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With the growing popularity of Linux and the advent of Darwin, Unix has metamorphosed into something new and exciting. No longer perceived as a difficult operating system, more and more users are discovering the advantages of Unix for the first time. But whether you are a newcomer or a Unix power user, you'll find yourself thumbing through the goldmine of information in the new edition of Unix Power Tools to add to your store of knowledge. Want to try something new? Check this book first, and you're sure to find a tip or trick that will prevent you from learning things the hard way. The latest edition of this best-selling favorite is loaded with advice about almost every aspect of Unix, covering all the new technologies that users need to know. In addition to vital information on Linux, Darwin, and BSD, Unix Power Tools 3rd Edition now offers more coverage of bash, zsh, and other new shells, along with discussions about modern utilities and applications. Several sections focus on security and Internet access. And there is a new chapter on access to Unix from Windows, addressing the heterogeneous nature of systems today.You'll also find expanded coverage of software installation and packaging, as well as basic information on Perl and Python. Unix Power Tools 3rd Edition is a browser's book...like a magazine that you don't read from start to finish, but leaf through repeatedly until you realize that you've read it all. Bursting with cross-references, interesting sidebars explore syntax or point out other directions for exploration, including relevant technical details that might not be immediately apparent. The book includes articles abstracted from other O'Reilly books, new information that highlights program tricks and gotchas, tips posted to the Net over the years, and other accumulated wisdom. Affectionately referred to by readers as "the" Unix book, UNIX Power Tools provides access to information every Unix user is going to need to know. It will help you think creatively about UNIX, and will help you get to the point where you can analyze your own problems. Your own solutions won't be far behind.

Freely available source code, with contributions from thousands of programmers around the world: this is the spirit of the software revolution known as Open Source. In this text, leaders of Open Source come together to discuss the new vision of the software industry they have created, through essays that explain how the movement works, why it succeeds, and where it is going.

Virtually everything--not just computers, but every kind of device--is coming on board the Internet, and the two principal applications are the World Wide Web and email. The POP3 model for online-only messaging is being taxed to its limit, and users clearly would like mail servers with more "oomph." More specifically, the demand is for email servers that take advantage of centralized resources to manage mail, rather than heap more tasks on end-user computers. This clamor has resulted in the IMAP protocol being incorporated into virtually every major email server on the market. Those who haven't already installed IMAP are probably planning to do so. Managing IMAP is a movable feast of IMAP help. It is a handy guide for everyday tasks common to most IMAP servers as well as a concise reference to help navigate the sometimes sparsely and obtusely documented open source software. Whether the goal is more insight into the IMAP server and client or utility software, or big-picture strategic suggestions to get off a legacy system, Managing IMAP is here to help. This book is both a conceptual and a mechanical IMAP road map.Managers, system integrators, and system administrators on the front lines of Internet messaging will find it a valuable tool for IMAP system provision, maintenance and support. It is also useful if you're considering IMAP for your messaging system. Managing IMAP covers the IMAP protocol, setting up a client, IMAP security, performance monitoring, and tools. Several chapters are devoted specifically to two of the most popular servers: the University of Washington server and Cyrus, and detailed appendixes cover topics such as TCL, procmail, Sieve, and sendmail.

The popular open source KDE desktop environment for Unix was built with Qt, a C++ class library for writing GUI applications that run on Unix, Linux, Windows 95/98, Windows 2000, and Windows NT platforms. Qt emulates the look and feel of Motif, but is much easier to use. Best of all, after you have written an application with Qt, all you have to do is recompile it to have a version that works on Windows. Qt also emulates the look and feel of Windows, so your users get native-looking interfaces. Platform independence is not the only benefit. Qt is flexible and highly optimized. You'll find that you need to write very little, if any, platform-dependent code because Qt already has what you need. And Qt is free for open source and Linux development. Although programming with Qt is straightforward and feels natural once you get the hang of it, the learning curve can be steep. Qt comes with excellent reference documentation, but beginners often find the included tutorial is not enough to really get started with Qt. That's where Programming with Qt steps in. You'll learn how to program in Qt as the book guides you through the steps of writing a simple paint application.Exercises with fully worked out answers help you deepen your understanding of the topics. The book presents all of the GUI elements in Qt, along with advice about when and how to use them, so you can make full use of the toolkit. For seasoned Qt programmers, there's also lots of information on advanced 2D transformations, drag-and-drop, writing custom image file filters, networking with the new Qt Network Extension, XML processing, Unicode handling, and more. Programming with Qt helps you get the most out of this powerful, easy-to-use, cross-platform toolkit. It's been completely updated for Qt Version 3.0 and includes entirely new information on rich text, Unicode/double byte characters, internationalization, and network programming.

