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Related Reading

Sequence Analysis in a Nutshell

Sequence Analysis in a Nutshell
A Guide to Common Tools and Databases

By Scott MarkelDarryl León
January 2003 
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis. The book contains details and examples of the common database formats (GenBank, EMBL, SWISS-PROT) and the GenBank/EMBL/DDBJ Feature Table Definitions. It also provides the command line syntax for popular analysis applications such as Readseq and MEME/MAST, BLAST, ClustalW, and the EMBOSS suite, as well as tables of nucleotide, genetic, and amino acid codes. Written in O'Reilly's enormously popular, straightforward "Nutshell" format, this book draws together essential information for bioinformaticians in industry and academia, as well as for students. If sequence analysis is part of your daily life, you'll want this easy-to-use book on your desk.




Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics

By James Tisdall
October 2001 
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This book shows biologists with little or no programming experience how to use Perl, the ideal language for biological data analysis. Each chapter focuses on solving a particular problem or class of problems, so you'll finish the book with a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to tackle more advanced bioinformatics programming.




CVS Pocket Reference

CVS Pocket Reference

By Gregor N. Purdy
August 2000 
CVS, the Concurrent Version System, is an open source tool for managing source code so that multiple users can make changes on the same file at the same time, using a shared directory, and then commit those changes back into the directory. The CVS Pocket Reference is a quick reference guide to help administrators and users set up and manage source code development. This small book, the ultimate companion for open source developers, covers CVS Version 1.10.8 and delivers the core concepts of version control, along with a complete command reference and guide to configuration and repository setup.




Developing Bioinformatics Computer Skills

Developing Bioinformatics Computer Skills

By Cynthia GibasPer Jambeck
April 2001 
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Developing Bioinformatics Computer Skills will help biologists, researchers, and students develop a structured approach to biological data and the computer tools they'll need to analyze it. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, data visualization, and tips for tailoring data analysis software to individual research needs.




Free as in Freedom

Free as in Freedom
Richard Stallman's Crusade for Free Software

By Sam Williams
March 2002 
Free as in Freedom interweaves biographical snapshots of GNU project founder Richard Stallman with the political, social and economic history of the free software movement. It examines Stallman's unique personality and how that personality has been at turns a driving force and a drawback in terms of the movement's overall success.




Java in a Nutshell, 4th Edition

Java in a Nutshell, 4th Edition

By David Flanagan
Fourth Edition March 2002 
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The 1.4 release of Java 2 Standard edition brings a load of new features - and the potential for frustration. Fret not, our new 4th edition has answers. The accelerated introduction lets you start writing code right away, and because the book's classic quick reference contains all the classes in the essential Java packages, you can find exactly what you need to make Java's new version work for you.




Learning Python

Learning Python

By Mark LutzDavid Ascher
April 1999 
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Learning Python is an introduction to the increasingly popular interpreted programming language that's portable, powerful, and remarkably easy to use in both stand-alone and scripting applications. This book thoroughly introduces the elements of Python: types, operators, statements, classes, functions, modules, and exceptions. It also demonstrates how to perform common programming tasks and write real applications.




Learning Red Hat Linux, 2nd Edition

Learning Red Hat Linux, 2nd Edition
A Guide to Red Hat Linux for New Users

By Bill McCarty
2nd Edition January 2002 
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This second edition of Learning Red Hat Linux is an excellent introduction to one of the most popular distributions of Linux in the U.S. It has been upgraded to cover installation and configuration of Red Hat version 7.2. Because the book is written specifically for the enclosed CDs, the reader needs nothing else to get started with their new Linux system. This is the book for first-time Linux users who want to learn how to use Red Hat Linux on their personal computer, or convert an existing system over to Linux.




Learning XML

Learning XML
Guide to Creating Self-Describing Data

By Erik T. Ray
January 2001 
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XML (Extensible Markup Language) is a flexible way to create "self-describing data"--and to share both the format and the data on the World Wide Web, intranets, and elsewhere. In Learning XML, the author explains XML and its capabilities succinctly and professionally, with references to real-life projects and other cogent examples. Learning XML shows the purpose of XML markup itself, the CSS and XSL styling languages, and the XLink and XPointer specifications for creating rich link structures.




