文件名称：Java.for.Bioinformatics.and.Biomedical.Applications.(2007).part1.rar
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更新时间：2010-08-23 12:41:35
Bioinformatics Biomedical Java
The book does not profess to be the comprehensive tome on J2EE;instead, it is designed to cover a few of the important topics that lend themselves to use in the situations that are commonly encountered in this domain. It is hoped that a more focused approach would lead to a better and clearer understanding of the core capabilities of the platform than would be achieved by a lengthier treatment of the subject that cover all its different aspects. Indeed, the vastness and the complexity of the biomedical space and the pace and profundity with which science,technology, policy and legislation affect it is at times daunting. The
authors acknowledge the challenge of writing on a topic this difficult and hope to address the concerns of the readers of this volume to identify gaps and produce a more inclusive title while providing time for the emerging technologies described in this book and others beyond the scope of this book to mature and gain wider acceptance by the user community.
The book begins with an overview of the state of biomedical research today and the challenges it faces due to the silo model that has perpetuated over decades across universities and research centers across the world. It establishes a case for and the rationale behind the current move towards integrative, collaborative and standards based research platform through an introduction to the NCI caBIG™ program. It next provides an overview of emerging architectural trends such as Web Services and Service-Oriented Architecture. The book is not as much about the J2EE platform as it is about its application to building useful software and does not dwell on the theoretical aspects of the language or the platform; the authors (as well as the readers) recognize that several excellent works on that topic already exist. Instead the uniqueness of this book is that after just a short introduction, it takes a deep dive into demonstrating how to build highly functional graphical user interfaces for common and widely used bioinformatics tools that most researchers are
familiar with and find indispensable for any kind of research activity. The reader is led through a step-wise and incremental software development
approach with two goals in mind - to demonstrate a systematic standard software engineering approach to application development and, to activate a thoughtful design process in the mind of the developer that is aimed at exploring ways to enhance the functionality and usefulness for end-users.The applications that are considered the backbone of modern genomic and bioinformatics-driven research - Basic Local Alignment Search Tool
(BLAST), Genscan gene prediction tool and others are used to illustrate this process. The reader will notice a significant amount of code in this
book and realize that this is so by design. Although there are many ways of architecting a solution for a particular problem, we have illustrated one such approach while encouraging users to build their own. In doing so, we
have also attempted to promote the reuse of tried and tested code from existing software libraries based on open source projects such as Apache,
BioJava, caBIG™, and others.