The Web services architecture offers a new way to think about and implement application-to-application integration and interoperability that makes the development platform irrelevant. Two applications, regardless of operating system, programming language, or any other technical implementation detail, communicate using XML messages over open Internet protocols such as HTTP or SMTP. The Simple Open Access Protocol (SOAP) is a specification that details how to encode that information and has become the messaging protocol of choice for Web services. This is a detailed guide to using SOAP and other Web services standards - WSDL (Web Service Description Language), and UDDI (Universal Description, Discovery, and Integration protocol). It covers the concepts of the Web services architecture and offers practical advice on building and deploying Web services in the enterprise. It decodes the standards, explaining the concepts and implementation in a clear, concise style. You'll also learn about the major toolkits for building and deploying Web services. Examples in Java, Perl, C#, and Visual Basic illustrate the principles.Significant applications developed using Java and Perl on the Apache Tomcat Web platform address real issues such as security, debugging, and interoperability.

Data is the lifeblood of modern business, and modern data centres have demanding requirements for size, speed, and reliability. Storage Area Networks (SANs) and Network Attached Storage (NAS) allow organizations to manage and back up huge file systems quickly, thereby keeping their lifeblood flowing. W. Curtis Preston's insightful book takes you through the ins and outs of building and managing large data centres using SANs and NAS. Network administrators are aware that multi-terabyte data stores are common and petabyte data stores are starting to appear. Given this much data, how can they ensure that it is available all the time, that access times and throughput are reasonable, and that the data can be backed up and restored in a timely manner? SANs and NAS provide solutions that help work through these problems, with special attention to the difficulty of backing up huge data stores. This book explains the similarities and differences of SANs and NAS to help determine which, or both, of these complementing technologies are appropriate for your network.Using SANs, for instance, is a way to share multiple devices (tape drives and disk drives) for storage, while NAS is a means for centrally storing files so they can be shared. Preston examines each technology with a vendor neutral approach, starting with the building blocks of a SAN and how they can be assembled for effective storage solutions. He covers day-to-day management and backup and recovery for both SANs and NAS in detail.

Network administrators, auditors and architects know the importance of securing networks and finding security solutions that can be implemented quickly. This book focuses on ways to secure Cisco routers, it is a reference for protecting the protectors. Topics covered include: the importance of router security and where routers fit into an overall security plan; different router configurations for various versions of Cisco's IOS; standard ways to access a Cisco router and the security implications of each; password and privilege levels in Cisco routers; authentication, authorization and accounting (AAA) control; router warning banner use (as recommended by the FBI); unnecessary protocols and services commonly run on Cisco routers; SNMP security; anti-spoofing; protocol security for RIP, OSPF, EIGRP, NTP and BGP; logging violations; incident response; and physical security. There is a checklist at the end of each chapter that summarizes the hardening techniques discussed in the chapter. The checklists help double-check the configurations that have been instructed, and serve as quick references for future security procedures.

The Korn shell is an interactive command and scripting language for accessing Unix(r) and other computer systems. As a complete and high-level programming language in itself, it's been a favorite since it was developed in the mid 1980s by David G. Korn at AT&T Bell Laboratories. Knowing how to use it is an essential skill for serious Unix users. Learning the Korn Shell shows you how to use the Korn shell as a user interface and as a programming environment. Writing applications is often easier and quicker with Korn than with other high-level languages. Because of this, the Korn shell is the most often used shell in commercial environments and among inexperienced users. There are two other widely used shells, the Bourne shell and the C shell. The Korn shell, or ksh, has the best features of both, plus many new features of its own. ksh can do much to enhance productivity and the quality of a user's work, both in interacting with the system, and in programming. The new version, ksh93, has the functionality of other scripting languages such as awk, icon, Perl, rexx, and tcl.Learning the Korn Shell is the key to gaining control of the Korn shell and becoming adept at using it as an interactive command and scripting language. Prior programming experience is not required in order to understand the chapters on basic shell programming. Readers will learn how to write many applications more easily and quickly than with other high-level languages. In addition, readers will also learn about Unix utilities and the way the Unix operating system works in general. The authors maintain that you shouldn't have to be an internals expert to use and program the shell effectively. The second edition covers all the features of the current version of the Korn shell, including many new features not in earlier versions of ksh93, making it the most up-to-date reference available on the Korn shell. It compares the current version of the Korn shell to several other Bourne-compatible shells, including several Unix emulation environments for MS-DOS and Windows. In addition, it describes how to download and build ksh93 from source code.A solid offering for many years, this newly revised title inherits a long tradition of trust among computer professionals who want to learn or refine an essential skill.

