Java for Bioinformatics and Biomedical Applications

By: Harshawardhan Bal, Johnny Hujol

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Hardcover | 25 October 2006

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Hardcover
364 Pages

Dimensions(cm)
23.39 x 15.6 x 2.06

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This book examines the tools being developed to meet the goal of eliminating suffering and death from cancer by 2015. It focuses on creating and integrating practical, useful tools for the scientific community in the context of real-life, real-value biomedical problems. From a software perspective, a functional approach is used to teach the Java platform and its features for enterprise-level application development. Under this approach, the various syntactical and operative elements of the language are taught in the context of definable research problems that enable the user to relate how the different parts of the language fit together. The book illustrates how individual bioinformatics applications can be stitched together into a pipeline so that users can direct the output of one tool to perform further analysis. All examples are derived from practical problems faced in biomedical/clinical data retrieval and analysis during routine bioinformatics and cancer research.

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Foreword	p. IX
Introduction	p. IX
Background and history	p. IX
Interfaces and standards	p. X
Java as a platform	p. X
The future	p. XI
Preface	p. XIII
	p. 1
Introduction to Bioinformatics and Java	p. 1
The Origins of Bioinformatics	p. 1
Current State of Biomedical Research	p. 3
The cancer Biomedical Informatics Grid program	p. 6
caBIG Organization and Architecture	p. 7
The Model-View-Controller Framework	p. 9
Web Services and Service-Oriented Architecture	p. 10
CaGrid	p. 11
Let's look at each of the tools in turn and understand how they sub-serve or address a small component of the bigger research problem	p. 14
CaArray	p. 14
CaWorkbench	p. 16
RProteomics	p. 17
cPath	p. 17
CaTissue Core, caTissue Clinical Annotation Engine and caTIES	p. 18
CaTissue Core	p. 18
Summary	p. 20
Questions and Exercises	p. 21
Additional Resources	p. 21
Selected Reading	p. 23
	p. 25
Introduction to Basic Local Alignment Search Tool	p. 25
The Purpose of Blast	p. 25
Performing a Blast Analysis	p. 27
Developing the SwingBlast Application	p. 32
Designing the SwingBlast Java Application	p. 35
Java Event Model	p. 36
Adding Events to Applications	p. 37
Designing the SwingBlast GUI	p. 39
Coding the SwingBlast GUI	p. 45
Coding the SwingBlast Business Logic	p. 48
Determining Sequence Type: Nucleotide or Protein?	p. 53
Displaying Valid Blast Options	p. 63
Summary	p. 80
Questions and Exercises	p. 81
Additional Resources	p. 81
Selected Reading	p. 81
	p. 83
Running Blast using SwingBlast	p. 83
Introduction	p. 83
The NCBI QBlast Package	p. 83
Strategy for Creating a QBlast Based System	p. 84
Designing the Blast API	p. 86
Description of Blast Classes	p. 88
Implementing JQBlast	p. 92
Enhancing the SwingBlast Application	p. 103
Retrieving Sequences From GenBank Using BioJava	p. 124
Retrieving GenBank Without BioJava	p. 129
Input Validation	p. 132
Controlling Program Events and Responses	p. 137
Reporting Blast Status	p. 139
Displaying Blast Results Interactively	p. 143
Summary	p. 151
Questions and Exercises	p. 152
Additional Resources	p. 152
Selected Reading	p. 153
	p. 155
Facilitating PubMed Searches: JavaServer Pages and Java Servlets	p. 155
Introduction	p. 155
HTTP and CGI	p. 155
HTTP Protocol	p. 156
Get and Post Methods	p. 157
CGI For Generating Dynamic Content	p. 157
Servlets and JavaServer Pages Technologies	p. 158
Java API for Servlets and JSPs	p. 159
JavaServer Pages Standard Tag Library (JSTL)	p. 160
Apache Tomcat Server	p. 160
The NCBI PubMed Literature Search and Retrieval Service	p. 161
Accessing Biomedical Literature Through Entrez	p. 161
Create Web Application With Servlets and JSPs	p. 165
Web Application Structure	p. 167
Creating a Servlet to Access Biomedical Literature	p. 169
Displaying PubMed Abstracts	p. 178
Highlighting Search Terms in Retrieved Abstracts	p. 193
Summary	p. 204
Questions and Exercises	p. 205
Additional Resources	p. 206
Selected Reading	p. 206
	p. 209
Creating a Gene Prediction and BLAST Analysis Pipeline	p. 209
Introduction	p. 209
Gene Prediction Programs	p. 209
DNA Transcription and Translation	p. 210
Gene Prediction with Genscan	p. 212
Running Genscan Analyses	p. 213
Analyzing GenScan Output	p. 215
Creating SwingGenscan	p. 221
Writing the Code for SwingGenScan	p. 222
The SwingGenScan User Interface	p. 235
Running SwingGenScan	p. 243
Summary	p. 246
Questions and Exercises	p. 247
Additional Resources	p. 247
Selected Reading	p. 247
	p. 249
Cancer Biomedical Informatics Grid (caBIG)	p. 249
Cancer Biomedical Informatics Grid	p. 249
Structure and Organization of caBIG	p. 250
Data Integration and ETL	p. 253
Cancer Common Ontologic Representation Environment (caCORE)	p. 255
Cancer Bioinformatics Infrastructure Objects (caBIO)	p. 257
Downloading and Configuring caBIO	p. 259
Creating the JcaBIO Application	p. 260
JcaBIO Classes and Application Structure	p. 261
Coding the SwingCaBIO Application	p. 263
Coding JcaBIO: The CaBIOReportEngine Class	p. 275
Coding JcaBIO: The CaBIOSearchEngine Class	p. 282
Running the JcaBIO Application	p. 286
Summary	p. 289
Questions and Exercises	p. 290
Additional Resources	p. 291
Selected Reading	p. 292
Appendix	p. 295
Apache Ant and Tomcat	p. 295
Downloading the Apache Tomcat server	p. 295
Managing the Apache Tomcat Server	p. 302
Installing and Configuring the Apache Ant Build Tool	p. 306
Configuring environmental variables for Ant	p. 309
Building and Deploying The Web Application	p. 310
Building the WAR file	p. 310
Deploying the application on Tomcat using Ant	p. 312
Version Control Systems	p. 314
Additional Resources	p. 315
Table of Contents provided by Ingram. All Rights Reserved.

Java for Bioinformatics and Biomedical Applications

At a Glance

Hardcover

Shipping

How to return your order

Defective items

You Can Find This Book In

Other Editions and Formats

Paperback

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2nd Edition

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