Java for Bioinformatics and Biomedical Applications (eBook)
XVIII, 342 Seiten
Springer US (Verlag)
978-0-387-37237-2 (ISBN)
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.
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(TM)) 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.
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
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
| Erscheint lt. Verlag | 16.1.2007 |
|---|---|
| Zusatzinfo | XVIII, 342 p. 108 illus., 16 illus. in color. |
| Verlagsort | New York |
| Sprache | englisch |
| Themenwelt | Informatik ► Programmiersprachen / -werkzeuge ► Java |
| Mathematik / Informatik ► Informatik ► Web / Internet | |
| Informatik ► Weitere Themen ► Bioinformatik | |
| Medizin / Pharmazie ► Medizinische Fachgebiete ► Biomedizin | |
| Medizin / Pharmazie ► Medizinische Fachgebiete ► Onkologie | |
| Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie | |
| Technik ► Medizintechnik | |
| Schlagworte | Bioinformatics • Biology • Biomedical Application • Biomedical Applications • biomedical informatics • Biotechnology • Cancer Research • Genome • Health Informatics • Java SDK • JavaServer Pages • Molecular Medicine • National Center for Biotechnology Information • Proteomics • PubMed • Servlets |
| ISBN-10 | 0-387-37237-7 / 0387372377 |
| ISBN-13 | 978-0-387-37237-2 / 9780387372372 |
| Haben Sie eine Frage zum Produkt? |
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