XML is a text-based markup language that has taken the programming world by storm. More powerful than HTML yet less demanding than SGML, XML has proven itself to be flexible and resilient. XML is the perfect tool for formatting documents with even the smallest bit of complexity, from Web pages to legal contracts to books. However, XML has also proven itself to be indispensable for organizing and conveying other sorts of data as well, thus its central role in web services like SOAP and XML-RPC. As the Perl programming language was tailor-made for manipulating text, few people have disputed the fact that Perl and XML are perfectly suited for one another. The only question has been what's the best way to do it. That's where this book comes in. Perl & XML is aimed at Perl programmers who need to work with XML documents and data. The book covers all the major modules for XML processing in Perl, including XML::Simple, XML::Parser, XML::LibXML, XML::XPath, XML::Writer, XML::Pyx, XML::Parser::PerlSAX, XML::SAX, XML::SimpleObject, XML::TreeBuilder, XML::Grove, XML::DOM, XML::RSS, XML::Generator::DBI, and SOAP::Lite.But this book is more than just a listing of modules; it gives a complete, comprehensive tour of the landscape of Perl and XML, making sense of the myriad of modules, terminology, and techniques. This book covers: *parsing XML documents and writing them out again *working with event streams and SAX *tree processing and the Document Object Model *advanced tree processing with XPath and XSLT Most valuably, the last two chapters of Perl & XML give complete examples of XML applications, pulling together all the tools at your disposal. All together, Perl & XML is the single book that gives you a solid grounding in XML processing with Perl.

Given Perl's natural fit for web applications development, it's no surprise that Perl is also a natural choice for web services development. It's the most popular web programming language, with strong implementations of both SOAP and XML-RPC, the leading ways to distribute applications using web services. But books on web services focus on writing these applications in Java or Visual Basic, leaving Perl programmers with few resources to get them started. Programming Web Services with Perl changes that, bringing Perl users all the information they need to create web services using their favorite language. Programming Web Services with Perl steers clear of the hype surrounding web services and concentrates on what is useful and practical. The book introduces the major web services standards, such as XML-RPC, SOAP, WSDL, and UDDI, and shows how to implement Perl servers and clients using these standards. You'll find detailed references on both the XML and SOAP toolkits, and learn when to use one technology in favor of the other. The book is rich with programming examples that you'll find useful well past the learning stage.And, moving beyond the basics, the book offers solutions to problems of security, authentication, and scalability. Some of the topics covered in the book are: * HTTP and XML basics * XML-RPC and the toolkits * SOAP and toolkits * SOAP::Lite * Using SOAP with SMTP and other protocols * Advertising and discovering with UDDI and WSDL * The REST methodology * The future of web services Programming Web Services with Perl was written for Perl programmers who have no prior knowledge of web services. You can pick up this book without any understanding of XML-RPC or SOAP and be able to apply these technologies easily, through the use of publicly available Perl modules detailed in the book. If you're interested in applying XML-RPC and SOAP technologies to distributed programming applications, then Programming Web Services with Perl is a book you'll want to have.

This guide takes a step-by-step approach to teaching developers how to build real graphics applications using Cocoa. By showing the basics of an application in one chapter and then layering additional functionality onto that application in subsequent chapters, the book keeps readers interested and motivated. Readers will see immediate results, and then go on to build onto what they've already achieved. The book is divided into four major parts: Part I introduces the Mac OS X graphical user interface (Aqua) from a developer's point of view, Cocoa developer tools (such as the Interface Builder, Project Builder, and gdb debugger), object-oriented concepts, the Objective-C language in which Cocoa is written, and the basics of Cocoa programming itself; Part II focuses on building the first complete application, calculator, a simple four-function calculator. The chapters in this part of the book extend the application, piece by piece, by introducing such features as nibs, icons, delegation, resizing, events, and responders.Part III focuses on building an application called MathPaper, which is similar to a word processor but which instead solves mathematical expressions the user supplies. The chapters in this part of the book extend MathPaper by developing both the front and back ends using a variety of Cocoa classes and methods. They introduce Cocoa'sdocument-based architecture, tasks, pipes, Rich Text format, handling document files, and using Quartz to draw in windows. Part IV focuses on building the GraphPaper application, a more complex multithreading application that graphs mathematical functions in multiple dimensions and that uses mouse-over capabilities to identify graph points. The chapters in this part of the book add more advanced Mac OS X features such as multithreading, colour, mouse events, zoom buttons, pasteboards, services, preferences, and the defaults database.

