O'Reilly's Computer E-Books

[MickC]

Beginning Perl for Bioinformatics



By James Tisdall
First Edition October 2001
Pages: 384
ISBN 10: 0-596-00080-4 | ISBN 13: 9780596000806


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 in data
• Arrays, hashes, and relational databases
• Regular expressions and restriction maps
• Using Perl to parse PDB records, annotations in GenBank, and BLAST output

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[MickC]

Better, Faster, Lighter Java



By Bruce A. Tate, Justin Gehtland
First Edition May 2004
Pages: 262
ISBN 10: 0-596-00676-4 | ISBN 13: 9780596006761


Sometimes the simplest answer is the best. Many Enterprise Java developers, accustomed to dealing with Java's spiraling complexity, have fallen into the habit of choosing overly complicated solutions to problems when simpler options are available. Building server applications with "heavyweight" Java-based architectures, such as WebLogic, JBoss, and WebSphere, can be costly and cumbersome. When you've reached the point where you spend more time writing code to support your chosen framework than to solve your actual problems, it's time to think in terms of simplicity. In Better, Faster, Lighter Java, authors Bruce Tate and Justin Gehtland argue that the old heavyweight architectures are unwieldy, complicated, and contribute to slow and buggy application code. As an alternative means for building better applications, the authors present two "lightweight" open source architectures: Hibernate--a persistence framework that does its job with a minimal API and gets out of the way, and Spring--a container that's not invasive, heavy or complicated. Hibernate and Spring are designed to be fairly simple to learn and use, and place reasonable demands on system resources. Better, Faster, Lighter Java shows you how they can help you create enterprise applications that are easier to maintain, write, and debug, and are ultimately much faster. Written for intermediate to advanced Java developers, Better, Faster, Lighter Java, offers fresh ideas--often unorthodox--to help you rethink the way you work, and techniques and principles you'll use to build simpler applications. You'll learn to spend more time on what's important. When you're finished with this book, you'll find that your Java is better, faster, and lighter than ever before.

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[MickC]

BSD Hacks



100 Industrial Tip & Tools
By Dru Lavigne
First Edition May 2004
Pages: 448
Series: Hacks
ISBN 10: 0-596-00679-9 | ISBN 13: 9780596006792


In the world of Unix operating systems, the various BSDs come with a long heritage of high-quality software and well-designed solutions, making them a favorite OS of a wide range of users. Among budget-minded users who adopted BSD early on to developers of some of today's largest Internet sites, the popularity of BSD systems continues to grow. If you use the BSD operating system, then you know that the secret of its success is not just in its price tag: practical, reliable, extraordinarily stable and flexible, BSD also offers plenty of fertile ground for creative, time-saving tweaks and tricks, and yes, even the chance to have some fun. "Fun?" you ask. Perhaps "fun" wasn't covered in the manual that taught you to install BSD and administer it effectively. But BSD Hacks, the latest in O'Reilly's popular Hacks series, offers a unique set of practical tips, tricks, tools--and even fun--for administrators and power users of BSD systems. BSD Hacks takes a creative approach to saving time and getting more done, with fewer resources. You'll take advantage of the tools and concepts that make the world's top Unix users more productive. Rather than spending hours with a dry technical document learning what switches go with a command, you'll learn concrete, practical uses for that command. The book begins with hacks to customize the user environment. You'll learn how to be more productive in the command line, timesaving tips for setting user-defaults, how to automate long commands, and save long sessions for later review. Other hacks in the book are grouped in the following areas:

• Customizing the User Environment
• Dealing with Files and Filesystems
• The Boot and Login Environments
• Backing Up
• Networking Hacks
• Securing the System
• Going Beyond the Basics
• Keeping Up-to-Date
• Grokking BSD

If you want more than your average BSD user--you want to explore and experiment, unearth shortcuts, create useful tools, and come up with fun things to try on your own--BSD Hacks is a must-have. This book will turn regular users into power users and system administrators into super system administrators.

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[MickC]

BLAST



By Ian Korf, Mark Yandell, Joseph Bedell
First Edition July 2003
Pages: 360
ISBN 10: 0-596-00299-8 | ISBN 13: 9780596002992


Sequence similarity is a powerful tool for discovering biological function. Just as the ancient Greeks used comparative anatomy to understand the human body and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, today we can use comparative sequence analysis to understand genomes. BLAST (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. It is one of the most important software packages used in sequence analysis and bioinformatics. Most users of BLAST, however, seldom move beyond the program's default parameters, and never take advantage of its full power. BLAST is the only book completely devoted to this popular suite of tools. It offers biologists, computational biology students, and bioinformatics professionals a clear understanding of BLAST as well as the science it supports. This book shows you how to move beyond the default parameters, get specific answers using BLAST, and how to interpret your results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material to help you understand the statistics behind BLAST, Perl scripts to help you prepare your data and analyze your results, and a wealth of tips and tricks for configuring BLAST to meet your own research needs. Some of the topics covered include:

• BLAST basics and the NCBI web interface
• How to select appropriate search parameters
• BLAST programs: BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, PHI-BLAST, and PSI BLAST
• Detailed BLAST references, including NCBI-BLAST and WU-BLAST
• Understanding biological sequences
• Sequence similarity, homology, scoring matrices, scores, and evolution
• Sequence Alignment
• Calculating BLAST statistics
• Industrial-strength BLAST, including developing applications with Perl and BLAST

BLAST is the only comprehensive reference with detailed, accurate information on optimizing BLAST searches for high-throughput sequence analysis. This is a book that any biologist should own.

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[MickC]

Building Embedded Linux Systems, Second Edition



By Karim Yaghmour, Jonathan Masters, Gilad Ben-Yossef
Second Edition August 2008 (est.)
Pages: 464
ISBN 10: 0-596-52968-6 | ISBN 13: 9780596529680


There's a great deal of excitement surrounding the use of Linux in embedded systems -- for everything from cell phones to car ABS systems and water-filtration plants -- but not a lot of practical information. Building Embedded Linux Systems offers an in-depth, hard-core guide to putting together embedded systems based on Linux.

Updated for the latest version of the Linux kernel, this new edition gives you the basics of building embedded Linux systems, along with the configuration, setup, and use of more than 40 different open source and free software packages in common use. The book also looks at the strengths and weaknesses of using Linux in an embedded system, plus a discussion of licensing issues, and an introduction to real-time, with a discussion of real-time options for Linux.

This indispensable book features arcane and previously undocumented procedures for: [list][*]Building your own GNU development toolchain [*]Using an efficient embedded development framework [*]Selecting, configuring, building, and installing a target-specific kernel [*]Creating a complete target root filesystem [*]Setting up, manipulating, and using solid-state storage devices [*]Installing and configuring a bootloader for the target [*]Cross-compiling a slew of utilities and packages [*]Debugging your embedded system using a plethora of tools and techniques [*]Using the uClibc, BusyBox, U-Boot, OpenSSH, thttpd, tftp, strace, and gdb packages
By presenting howto build the operating system components from pristine sources and how to find more documentation or help, Building Embedded Linux Systems greatly simplifies the task of keeping complete control over your embedded operating system.

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[MickC]

Building Java Enterprise Applications



By Brett McLaughlin
First Edition March 2002
Pages: 318
ISBN 10: 0-596-00123-1 | ISBN 13: 9780596001230


What are the key decisions and tradeoffs you face as you design and develop enterprise applications? How do you build the back end so that it not only handles your current needs but is flexible enough to allow your system to evolve as your needs expand? Answer these questions and many more with Building Java Enterprise Applications, an advanced guide to building complex Java Enterprise Applications from the ground up that addresses design issues along the way. These practical books take a step back from detailed examination of the APIs and focus on the entire picture, so you can put the pieces together and build something that works! This book explores the infrastructure issues so important to good application design. It isn't just a book about doing things with Entity Beans, JDBC and JMS and JNDI. It takes you step by step through building the back end, designing the data store so that it gives you convenient access to the data your application needs; designing a directory; figuring out how to handle security and where to store security credentials you need; and so on. On top of this, it shows -- as easily as possible --how to build the entity bean layer that makes information available to the rest of the application. Throughout this guide, author Brett McLaughlin uses his wealth of real-world experience with enterprise development to show you one step at a time how to design and build a comprehensive enterprise application from the ground up, starting with the back end.

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[MickC]

Building Oracle XML Applications



By Steve Muench
First Edition October 2000
Pages: 812
ISBN 10: 1-56592-691-9 | ISBN 13: 9781565926912


This rich and detailed look at the many Oracle tools that support XML development shows Java and PL/SQL developers how to combine the power of XML and XSLT with the speed, functionality, and reliability of the Oracle database. The nearly 800 pages of entertaining text, helpful and time-saving hints, and extensive examples can be put to use immediately to build custom XML applications.