Mac OS X Pocket Reference

Mac OS X Pocket Reference
A User's Guide to Mac OS X

By Chuck Toporek
May 2002 
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The Mac OS X Pocket Reference introduces Mac, Windows, and Unix users to the fundamental concepts of Mac OS X. The book starts out with a "Mac OS X Survival Guide," which shows Mac users what’s changed from Mac OS 9, and also helps Windows and Unix converts get acclimated with their new OS. The Mac OS X Pocket Reference concludes with a 30+-page "Task and Setting" index, which answers questions that users might have when trying to configure their system.




Mac OS X for Unix Geeks

Mac OS X for Unix Geeks

By Brian JepsonErnest E. Rothman
October 2002  (est.)
If you're one of the many Unix developers drawn to Mac OS X for its BSD core, you'll find yourself in surprisingly unfamiliar territory. Even if you're an experienced Mac user, Mac OS X is unlike earlier Macs, and it's radically different from the Unix you've used before, too.

Enter "Mac OS X for Unix Developers and Administrators" by Brian Jepson and Ernest E. Rothman, two Unix geeks who found themselves in the same place you are. Their new book is your guide to figuring out the BSD Unix system and Mac-specific components that are making your life difficult and to help ease you into the Unix inside Mac OS X.




Learning Unix for Mac OS X

Learning Unix for Mac OS X

By Dave TaylorJerry Peek
May 2002 
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Learning Unix for Mac OS X is a concise introduction to just what a reader needs to know to get started with Unix on Mac OS X. With Mac OS X, they now have the ability to not only continue to use their preferred platform, but to explore the powerful capabilities of Unix. This title gives the reader information on how to use the Terminal application, become functional with the command interface and explore many Unix applications.




Managing & Using MySQL, 2nd Edition

Managing & Using MySQL, 2nd Edition
Open Source SQL Databases for Managing Information & Web Sites

By George ReeseRandy Jay YargerTim King
With Hugh E. Williams
2nd Edition April 2002 
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Learn how to use MySQL, a popular database product that supports key subsets of SQL on Linux and Unix systems. Using C/C++, Java, Perl, PHP, or Python, you can write programs to interact with a MySQL database, either as a stand-alone application or through a web page. This book covers the whole process, from installation to programming interfaces and database administration. It includes ample tutorial material and examples.




Mastering Regular Expressions, 2nd Edition

Mastering Regular Expressions, 2nd Edition

By Jeffrey E. F. Friedl
2nd Edition July 2002 
Regular expressions are an extremely powerful tool for manipulating text and data. They are now standard features in a wide range of languages and popular tools, including Perl, Java, VB.NET and C# (and any language using the .NET Framework), PHP, Python, Ruby, Tcl, MySQL, awk, and Emacs.
If you don't use regular expressions yet, you will discover in this book a whole new world of mastery over your data. If you already use them, you'll appreciate this book's unprecedented detail and breadth of coverage.




Perl & LWP

Perl & LWP

By Sean M. Burke
June 2002 
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The LWP (Library for WWW in Perl) suite of modules lets your programs download and extract information from the Web. Perl & LWP shows how to make web requests, submit forms, and even provide authentication information, and it demonstrates using regular expressions, tokens, and trees to parse HTML.. This book is a must have for Perl programmers who want to automate and mine the Web.




Perl & XML

Perl & XML

By Erik T. RayJason McIntosh
April 2002 
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Perl & XML is aimed at Perl programmers who need to work with XML documents and data. This book gives a complete, comprehensive tour of the landscape of Perl and XML, making sense of the myriad of modules, terminology, and techniques. The last two chapters of Perl and XML give complete examples of XML applications, pulling together all the tools at your disposal.