Web services are poised to become a key technology for a wide range of Internet-enabled applications, spanning everything from straight B2B systems to mobile devices and proprietary in-house software. While there are several tools and platforms that can be used for building web services, developers are finding a powerful tool in Microsoft's .NET Framework and Visual Studio .NET. Designed from scratch to support the development of web services, the .NET Framework simplifies the process--programmers find that tasks that took an hour using the SOAP Toolkit take just minutes. Programming .NET Web Services is a comprehensive tutorial that teaches you the skills needed to develop web services hosted on the .NET platform. Written for experienced programmers, this book takes you beyond the obvious functionality of ASP.NET or Visual Studio .NET to give you a solid foundation in the building blocks of web services, and leads you step-by-step through the process of creating your own. Beginning with a close look at the underlying technologies of web services, including the benefits and limitations, Programming .NET Web Services discusses the unique features of the .NET Framework that make creating web services easier, including the Common Language Runtime (CLR) and the namespaces used in .NET programming. Filled with numerous code examples using the C# language, the book leads you through some of the more challenging issues of web services development, including the use of proxies, marshalling of complex data types, state management, security, performance tuning and cross-platform implementation. The book also covers: * Creating and publishing your first web service * The UDDI project, tModels and what they mean for web service publishers Securing web service applications Written for programmers who are familiar with the .NET Framework and interested in building industrial-strength web services, Programming .NET Web Services is full of practical information and good old-fashioned advice.

For creating or using formal descriptions of XML vocabularies, this text offers a set of tools for defining acceptable document structures and content. An alternative to DTDs as the way to describe and validate data in an XML environment, the book should enable developers to create precise descriptions with a richer set of datatypes-such as booleans, numbers, currencies, dates and times - that are useful for modern applications. It explains the ins and outs of XML Schema, including design choices, best practices, and limitations. Particularly valuable are discussions of how the type structures fit with existing database and object-oriented program contexts. With XML Schema, you can define acceptable content models and annotate those models with additional type information, making them more readily bound to programs and objects. Schemas combine the easy interchange of text-based XML with the more stringent requirements of data exchange, and make it easier to validate documents based on namespaces. Examples are included that demonstrate the details necessary for precise vocabulary definitions.Topics covered within the book include: foundations of XML Schema syntax; flat, "russian-doll", and other schema approaches; working with simple and complex types in a variety of contexts; the built-in datatypes provided by XML Schema; using facets to extend datatypes, including regular expression-based patterns; using keys and uniqueness rules to limit how and where information may appear; creating extensible schemas and managing extensibility; and documenting schemas and extending XML schema capabilities. In addition to the explanatory content, XML Schema offers a complete reference to all parts of both the XML Schema structures and XML Schema datatypes specifications, as well as a glossary. Appendices explore the relationships between XML Schema and other tools for describing document structures, including DTDs, RELAX NG, and Schematron, as well as work in progress at the W3C to more tightly integrate XML Schema with existing specifications.

If you've ever wondered how Linux carries out the complicated tasks assigned to it by the IP protocols -- or if you just want to learn about modern networking through real-life examples -- Understanding Linux Network Internals is for you. Like the popular O'Reilly book, Understanding the Linux Kernel, this book clearly explains the underlying concepts and teaches you how to follow the actual C code that implements it. Although some background in the TCP/IP protocols is helpful, you can learn a great deal from this text about the protocols themselves and their uses. And if you already have a base knowledge of C, you can use the book's code walkthroughs to figure out exactly what this sophisticated part of the Linux kernel is doing. Part of the difficulty in understanding networks -- and implementing them -- is that the tasks are broken up and performed at many different times by different pieces of code. One of the strengths of this book is to integrate the pieces and reveal the relationships between far-flung functions and data structures. Understanding Linux Network Internals is both a big-picture discussion and a no-nonsense guide to the details of Linux networking.Topics include: * Key problems with networking * Network interface card (NIC) device drivers * System initialization * Layer 2 (link-layer) tasks and implementation * Layer 3 (IPv4) tasks and implementation * Neighbor infrastructure and protocols (ARP) * Bridging * Routing * ICMP Author Christian Benvenuti, an operating system designer specializing in networking, explains much more than how Linux code works. He shows the purposes of major networking features and the trade-offs involved in choosing one solution over another. A large number of flowcharts and other diagrams enhance the book's understandability.

