Useful Books and Software

As you'd expect, this book teaches you all the core Java skills you need on the job, showing you how to take advantage of time-saving Java features like:

* the Scanner class
* type-safe enumerations
* enhanced for loops
* typed collections
* generics
* autoboxing
* the StringBuilder class

But beyond that, it gives you the practical training you need in both object-oriented programming and data access programming. In particular, it shows you how to use a 3-tiered architecture to separate the business classes, presentation classes, and database classes of an application. It shows you practical techniques for populating business objects with data from files or databases. And it shows you how to use inheritance, polymorphism, interfaces, and the factory pattern in a way that is not just understandable but also reflects what's done in the real world. The result is, you'll soon be writing Java applications the way the best professionals do.

To download the book applications...
You can download the code for the book applications, the starting code and test data for the exercises in the book, and sample chapters from the Murach web site.

Publisher: Mike Murach & Associates
Authors: Doug Lowe, Joel Murach, Andrea Steelman
Release Date: 2005-01-15
ISBN/EAN: 1890774294 / 9781890774295

New Price: $30.00 / Used Price: $13.95

But if you're serious about your profession, intuition isn't enough. Perl Best Practices author Damian Conway explains that rules, conventions, standards, and practices not only help programmers communicate and coordinate with one another, they also provide a reliable framework for thinking about problems, and a common language for expressing solutions. This is especially critical in Perl, because the language is designed to offer many ways to accomplish the same task, and consequently it supports many incompatible dialects.

With a good dose of Aussie humor, Dr. Conway (familiar to many in the Perl community) offers 256 guidelines on the art of coding to help you write better Perl code--in fact, the best Perl code you possibly can. The guidelines cover code layout, naming conventions, choice of data and control structures, program decomposition, interface design and implementation, modularity, object orientation, error handling, testing, and debugging.

They're designed to work together to produce code that is clear, robust, efficient, maintainable, and concise, but Dr. Conway doesn't pretend that this is the one true universal and unequivocal set of best practices. Instead, Perl Best Practices offers coherent and widely applicable suggestions based on real-world experience of how code is actually written, rather than on someone's ivory-tower theories on how software ought to be created.

Most of all, Perl Best Practices offers guidelines that actually work, and that many developers around the world are already using. Much like Perl itself, these guidelines are about helping you to get your job done, without getting in the way.

Praise for Perl Best Practices from Perl community members:

"As a manager of a large Perl project, I'd ensure that every member of my team has a copy of Perl Best Practices on their desk, and use it as the basis for an in-house style guide." -- Randal Schwartz

"There are no more excuses for writing bad Perl programs. All levels of Perl programmer will be more productive after reading this book." -- Peter Scott

"Perl Best Practices will be the next big important book in the evolution of Perl. The ideas and practices Damian lays down will help bring Perl out from under the embarrassing heading of "scripting languages". Many of us have known Perl is a real programming language, worthy of all the tasks normally delegated to Java and C++. With Perl Best Practices, Damian shows specifically how and why, so everyone else can see, too." -- Andy Lester

"Damian's done what many thought impossible: show how to build large, maintainable Perl applications, while still letting Perl be the powerful, expressive language that programmers have loved for years." -- Bill Odom

"Finally, a means to bring lasting order to the process and product of real Perl development teams." -- Andrew Sundstrom

New Price: $21.96 / Used Price: $24.50

New Price: $54.98 / Used Price: $84.97

But with so many changes, where do you start? You could read through the lengthy, often boring language specification; you could wait for the latest 500 page tome on concepts and theory; you could even play around with the new JDK, hoping you figure things out--or you can get straight to work with "Java 5.0 Tiger: A Developer's Notebook,"

This no-nonsense, down-and-dirty guide by bestselling Java authors Brett McLaughlin and David Flanagan skips all the boring prose and lecture, and jumps right into Tiger. You'll have a handle on the important new features of the language by the end of the first chapter, and be neck-deep in code before you hit the halfway point. Using the task-oriented format of this new series, you'll get complete practical coverage of generics, learn how boxing and unboxing affects your type conversions, understand the power of varargs, learn how to write enumerated types and annotations, master Java's new formatting methods and the for/in loop, and even get a grip on concurrency in the JVM.

