Bal / Hujol Java for Bioinformatics and Biomedical Applications

1. Auflage 2007
ISBN: 978-0-387-37237-2
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 342 Seiten

Medical science and practice have undergone fundamental changes in the last 5 years, as large-scale genome projects have resulted in the sequencing of a number of important microbial, plant and animal genomes. This book aims to combine industry standard software engineering and design principles with genomics, bioinformatics and cancer research. Rather than an exercise in learning a programming platform, the text focuses on useful analytical tools for the scientific community.

Autoren/Hrsg.

Bal, Harshawardhan

Hujol, Johnny

Inhaltsverzeichnis

1;Contents;5
2;Foreword;9
2.1;Introduction;9
2.2;Background and history;9
2.3;Interfaces and standards;10
2.4;Java as a platform;10
2.5;The future;11
3;Preface;12
4;Introduction to Bioinformatics and Java;17
4.1;The Origins of Bioinformatics;17
4.2;Current State of Biomedical Research;19
4.3;The cancer Biomedical Informatics Grid program;22
4.4;caBIG ™ Organization and Architecture;23
4.5;The Model-View-Controller Framework;25
4.6;Web Services and Service-Oriented Architecture;26
4.7;CaGrid;27
4.8;Questions and Exercises;37
4.9;Additional Resources;37
4.10;Selected Reading;39
5;Introduction to Basic Local Alignment Search Tool;40
5.1;The Purpose of BLAST;40
5.2;Performing a BLAST Analysis;42
5.3;Java Event Model;51
5.4;Adding Events to Applications;52
5.5;Coding the SwingBlast Business Logic;63
5.6;Determining Sequence Type: Nucleotide or Protein?;68
5.7;Displaying Valid BLAST Options;78
5.8;Summary;95
5.9;Questions and Exercises;96
5.10;Selected Reading;96
6;Running BLAST using SwingBlast;98
6.1;Introduction;98
6.2;The NCBI QBLAST Package;98
6.3;Implementing JQBIast;107
6.4;Enhancing the SwingBlast Application;118
6.5;Retrieving Sequences From GenBanl< Using BioJava;139
6.6;Retrieving GenBanIc Without BioJava;144
6.7;Input Validation;147
6.8;Controlling Program Events and Responses;152
6.9;Displaying BLAST Results Interactively;158
6.10;Summary;166
6.11;Selected Reading;168
7;Facilitating PubMed Searches: JavaServer Pages and Java Servlets;169
7.1;JavaServer Pages Standard Tag Library ( JSTL);174
7.2;Apache Tomcat Server;174
7.3;Create Web Application With Servlets and JSPs;179
7.4;Questions and Exercises;219
7.5;Additional Resources;220
7.6;Selected Reading;220
8;Creating a Gene Prediction and BLAST Analysis Pipeline;222
8.1;Introduction;222
8.2;Gene Prediction Programs;222
8.3;DNA Transcription and Translation;223
8.4;Gene Prediction with Genscan;225
8.5;Running Genscan Analyses;226
8.6;Analyzing GenScan Output;228
8.7;Creating SwingGenscan;233
8.8;Writing the Code for SwingGenScan;234
8.9;The SwingGenScan User Interface;247
8.10;Running SwingGenScan;255
8.11;Summary;258
8.12;Questions and Exercises;259
8.13;Additional Resources;259
8.14;Selected Reading;259
9;cancer Biomedical Informatics Grid (caBIG™);261
9.1;Structure and Organization of caBIG ™;262
9.2;Cancer Bioinformatics Infrastructure Objects ( caBIO);269
9.3;Downloading and Configuring caBIO;271
9.4;Creating the JcaBIO Application;272
9.5;JcaBIO Classes and Application Structure;273
9.6;Coding the SwingCaBIO Application;275
9.7;Coding JcaBIO: The CaBIOReportEngine Class;287
9.8;Coding JcaBIO: The CaBIOSearchEngine Class;294
9.9;Running the JcaBIO Application;298
9.10;Additionaf Resources;303
9.11;Selected Reading;304
10;Appendix;306
10.1;Apache Ant and Tomcat;306
10.2;Downloading the Apache Tomcat server;306
10.3;Installing and Configuring the Apache Ant Build Tool;317
10.4;Version Control Systems;325
10.5;Additional Resources;326
11;Index;328