Most applications these days are at least somewhat network aware, but how do you protect those applications against common network security threats? Many developers are turning to OpenSSL, an open source version of SSL/TLS, which is the most widely used protocol for secure network communications. The OpenSSL library is seeing widespread adoption for web sites that require cryptographic functions to protect a broad range of sensitive information, such as credit card numbers and other financial transactions. The library is the only free, full-featured SSL implementation for C and C++, and it can be used programmatically or from the command line to secure most TCP-based network protocols. Network Security with OpenSSL enables developers to use this protocol much more effectively. Traditionally, getting something simple done in OpenSSL could easily take weeks. This concise book gives you the guidance you need to avoid pitfalls, while allowing you to take advantage of the library?s advanced features. And, instead of bogging you down in the technical details of how SSL works under the hood, this book provides only the information that is necessary to use OpenSSL safely and effectively.In step-by-step fashion, the book details the challenges in securing network communications, and shows you how to use OpenSSL tools to best meet those challenges. As a system or network administrator, you will benefit from the thorough treatment of the OpenSSL command-line interface, as well as from step-by-step directions for obtaining certificates and setting up your own certification authority. As a developer, you will further benefit from the in-depth discussions and examples of how to use OpenSSL in your own programs. Although OpenSSL is written in C, information on how to use OpenSSL with Perl, Python and PHP is also included. OpenSSL may well answer your need to protect sensitive data. If that?s the case, Network Security with OpenSSL is the only guide available on the subject.

This concise guide offers the basic concepts of IP routing, free of hype and jargon. It begins with the simplest routing protocol, RIP, and then proceeds, in order of complexity, to IGRP, EIGRP, RIP2, OSPF, and finally to BGP. New concepts are presented one at a time in successive chapters. By the end, you will have mastered not only the fundamentals of all the major routing protocols, but also the underlying principles on which they are based. The basic information in IP Routing is designed to help you begin configuring protocols for Cisco routers. Although author Ravi Malhotra assumes that readers have a basic understanding of TCP/IP and are somewhat familiar with Cisco router configurations, he also assumes that you find some or all of these protocols difficult to work with. His book presents concepts simply, as nuts and bolts. Malhotra's use of plain language, analogy, and the recurring example of an imaginary network, which grows in complexity as the book progresses, will help you understand fundamental concepts behind each protocol.Once you master these concepts, you will benefit from the detailed information contained in Cisco manuals and web pages (such as bug lists, new features, design guides, etc). Depending on your skill level, you can either read IP Routing from cover to cover or use it as a reference for any of the protocols presented. The book describes administrative tools available to all the routing protocols, including those that block the advertisement of routing updates, and those that set up preferences for one routing protocol over another. Honed by years of teaching Data Communications at major universities and managing IP networks in production environments, Ravi Malhotra's knowledge of this subject makes IP Routing is the ideal primer to Internet routing protocols.

Mention wireless networks, and the question of security will soon follow. It's not surprising that in spite of compelling business arguments for going wireless, many companies are holding back because of security concerns. But, while it's true that wireless networks create security issues that don't exist in wired networks, the issues are not insurmountable. 802.11 Security shows how you can plan for and successfully contend with security obstacles in your wireless deployment. This authoritative book not only explains the security issues, but shows you how to design and build a your own secure wireless network. 802.11 Security covers the entire process of building secure 802.11-based wireless networks, in particular, the 802.11b ("Wi-Fi") specification. The authors provide detailed coverage of security issues unique to wireless networking, such as Wireless Access Points (WAP), bandwidth stealing, and the problematic Wired Equivalent Privacy component of 802.11. You'll learn how to configure a wireless client and to set up a WAP using either Linux or Free BSD. You'll also find thorough information on controlling network access and encrypting client traffic.Beginning with an introduction to 802.11b in general, the book gives you a broad basis in theory and practice of wireless security, dispelling some of the myths along the way. In doing so, they provide you with the technical grounding required to think about how the rest of the book applies to your specific needs and situations. Next, the book details the technical setup instructions needed for both the Linux and FreeBSD operating systems. Some of the topics covered include: Station Security for Linux, FreeBSD, Open BSD, Mac OS X and Windows; Setting Up Access Point Security Gateway Security, including building Gateways, firewall Rules, Auditing, etc.; Authentication and Encryption; FreeBSD IPsec client and gateway configuration; Linux IPsec client and gateway configuration; 802.1x authentication. 802.11 Security is a book whose time has come. If you are a network, security, or systems engineer, or anyone interested in deploying 802.11b-based systems, you'll want this book beside you every step of the way.