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[MickC]

Building Secure Servers with Linux



By Michael D. Bauer
First Edition October 2002
Pages: 448
ISBN 10: 0-596-00217-3 | ISBN 13: 9780596002176


Linux consistently turns up high in the list of popular Internet servers, whether it's for the Web, anonymous FTP, or general services like DNS and routing mail. But security is uppermost on the mind of anyone providing such a service. Any server experiences casual probe attempts dozens of time a day, and serious break-in attempts with some frequency as well. As the cost of broadband and other high-speed Internet connectivity has gone down, and its availability has increased, more Linux users are providing or considering providing Internet services such as HTTP, Anonymous FTP, etc., to the world at large. At the same time, some important, powerful, and popular Open Source tools have emerged and rapidly matured--some of which rival expensive commercial equivalents--making Linux a particularly appropriate platform for providing secure Internet services. Building Secure Servers with Linux will help you master the principles of reliable system and network security by combining practical advice with a firm knowledge of the technical tools needed to ensure security. The book focuses on the most common use of Linux--as a hub offering services to an organization or the larger Internet--and shows readers how to harden their hosts against attacks. Author Mick Bauer, a security consultant, network architect, and lead author of the popular Paranoid Penguin column in Linux Journal, carefully outlines the security risks, defines precautions that can minimize those risks, and offers recipes for robust security. The book does not cover firewalls, but covers the more common situation where an organization protects its hub using other systems as firewalls, often proprietary firewalls. The book includes:

• Precise directions for securing common services, including the Web, mail, DNS, and file transfer.
• Ancillary tasks, such as hardening Linux, using SSH and certificates for tunneling, and using iptables for firewalling.
• Basic installation of intrusion detection tools.

Writing for Linux users with little security expertise, the author explains security concepts and techniques in clear language, beginning with the fundamentals. Building Secure Servers with Linux provides a unique balance of "big picture" principles that transcend specific software packages and version numbers, and very clear procedures on securing some of those software packages. An all-inclusive resource for Linux users who wish to harden their systems, the book covers general security as well as key services such as DNS, the Apache Web server, mail, file transfer, and secure shell. With this book in hand, you'll have everything you need to ensure robust security of your Linux system.

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[MickC]

Building Wireless Community Networks, Second Edition



By Rob Flickenger
Second Edition June 2003
Pages: 182
ISBN 10: 0-596-00502-4 | ISBN 13: 9780596005023


Building Wireless Community Networks is about getting people online using wireless network technology. The 802.11b standard (also known as WiFi) makes it possible to network towns, schools, neighborhoods, small business, and almost any kind of organization. All that's required is a willingness to cooperate and share resources. The first edition of this book helped thousands of people engage in community networking activities. At the time, it was impossible to predict how quickly and thoroughly WiFi would penetrate the marketplace. Today, with WiFi-enabled computers almost as common as Ethernet, it makes even more sense to take the next step and network your community using nothing but freely available radio spectrum. This book has showed many people how to make their network available, even from the park bench, how to extend high-speed Internet access into the many areas not served by DSL and cable providers, and how to build working communities and a shared though intangible network. All that's required to create an access point for high-speed Internet connection is a gateway or base station. Once that is set up, any computer with a wireless card can log onto the network and share its resources. Rob Flickenger built such a network in northern California, and continues to participate in network-building efforts. His nuts-and-bolts guide covers:

• Selecting the appropriate equipment
• Finding antenna sites, and building and installing antennas
• Protecting your network from inappropriate access
• New network monitoring tools and techniques (new)
• Regulations affecting wireless deployment (new)
• IP network administration, including DNS and IP Tunneling (new)

His expertise, as well as his sense of humor and enthusiasm for the topic, makes Building Wireless Community Networks a very useful and readable book for anyone interested in wireless connectivity.

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[MickC]

Cascading Style Sheets: The Definitive Guide, Second Edition



By Eric A. Meyer
Second Edition March 2004
Pages: 528
ISBN 10: 0-596-00525-3 | ISBN 13: 9780596005252


Simply put, Cascading Style Sheets (CSS) is a way to separate a document's structure from its presentation. The benefits of this can be quite profound: CSS allows a much richer document appearance than HTML; CSS saves time--you can create or change the appearance of an entire document in just one place; and its compact file size makes web pages load quickly. Eric Meyer, a member of the CSS&FP Working Group and an internationally known expert on HTML and CSS, tackles the subject with passion and delivers a comprehensive and thorough update to his groundbreaking book. All readers will benefit from both the depth and breadth of his experience and his clear and honest style. Cascading Style Sheets: The Definitive Guide, 2nd Edition is a thorough review of all aspects of CSS2.1 and a comprehensive guide to CSS implementation. The book includes new content on positioning, lists and generated content, table layout, user interface, paged media, and more. It explores in detail each individual CSS property and how it interacts with other properties, and shows how to avoid common mistakes in interpretation. If you're ready to take the next step with your HTML coding and incorporate CSS or are already a CSS code warrior, you'll find Cascading Style Sheets: The Definitive Guide, 2nd Edition is the book you've been craving.

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