"In this book, Andy Baxevanis and Francis Ouellette . . . have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt."–Eric Lander from the Foreword

Reviews from the First Edition

"...provides a broad overview of the basic tools for sequence analysis ... For biologists approaching this subject for the first time, it will be a very useful handbook to keep on the shelf after the first reading, close to the computer."–Nature Structural Biology

"...should be in the personal library of any biologist who uses the Internet for the analysis of DNA and protein sequence data." –Science

"...a wonderful primer designed to navigate the novice through the intricacies of in scripto analysis ... The accomplished gene searcher will also find this book a useful addition to their library ... an excellent reference to the principles of bioinformatics."–Trends in Biochemical Sciences

This new edition of the highly successful Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins provides a sound foundation of basic concepts, with practical discussions and comparisons of both computational tools and databases relevant to biological research.

Equipping biologists with the modern tools necessary to solve practical problems in sequence data analysis, the Second Edition covers the broad spectrum of topics in bioinformatics, ranging from Internet concepts to predictive algorithms used on sequence, structure, and expression data. With chapters written by experts in the field, this up-to-date reference thoroughly covers vital concepts and is appropriate for both the novice and the experienced practitioner. Written in clear, simple language, the book is accessible to users without an advanced mathematical or computer science background. This new edition includes:

• All new end-of-chapter Web resources, bibliographies, and problem sets
• Accompanying Web site containing the answers to the problems, as well as links to relevant Web resources
• New coverage of comparative genomics, large-scale genome analysis, sequence assembly, and expressed sequence tags
• A glossary of commonly used terms in bioinformatics and genomics

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, positional cloning, clinical research, and computational biology.

About the Author

Andy Baxevanis is the Associate Director for Intramural Research and the Director, Computational Genomics, at the National Human Genome Research Institute, National Institutes of Health. He received his B.S. in biological sciences from Cornell University in 1984 and his Ph.D. in the Department of Biology at The Johns Hopkins University in 1991. His research focuses on protein structure-function relationships, positional cloning, and the development of new methods for the analysis of gene expression data. His accomplishments have been recognized by the Bodossaki Foundation in Greece, who awarded him their 1999 Academic Prize in Medicine and Biology.

Francis Ouellette is Director of the Bioinformatics Core Facility at the Center for Molecular Medicine and Therapeutics, The University of British Columbia, and the Director of Bioinformatics for the Canadian Genetic Diseases Network. He previously held the position of GenBank Coordinator for the National Center for Biotechnology Information at the National Institutes of Health. He earned his B.Sc. in the Department of Biology at McGill University in 1991, and is the founder and moderator of bionet.molbio.yeast, a Usenet discussion forum for the yeast genomics community.

The Java 2 Platform, Enterprise Edition, offers enterprise developers a simplified, component-based approach to creating applications for both intranets and the Internet.

Created by the Enterprise Team of the Java Software group at Sun Microsystems, Designing Enterprise Applications with the Java™ 2 Platform, Enterprise Edition describes the application configurations supported by the J2EE platform and presents practical guidelines for determining the best design for particular needs. It explores web-based clients based on Java servlets and Java ServerPages, middle-tier solutions using Enterprise JavaBeans technology, and backend connections based on JDBC technology. It also presents security, deployment, transaction management, and other key issues for today's applications.

Using both smaller code samples and a full-scale e-commerce example, this book provides concrete guidelines to assist with mastering the features and benefits of the J2EE platform.

Chapters include:
* An introduction to the J2EE platform and several scenarios for Internet and intranet applications built on the J2EE platform
* An in-depth discussion of the technologies provided by the J2EE platform
* How to create Web-based applications implemented with Java servlets and JavaServer Pages technologies
* How to implement the middle tier of J2EE applications using Enterprise JavaBeans component technology
* How to connect new J2EE applications to existing information systems using JDBC and other technologies
* A discussion of packaging and deploying applications for the J2EE platform
* Information on techniques, both automatic and programmatic, for managing transactions
* An in-depth exploration of the security features provided by the J2EE platform
* A complete hands-on example of an e-commerce application--the Java Pet Store Demo--written using these design guidelines
* A glossary of terms used in discussing the Java 2 Platform, Enterprise Edition and its technologies

About the Author

Nicholas Kassem is a Senior Staff Engineer with Sun Microsystems. He has influenced and had responsibility for a number of technologies and initiatives within Java Software, including the Java Web Server, Java Embedded Server, Java Servlet API, JavaServer Pages, Java Message Queuing, and the J2EE programming model.

"The best logic of our time is to be found in computer science departments....Computer scientists (many of whom are former logicians) are developing the logic that really matters, the one that really meets the challenges of today's demands for automated reasoning. This book is a prime example of such triumph of useful logic." --The Bulletin of Mathematics Books

This book develops a type theory, studies its properties, and explains its uses in computer science. The book focuses in particular on how the study of type theory may offer a powerful and uniform language for programming, program specification and development, and logical reasoning. The type theory developed here reflects a conceptual distinction between logical propositions and computational data types. Starting from an introduction of the basic concepts, the author explains the meaning and use of the type-theoretic language with proof-theoretic justifications, and discusses various issues in the study of type theory. The practical use of the language is illustrated by developing an approach to specification and data refinement in type theory, which supports modular development of specification, programs, and proofs. Students and researchers in computer science and logic will welcome this exciting new book.

Studies a type theory and its applications to computer science. Basic ideas in the development of the type theory are explained.

About the Author

Zhaohui Luo is at JCMB, Edinburgh.

First impressions are important.

To introduce your Assembly Language programming students to the fundamental concepts of contemporary computer architecture, start with a Reduced Instruction Set Computer (RISC).

When students first encounter computer architecture, they need to begin with the basics of modern computer organization. The MIPS architecture embodies the fundamental design principles of all contemporary RISC architectures:

• All instructions are directly executed in hardware
• The rate at which instructions are issued is maximized
• Instructions are easy to decode
• Only load and store instructions reference memory
• Plenty of general purpose registers are provided (32 for MIPS)

MIPS Assembly Language Programming offers students an understanding of how the functional components of modern computers are put together and how a computer works at the machine-language level. The book begins with a datapath diagram that shows a simple implementation of the MIPS architecture, consisting of a register file, an ALU, a memory. a program counter, and an instruction register. As students progress through the text, they will elaborate on this established datapath diagram model, allowing them to visualize how the instructions are fetched and executed as they write their programs.

The Spim simulator for the MIPS architecture runs on PC's and Unix^® systems. All the programming exercises are done using this simulator, which can be downloaded for free from the Internet. Using the MIPS simulator allows students to observe the contents of the registers and memory change as their programs execute. The students are not isolated by a particular operating system from experiencing and writing code dealing with:

• Memory-mapped I/0
• Interrupts and exception processing
• Delayed loads and delayed branches for a pipelined implementation

It is assumed that students using this text already have some experience in developing algorithms, and running programs in a high-level language. The skills they will learn with MIPS Assembly Language Programming offer a sound basis for advanced work in computer architectures and complex assembly languages.

Welcome to XML programming! In this book we're going to take a guided tour of what XML has to offer[md]we'll see it all, from the basics of XML to the advanced topics, from creating our own XML documents to using XML stylesheets, from creating XML links to creating XML browsers.

HTML is like Latin-a language that soon won't be spoken anymore. The new mother tongue for creating pages on the Web is XML (eXtensible Markup Language), the second-generation HTML available with Internet Explorer 4. How can you put it to work fast? This professional learn-it and do-it guide explains what XML is, shows how to implement it, and helps you master the intricacies. Invaluable for Web developers and content providers alike.