This complete guide to setting up and running a TCP/IP network is essential for network administrators, and invaluable for users of home systems that access the Internet. The book starts with the fundamentals -- what protocols do and how they work, how addresses and routing are used to move data through the network, how to set up your network connection -- and then covers, in detail, everything you need to know to exchange information via the Internet. Included are discussions on advanced routing protocols (RIPv2, OSPF, and BGP) and the gated software package that implements them, a tutorial on configuring important network services -- including DNS, Apache, sendmail, Samba, PPP, and DHCP -- as well as expanded chapters on troubleshooting and security. TCP/IP Network Administration is also a command and syntax reference for important packages such as gated, pppd, named, dhcpd, and sendmail.With coverage that includes Linux, Solaris, BSD, and System V TCP/IP implementations, the third edition contains: *Overview of TCP/IP *Delivering the data *Network services *Getting startedM *Basic configuration *Configuring the interface *Configuring routing *Configuring DNS *Configuring network servers *Configuring sendmail *Configuring Apache *Network security *Troubleshooting *Appendices include dip, ppd, and chat reference, a gated reference, a dhcpd reference, and a sendmail reference This new edition includes ways of configuring Samba to provide file and print sharing on networks that integrate Unix and Windows, and a new chapter is dedicated to the important task of configuring the Apache web server. Coverage of network security now includes details on OpenSSH, stunnel, gpg, iptables, and the access control mechanism in xinetd. Plus, the book offers updated information about DNS, including details on BIND 8 and BIND 9, the role of classless IP addressing and network prefixes, and the changing role of registrars.Without a doubt, TCP/IP Network Administration, 3rd Edition is a must-have for all network administrators and anyone who deals with a network that transmits data over the Internet.

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 BLASTBLAST 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.

Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis. This text covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with "Beginning Perl for Bioinformatics", forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics.The range of topics covered in the book prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as: gene finding; string alignment; methods of data storage and retrieval (SML and databases); modelling of networks (graphs and Petri nets); graphics (Tk); parallelization; interfacing with other programming languages; statistics (PDL); protein structure determination; and biological models of computation (DNA Computers). Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.

Remote Authentication Dial-In User Radius (RADIUS) is a widely deployed protocol that enables companies to authenticate, authorize and account for remote users who want access to a system or service from a central network server. This text is a detailed guide to the underpinnings of RADIUS protocol, with particular emphasis on the utility of user accounting. Author Jonathan Hassell draws from his extensive experience in Internet service provider operations to bring practical suggestions and advice for implementing RADIUS. He also provides instructions for using an open-source variation called FreeRADIUS. This book covers RADIUS completely, from the history and theory of the architecture around which it was designed, to how the protocol and its ancillaries function on a day-to-day basis, to implementing RADIUS-based security in a variety of corporate and service provider environments. If you are an ISP owner or administrator, corporate IT professional responsible for maintaining mobile user connectivity, or a web presence provider responsible for providing multiple communications resources, you'll want this book to help you master this widely implemented but little understood protoc

No matter how flexible and convenient digital information has become, we haven't done away with the need to see information in print. Extensible Style Language-Formatting Objects, or XSL-FO, is a set of tools developers and web designers use to describe page printouts of their XML (including XHTML) documents. If you need to produce high quality printed material from your XML documents, then XSL-FO provides the bridge. XSL-FO is one of the few books to go beyond a basic introduction to the technology. While many books touch on XSL-FO in their treatment of XSLT, this book offers in-depth coverage of XSL-FO's features and strengths. Author Dave Pawson is well known in the XSLT and XSL-FO communities, and maintains the XSLT FAQ. An online version of this book has helped many developers master this technology. XSL-FO is the first time this reference is available in print. The first part of the book provides an overview of the technology and introduces the XSL-FO vocabulary. The author discusses how to choose among today's implementations, explains how to describe pages, and shows you what is going on in the processor in terms of layout.You'll learn about the basics of formatting and layout as well as readability. The second part focuses on smaller pieces: blocks, inline structures, graphics, color and character level formatting, concluding by showing how to integrate these parts into a coherent whole. XSL-FO also explores organizational aspects you'll need to consider?how to design your stylesheets strategically rather than letting them evolve on their own. XSL-FO is more than just a guide to the technology; the book teaches you how to think about the formatting of your documents and guides you through the questions you'll need to ask to ensure that your printed documents meet the same high standards as your computer-generated content. Written for experienced XML developers and web designers, no other book contains as much useful information on this practical technology.

Updated for Excel 2002, this text offers Excel power-users, as well as programmers who are unfamiliar with the Excel object model, with an introduction to writing Visual Basic for Applications (VBA) macros and programs for Excel. In particular, the book focuses on: the Visual Basic Editor and the Excel VBA programming environment. Excel features a complete , state-of-the-art integ rated development environment for writing, running, testing, and debugging VBA macros. The VBA programming language, the same programming language used by the other applications in Microsoft Office XP and 2000, as well as by the retail editions of Visual Basic 6.0. The Excel object model, including new objects and new members of existing objects in Excel 2002. Excel exposes nearly all of its functionality through its object model, which is the means by which Excel can be controlled programmatically using VBA. While the Excel object model, with 192 objects, is the second largest among the Office applications, you need to be familiar with only a handful of objects to write effective macros. Writing Excel Macros focuses on these essential objects, but includes a discussion of many more objects as well.