Light on theory and long on practical application, "Java 5.0 Tiger: A Developer's Notebook" allows you to cut to the chase, getting straight to work with Tiger's new features. The new Developer's Notebooks series from O'Reilly covers important new tools for software developers. Emphasizing example over explanation and practice over theory, they focus onlearning by doing--you'll get the goods straight from the masters, in an informal and code-intensive style that suits developers. If you've been curious about Tiger, but haven't known where to start, this no-fluff, lab-style guide is the solution.

Publisher: O'Reilly Media, Inc.
Authors: David Flanagan, Brett McLaughlin
Release Date: 2004-06-25
ISBN/EAN: 0596007388 / 9780596007386

New Price: $4.70 / Used Price: $4.73

• Create dynamic websites with design and usability in mind, as well as functionality
• Understand how PHP scripts work, giving you confidence to adapt them to your own needs
• Bring online forms to life, check required fields, and ensure user input is safe to process
• Upload files and automatically create thumbnails from larger images
• Manage website content with a searchable database

• Chapter 1: What Is PHPAnd Why Should I Care?
• Chapter 2: Getting Ready to Work with PHP
• Chapter 3: How to Write PHP Scripts
• Chapter 4: Lightening Your Workload with Includes
• Chapter 5: Bringing Forms to Life
• Chapter 6: Uploading Files
• Chapter 7: Using PHP to Manage Files
• Chapter 8: Generating Thumbnail Images
• Chapter 9: Pages That Remember: Simple Login and Multipage Forms
• Chapter 10: Setting Up MySQL and phpMyAdmin
• Chapter 11: Getting Started with a Database
• Chapter 12: Creating a Dynamic Online Gallery
• Chapter 13: Managing Content
• Chapter 14: Solutions to Common PHP/MySQL Problems
• Chapter 15: Keeping Intruders at Bay

New Price: $20.00 / Used Price: $24.74

Do you want to push Ruby to its limits? The Ruby Cookbook is the most comprehensive problem-solving guide to today's hottest programming language. It gives you hundreds of solutions to real-world problems, with clear explanations and thousands of lines of code you can use in your own projects.

From data structures and algorithms, to integration with cutting-edge technologies, the Ruby Cookbook has something for every programmer. Beginners and advanced Rubyists alike will learn how to program with:

• Strings and numbers
• Arrays and hashes
• Classes, modules, and namespaces
• Reflection and metaprogramming
• XML and HTML processing
• Ruby on Rails (including Ajax integration)
• Databases
• Graphics
• Internet services like email, SSH, and BitTorrent
• Web services
• Multitasking
• Graphical and terminal interfaces

If you need to write a web application, this book shows you how to get started with Rails. If you're a system administrator who needs to rename thousands of files, you'll see how to use Ruby for this and other everyday tasks. You'll learn how to read and write Excel spreadsheets, classify text with Bayesian filters, and create PDF files. We've even included a few silly tricks that were too cool to leave out, like how to blink the lights on your keyboard.

The Ruby Cookbook is the most useful book yet written about Ruby. When you need to solve a problem, don't reinvent the wheel: look it up in the Cookbook.

New Price: $21.95 / Used Price: $9.67

• Working with interactive forms and style sheets
• Presenting user-friendly page navigation
• Creating dynamic content
• Producing visual effects for stationary content
• Positioning HTML elements
• Managing browser windows and multiple frames

New Price: $7.00 / Used Price: $1.63

New Price: n.a. / Used Price: $2.33

The book is perfect for developers of Web sites running on Apache on Unix. Loyalties vary in terms of operating systems, Web servers, and scripting languages, but those who find their home in the Unix and Perl environments will find this book right up their alleys. The target audience is developers somewhat familiar with Perl and the Unix-based Web server environment, but you'll find the book illustrative even if your knowledge is sketchy.

