ABSTRACT
SECTION 1 APPLICATION OF PERL IN BIOLOGY 451 Part I Introduction 451
1. What Is Perl Programming? 451 2. Why Is Perl Popular in Biology? 452 3. Some Perl Basics 456
Part II Step-By-Step Tutorial 458 1. Download and Install Perl 458 2. Download and Install TextPad 458 3. Install Bioperl Module 460 4. Start TextPad, Configure for Syntax Highlight and Running Perl 460 5. Test Bioperl Scripts 462
Part III An Application Example 463 1. Background 463 2. Read the File 465 3. Store the Data into MySQL 467 4. Retrieve the Data from MySQL 469
5. Web Application 470 SECTION 2 APPLICATION OF JAVA IN BIOLOGY 473
Part I Introduction 473 1. What Is JAVA? 473 2. Why Is JAVA Popular in Biology? 474 3. Some JAVA Basics 477
Part II Step-By-Step Tutorial 480 1. Download and Install Java 480 2. Download and Install TextPad 481 3. Install Biojava Module 482 4. Start TextPad, Configure for Syntax Highlight as well as Compiling and Running JAVA 483 5. Program Using Biojava 483
Part III An Application Example 487 SECTION 3 APPLICATION OF R IN BIOLOGY 494
Part I Introduction 494 1. What Is R Programming? 494 2. Why Is R Popular in Biology? 495 3. Some R Basics 495
Part II Step-By-Step Tutorials 497 1. Download and Install R 497 2. Install BioConductor 498 3. Perform Microarray Data Analysis Using BioConductor 499
With a large number of prokaryotic and eukaryotic genomes completely sequenced and more forthcoming, the use of genomic information and accumulated biomedical knowledge for the discovery of new knowledge has become the central theme of modern biomedical research. The exploration of the Internet and the use of the World Wide Web (WWW) have enabled various data sources like GenBank and a variety of bioinformatics tools like BLAST accessible to biomedical researchers. However, to truly exploit various sources and bioinformatics tools, biologists need to understand and be able to use programming languages for managing, presenting, and analyzing large amounts of data or results obtained from many different sources or tools.
