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Java for Bioinformatics and Biomedical Applications
von: Harshawardhan Bal, Johnny Hujol
Springer-Verlag, 2007
ISBN: 9780387372372 , 342 Seiten
Format: PDF
Kopierschutz: Wasserzeichen
Preis: 149,79 EUR
Contents
5
Foreword
9
Introduction
9
Background and history
9
Interfaces and standards
10
Java as a platform
10
The future
11
Preface
12
Introduction to Bioinformatics and Java
17
The Origins of Bioinformatics
17
Current State of Biomedical Research
19
The cancer Biomedical Informatics Grid program
22
caBIG ™ Organization and Architecture
23
The Model-View-Controller Framework
25
Web Services and Service-Oriented Architecture
26
CaGrid
27
Questions and Exercises
37
Additional Resources
37
Selected Reading
39
Introduction to Basic Local Alignment Search Tool
40
The Purpose of BLAST
40
Performing a BLAST Analysis
42
Java Event Model
51
Adding Events to Applications
52
Coding the SwingBlast Business Logic
63
Determining Sequence Type: Nucleotide or Protein?
68
Displaying Valid BLAST Options
78
Summary
95
Questions and Exercises
96
Selected Reading
96
Running BLAST using SwingBlast
98
Introduction
98
The NCBI QBLAST Package
98
Implementing JQBIast
107
Enhancing the SwingBlast Application
118
Retrieving Sequences From GenBanl< Using BioJava
139
Retrieving GenBanIc Without BioJava
144
Input Validation
147
Controlling Program Events and Responses
152
Displaying BLAST Results Interactively
158
Summary
166
Selected Reading
168
Facilitating PubMed Searches: JavaServer Pages and Java Servlets
169
JavaServer Pages Standard Tag Library ( JSTL)
174
Apache Tomcat Server
174
Create Web Application With Servlets and JSPs
179
Questions and Exercises
219
Additional Resources
220
Selected Reading
220
Creating a Gene Prediction and BLAST Analysis Pipeline
222
Introduction
222
Gene Prediction Programs
222
DNA Transcription and Translation
223
Gene Prediction with Genscan
225
Running Genscan Analyses
226
Analyzing GenScan Output
228
Creating SwingGenscan
233
Writing the Code for SwingGenScan
234
The SwingGenScan User Interface
247
Running SwingGenScan
255
Summary
258
Questions and Exercises
259
Additional Resources
259
Selected Reading
259
cancer Biomedical Informatics Grid (caBIG™)
261
Structure and Organization of caBIG ™
262
Cancer Bioinformatics Infrastructure Objects ( caBIO)
269
Downloading and Configuring caBIO
271
Creating the JcaBIO Application
272
JcaBIO Classes and Application Structure
273
Coding the SwingCaBIO Application
275
Coding JcaBIO: The CaBIOReportEngine Class
287
Coding JcaBIO: The CaBIOSearchEngine Class
294
Running the JcaBIO Application
298
Additionaf Resources
303
Selected Reading
304
Appendix
306
Apache Ant and Tomcat
306
Downloading the Apache Tomcat server
306
Installing and Configuring the Apache Ant Build Tool
317
Version Control Systems
325
Additional Resources
326
Index
328
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