Recognition Sites; 5.4 Drawing Restriction Maps; 5.5 Resources; 5.6 Exercises; Part II: Perl and Bioinformatics; Chapter 6: Perl and Relational Databases; 6.1 One Perl, Many Databases; 6.2 Popular Relational Databases; 6.3 Relational Database Definitions; 6.4 Structured Query Language; 6.5 Administering Your Database; 6.6 Relational Database Design; 6.7 Perl DBI and DBD Interface Modules; 6.8 A Rebase Database Implementation; 6.9 Additional Topics; 6.10 Resources; 6.11 Exercises; Chapter 7: Perl and the Web; 7.1 How the Web Works; 7.2 Web Servers and Browsers; 7.3 The Common Gateway Interface; 7.4 Rebase: Building Dynamic Web Pages; 7.5 Exercises; Chapter 8: Perl and Graphics; 8.1 Computer Graphics; 8.2 GD; 8.3 Adding GD Graphics to Restrictionmap.pm; 8.4 Making Graphs; 8.5 Resources; 8.6 Exercises; Chapter 9: Introduction to Bioperl; 9.1 The Growth of Bioperl; 9.2 Installing Bioperl; 9.3 Testing Bioperl; 9.4 Bioperl Problems; 9.5 Overview of Objects; 9.6 bptutorial.pl; 9.7 bptutorial.pl: sequencemanipulation Demo; 9.8 Using Bioperl Modules; Part III: Appendixes; Appendix A: Perl Summary; A.1 Command Interpretation; A.2 Comments; A.3 Scalar Values and Scalar Variables; A.4 Assignment; A.5 Statements and Blocks; A.6 Arrays; A.7 Hashes; A.8 Complex Data Structures; A.9 Operators; A.10 Operator Precedence; A.11 Basic Operators; A.12 Conditionals and Logical Operators; A.13 Binding Operators; A.14 Loops; A.15 Input/Output; A.16 Regular Expressions; A.17 Scalar and List Context; A.18 Subroutines; A.19 Modules and Packages; A.20 Object-Oriented Programming; A.21 Built-in Functions; Appendix B: Installing Perl; B.1 Installing Perl on Your Computer; B.2 Versions of Perl; B.3 Internet Access; B.4 Downloading; B.5 How to Run Perl Programs; B.6 Finding Help; Colophon.