Anyone can run a blog (an online journal). From personal diaries to political commentary and technology observations, bloggers are making their voices heard around the world. Essential Blogging helps you select the right blogging software for your needs and show how to get your blog up and running. You'll learn the ingredients of a successful blog, and then get detailed installation, configuration and operation instructions for the leading blogging software: Blogger, Radio Userland, Movable Type, and Blosxom. After showing you how to acquire, set-up, and run these leading software packages, Essential Blogging takes you through the more advanced features, so that by the time you finish, you'll be up and blogging with the best of them.Essential Blogging covers: * the important components of a blog and a blog post * installing and configuring the tools * a survey of desktop blogging clients * advice and experience from real-world bloggers * hosted blogging with Blogger and Blogger Pro * desktop blogging with Radio Userland * server blogging with Movable Type * posting, editing, and deleting blog entries * adding pictures to blog entries * syndicating your stories with RSS * consuming RSS feeds with Radio Userland * customizing the appearance of your blog with templates * managing and customizing archives of blog entries * adding comments to your blog * self-hosting your blog vs using a blog-hosting service * going under the hood with the Blosxom blogging system Written by prominent bloggers and authors of blogging tools, Essential Blogging is a no-nonsense guide to the technology of blogging.

If you're seeking ways to build network-based applications or XML-based web services, Microsoft provides most of the tools you'll need. XML is integrated into the .NET Framework and Visual Studio .NET, but if you want to get a grasp on how .NET and XML actually work together, that's a different story. With .NET & XML, you can get under the hood to see how the .NET Framework implements XML, giving you the skills to write understandable XML-based code that interoperates with code written with other tools, and even other languages. .NET & XML starts by introducing XML and the .NET Framework, and then teaches you how to read and write XML before moving on to complex methods for manipulating, navigating, transforming, and constraining it. To demonstrate the power of XML in .NET, author Niel Bornstein builds a simple hardware store inventory system throughout the book. As you move from chapter to chapter, you'll absorb increasingly complex information until you have enough knowledge to successfully program your own XML-based applications. This tutorial also contains a quick reference to the API, plus appendices present additional .NET assemblies that you can use to work with XML, and how to work with the .NET XML configuration file format. One study puts the potential market for new software based on XML at or near $100 billion over the next five years. The .NET Framework gives you a way to become a part of it. But to use XML and .NET effectively, you need to understand how these two technologies work together. This book gives you the insight to take full advantage of the power the two provide.

As developers know, the beauty of XML is that it is extensible, even to the point that you can invent new elements and attributes as you write XML documents. Then, however, you need to define your changes so that applications will be able to make sense of them and this is where XML schema languages come into play. RELAX NG (pronounced relaxing), the Regular Language Description for XML Core--New Generation is quickly gaining momentum as an alternative to other schema languages. Designed to solve a variety of common problems raised in the creation and sharing of XML vocabularies, RELAX NG is less complex than The W3C's XML Schema Recommendation and much more powerful and flexible than DTDs. RELAX NG is a grammar-based schema language that's both easy to learn for schema creators and easy to implement for software developers In RELAX NG, developers are introduced to this unique language and will learn a no-nonsense method for creating XML schemas. This book offers a clear-cut explanation of RELAX NG that enables intermediate and advanced XML developers to focus on XML document structures and content rather than battle the intricacies of yet another convoluted standard.RELAX NG covers the following topics in depth: Introduction to RELAX NG Building RELAX NG schemas using XML syntax Building RELAX NG schemas using compact syntax, an alternative non-XML syntax Flattening schemas to limit depth and provide reusability Using external datatype libraries with RELAX NG W3C XML Schema regular expressions Writing extensible schemas Annotating schemas Generating schemas form different sources Determinism and datatype assignment and much more. If you're looking for a schema language that's easy to use and won't leave you in a labyrinth of obscure limitations, RELAX NG is the language you should be using. And only O'Reilly's RELAX NG gives you the straightforward information and everything else you'll need to take advantage of this powerful and intelligible language.