Perl Pocket Reference, 4th Edition

Perl Pocket Reference, 4th Edition

By Johan Vromans
Fourth Edition July 2002 
The Perl Pocket Reference, 4th Edition provides a complete overview of the Perl programming language, all packed into a convenient, carry-around booklet. It is updated for Perl 5.8, and covers a summary of Perl syntax rules, a complete list of operators, built-in functions, and standard library modules, all with brief descriptions. Also included are the newest Perl features, such as enhanced regular expressions, multithreading, the Perl compiler, and Unicode support.




Programming Perl, 3rd Edition

Programming Perl, 3rd Edition

By Larry WallTom ChristiansenJon Orwant
3rd Edition July 2000 
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Programming Perl is not just a book about Perl; it is also a unique introduction to the language and its culture, as one might expect only from its authors. This third edition has been expanded to cover Version 5.6 of Perl. New topics include threading, the compiler, Unicode, and other features that have been added or improved since the previous edition.




Programming PHP

Programming PHP

By Rasmus LerdorfKevin Tatroe
March 2002 
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Programming PHP is a comprehensive guide to PHP, a simple yet powerful language for creating dynamic web content. Filled with the unique knowledge of the creator of PHP, Rasmus Lerdorf, this book is a detailed reference to the language and its applications, including such topics as form processing, sessions, databases, XML, and graphics. Covers PHP 4, the latest version of the language.




Programming Python

Programming Python
Object-Oriented Scripting

By Mark Lutz
October 1996 
This book describes how to use Python, an increasingly popular object- oriented scripting language. Endorsed by Python creator Guido van Rossum, it contains the most comprehensive user material available on Python and complements reference materials that accompany the software. Includes a CD-ROM with Python software for all major UNIX platforms, as well as Windows, NT, and the Mac.




Programming Web Services with SOAP

Programming Web Services with SOAP

By Doug TidwellJames SnellPavel Kulchenko
December 2001 
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Programming Web Services with SOAP introduces you to building distributed Web-based applications using the SOAP, WSDL, and UDDI protocols. You'll learn the XML underlying these standards, as well as how to use the popular toolkits for Java and Perl. The book also addresses security and other enterprise issues.




Python Cookbook

Python Cookbook
Edited by David AscherAlex Martelli
July 2002 
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The Python Cookbook is a collection of problems, solutions, and practical examples for Python programmers, written by Python programmers. It contains over two hundred recipes for text manipulation, object oriented programming, XML processing, system administration, and much more. This book is a treasure trove of useful code for both novices and advanced practitioners, with contributions from such Python luminaries as Guido Van Rossum, Tim Peters, Paul Prescod, and Mark Hammond.




vi Editor Pocket Reference

vi Editor Pocket Reference

By Arnold Robbins
1st Edition January 1999 
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The vi Editor Pocket Reference is a companion volume to O'Reilly's updated sixth edition of Learning the vi Editor, presenting movement and editing commands, the command-line options, and other elements of the vi editor in an easy-to-use tabular format.




XML in a Nutshell, 2nd Edition

XML in a Nutshell, 2nd Edition
A Desktop Quick Reference

By Elliotte Rusty HaroldW. Scott Means
Second Edition June 2002 
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This powerful new edition provides developers with a comprehensive guide to the rapidly evolving XML space. Serious users of XML will find topics on just about everything they need, from fundamental syntax rules, to details of DTD and XML Schema creation, to XSLT transformations, to APIs used for processing XML documents. Simply put, this is the only reference of its kind among XML books.




XML Pocket Reference, 2nd Edition

XML Pocket Reference, 2nd Edition
Extensible Markup Language

By Robert Eckstein
With Michel Casabianca
2nd Edition April 2001 
Read Online--Safari
The XML Pocket Reference is both a handy introduction to XML terminology and syntax, and a quick reference to XML instructions, attributes, entities, and datatypes. Although XML itself is complex, its basic concepts are simple. This small book combines a perfect tutorial for learning the basics of XML with a reference to the XML and XSL specifications. The new edition introduces information on XSLT (Extensible Stylesheet Language Transformations) and Xpath.






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