After showing how to make database connections using Perl and MySQL, author Paul DuBois dives into some useful real-world examples to help you build your skills. He shows how to implement a simple to-do list application, an online product registration site, contests, online polls, image databases, an online greeting card service, and more. There is also excellent coverage of search facilities and session management.

The sample code for the applications in this text is presented in small pieces in context with the discussion; most of the space is devoted to explanations of the issues and implementation. All of the code is available, however, from the book's companion Web site. This tutorial is an excellent way for Perl developers to move to the next level of development and make the most of some powerful, free tools. --Stephen W. Plain

MySQL and Perl for the Web provides a much-needed handbook for database and Web developers seeking an extensive and detailed guide for using the combination of MySQL and Perl to build dynamic and interactive database-backed Web sites. It shows how to use Perl's DBI database access module, pairing it with with the CGI.pm module that allows Web pages and forms to be generated and processed easily. These tools provide developers with a solid foundation for creating applications that incorporate database content to create dynamic, up-to-date Web sites.

The book employs a practical learn-by-doing approach that demonstrates development techniques by building complete applications, not just fragmentary pieces. It shows what to do at each step of the way during the process of building live, working examples. Applications are fully explained so you can understand how they work and apply the techniques they illustrate to your own projects.

New Price: $32.20 / Used Price: $14.00

Departing from O'Reilly's earlier monograph Developing Bioinformatic Computer Skills, Tisdall's text is organized aggressively along didactic lines. Nearly all of the 13 chapters begin with twin bullet lists of Perl programming tools and the bioinformatic methods that require them. Likewise, the chapters end with exercises. String concatenation is illustrated with gene splicing, and regular expressions are taught with gene transcription and motif searching.

Tisdall emphasizes sequence examples throughout, leading up to an introduction to a Perl interface for the NIH GenBank biological database and the widely used BLAST sequence alignment tool. After a brief discussion of three-dimensional protein structure, he returns to sequence extraction and secondary structure prediction.

Tisdall's goal is to boost the beginning programmer into a domain of self-learning. He imparts essential etiquette for the success of programming newbies: use the wealth or resources available, from user documentation to Web site surveys to FAQs to How-To's to news groups and finally to direct personal appeals for help from a senior colleague. A well-plugged-in bioinformatics Perl student will soon discover Bioperl, an open-source effort to bring research-grade bioinformatic tools to the Perl community. Bioperl is described briefly at the end of Tisdall's book and will reportedly be a forthcoming title of its own in the O'Reilly bioinformatics series.

Although he introduces bioinformatics as an academic discipline, Tisdall treats it as a trade throughout his book. He indicates that open questions and computational hard problems exist, but does not describe what they are or how they are being tackled. Ultimately, Tisdall presents bioinformatics as another arrow in a bench scientist's quiver, very much like HPLC, 2D-PAGE, and the various spectroscopies.

As odd as a "bioinformatics-as-tool" book may be to its research proponents, the reduction of bioinformatics to trade status both deflates and vindicates the years of research, as Tisdall's work attests. --Peter Leopold

With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.

"Beginning Perl for Bioinformatics" is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.

The book covers:

Programming basics and working with DNA sequences and strings

Debugging your code

Simulating gene mutations using random number generators

Regular expressions and finding motifs indata

Arrays, hashes, and relational databases

Regular expressions and restriction maps

Using Perl to parse PDB records, annotations in GenBank, and BLAST output

Publisher: O'Reilly Media, Inc.
Author: James Tisdall
Release Date: 2001-10-15
ISBN/EAN: 0596000804 / 9780596000806

New Price: $19.95 / Used Price: $17.88