Architects of buildings and architects of software have more in common than most people think. Both professions require attention to detail, and both practitioners will see their work collapse around them if they make too many mistakes. It's impossible to imagine a world in which buildings get built without blueprints, but it's still common for software applications to be designed and built without blueprints, or in this case, design patterns. A software design pattern can be identified as "a recurring solution to a recurring problem." Using design patterns for software development makes sense in the same way that architectural design patterns make sense--if it works well in one place, why not use it in another? But developers have had enough of books that simply catalog design patterns without extending into new areas, and books that are so theoretical that you can't actually do anything better after reading them than you could before you started. Crawford and Kaplan's J2EE Design Patterns approaches the subject in a unique, highly practical and pragmatic way.Rather than simply present another catalog of design patterns, the authors broaden the scope by discussing ways to choose design patterns when building an enterprise application from scratch, looking closely at the real world tradeoffs that Java developers must weigh when architecting their applications. Then they go on to show how to apply the patterns when writing realworld software. They also extend design patterns into areas not covered in other books, presenting original patterns for data modeling, transaction / process modeling, and interoperability. J2EE Design Patterns offers extensive coverage of the five problem areas enterprise developers face: * Maintenance (Extensibility) * Performance (System Scalability) * Data Modeling (Business Object Modeling) * Transactions (process Modeling) * Messaging (Interoperability) And with its careful balance between theory and practice, J2EE Design Patterns will give developers new to the Java enterprise development arena a solid understanding of how to approach a wide variety of architectural and procedural problems, and will give experienced J2EE pros an opportunity to extend and improve on their existing experience.

With a worldwide community of users and more than a million dedicated programmers, Perl has proven to be the most effective language for the latest trends in computing and business. Every programmer must keep up with the latest tools and techniques. This updated version of Advanced Perl Programming from O'Reilly gives you the essential knowledge of the modern Perl programmer. Whatever your current level of Perl expertise, this book will help you push your skills to the next level and become a more accomplished programmer. O'Reilly's most high-level Perl tutorial to date, Advanced Perl Programming, Second Edition teaches you all the complex techniques for production-ready Perl programs. This completely updated guide clearly explains concepts such as introspection, overriding built-ins, extending Perl's object-oriented model, and testing your code for greater stability.Other topics include: * Complex data structures * Parsing * Templating toolkits * Working with natural language data * Unicode * Interaction with C and other languages In addition, this guide demystifies once complex topics like object-relational mapping and event-based development-arming you with everything you need to completely upgrade your skills. Praise for the Second Edition: "Sometimes the biggest hurdle to problem solving isn't the subject itself but rather the sheer number of modules Perl provides. Advanced Perl Programming walks you through Perl's TMTOWTDI ("There's More Than One Way To Do It") forest, explaining and comparing the best modules for each task so you can intelligently apply them in a variety of situations." --Rocco Caputo, lead developer of POE "It has been said that sufficiently advanced Perl code is indistinguishable from magic. This book of spells goes a long way to unlocking those secrets. It has the power to transform the most humble programmer into a Perl wizard." --Andy Wardley "The information here isn't theoretical. It presents tools and techniques for solving real problems cleanly and elegantly."--Curtis 'Ovid' Poe " Advanced Perl Programming collects hard-earned knowledge from some of the best programmers in the Perl community, and explains it in a way that even novices can apply immediately." --chromatic, Editor of Perl.com

A competent system administrator knows that a Linux server is a high performance system for routing large amounts of information through a network connection. Setting up and maintaining a Linux server requires understanding not only the hardware, but the ins and outs of the Linux operating system along with its supporting cast of utilities as well as layers of applications software. There's basic documentation online but there's a lot beyond the basics you have to know, and this only comes from people with hands-on, real-world experience. This kind of "know how" is what we sought to capture in Linux Server Hacks. Linux Server Hacks is a collection of 100 industrial-strength hacks, providing tips and tools that solve practical problems for Linux system administrators. Every hack can be read in just a few minutes but will save hours of searching for the right answer. Some of the hacks are subtle, many of them are non-obvious, and all of them demonstrate the power and flexibility of a Linux system. You'll find hacks devoted to tuning the Linux kernel to make your system run more efficiently, as well as using CVS or RCS to track the revision to system files.You'll learn alternative ways to do backups, how to use system monitoring tools to track system performance and a variety of secure networking solutions. Linux Server Hacks also helps you manage large-scale Web installations running Apache, MySQL, and other open source tools that are typically part of a Linux system. O'Reilly's new Hacks Series proudly reclaims the term "hacking" for the good guys. Hackers use their ingenuity to solve interesting problems. Rob Flickenger is an experienced system administrator, having managed the systems for O'Reilly Network for several years. (He's also into community wireless networking and he's written a book on that subject for O'Reilly.) Rob has also collected the best ideas and tools from a number of other highly skilled contributors. Written for users who already understand the basics, Linux Server Hacks is built upon the expertise of people who really know what they're doing.