Bal / Hujol Java for Bioinformatics and Biomedical Applications

1. Auflage 2007
ISBN: 978-0-387-37237-2
Verlag: Springer-Verlag
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 342 Seiten

April 2006 Introduction Bioinformatics is at a crossroads. We work in a field that is changing every day, increasingly moving from specific solutions created by single researchers working alone or in small groups to larger, often geographically dispersed programs enabled by collaborative computing and open software. This book represents an important development, giving the reader an opportunity to discover how the use of open and reusable Java code can solve large bioinformatics problems in a software engineered and robust way. I work with one of the authors of this book every day, on the National Cancer Institute's cancer Biomedical Informatics Grid (caBIG™) project, and I can attest that they are well suited to share with their readers both their experience in the development and use of bioinformatics software, as well as their interest in solid software engineering and interoperability. Background and history In its short history, bioinformatics has become an increasingly important part of how scientists involved in biological research go about their work. This has lead to an explosion of interest in the subject, and a similar explosion in tools and data resources for researchers to learn and use in their work. Historically, tools for bioinformatics have been idiosyncratic and are custom-developed by the end-users (or those close to them) in an iterative fashion until the specific immediate problem is solved. This has led to a balkanization of informatics systems, sometimes yielding multiple, incompatible systems at a single institution for a single application.

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