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PROGRAMMING BOOKS

Posted in Programming (Friday, July 4, 2008)

Written by David D. Busch. By Course Technology PTR. The regular list price is $39.99. Sells new for $25.02. There are some available for $25.06.
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5 comments about David Buschs Digital Infrared Pro Secrets.
  1. Infrared light is close in the spectrum to heat. As a result, cold things like trees and water dramatically change their appearance. And the warm skin of people put out a more intense image. Again because of the heat effect, skin blemishes such as acne tend to disappear. This may offer some distinct advantages in photographing young people. Likewise the somewhat strange effect produced by infrared photography may have effects that appeal in industrial or commercial shoots.

    While there are a lot of books on taking, using, processing infrared pictures, in this book that only takes up about half the content of the book. The most interesting half is on getting yourself an infrared camera. At the minimal end of the game there's building yourself a filter that can be put on the front of a camera. Or, you might consider that some cameras are easy to convert to infrared photography only. He gives a list (many of these are under $100 on eBay that can be professionally or perhaps even converted by you.


  2. Actually, as the author points out in several places in this book, digital infrared photography is exclusively near infrared (NIR)photography, and should not be confused with heat/thermal photography, which, as Busch says, is something else entirely.

    Indeed, the technical accuracy and depth of coverage are one of the strengths of this book. It explains the process of IR photography in enough detail that even those new to this type of shooting will be comfortable with the technical demands, which, after you've read the book, aren't that complicated at all.

    There are two other aspects that I particularly enjoyed. First, unlike most other books in IR photography, this one doesn't deal exclusively with landscape photography. Instead, the author invites you to explore architectural photography, close-ups, even sports (!) and other varied subject matter. If you thought of IR photography as a quirky special effect, you'll discover that it's a genre of its own.

    Second, the do-it-yourself parts of this book are commendable. The author shows you how to build an auxiliary viewfinder from parts salvaged from a single-use film camera, how to make your own IR filter on the cheap, and how to convert your own camera to full time infrared shooting. There are even step-by-step illustrated instructions for converting a popular camera model.

    None of the other IR books I've read touch on all the topics found here. This is highly recommended.


  3. I picked up this book after already being really interested in IR photography, or as David corrects, is near IR photography.

    He shows you how you can convert your camera, but also recommends LifePixel for conversion, which I had done. He does not steer you wrong there with that suggestion. I do have some sample images on my blog at [...]

    David gives you several ideas for dIR photography and more than just typical IR subjects as well. This is a definate keeper.


  4. This book is great. The information provided will help anyone that is thinking about trying infrared photography. Digital cameras make the process so much easier without the hassle of trying to find a pro lab that will develop infrared film. This was a good purchase and I intend to get lots of use out of it.


  5. The overwhelming majority of this book is devoted to photography basics. There are no pro secrets. Everything in this book is available on the Internet at a number of IR photography web sites. It's unlikely that a pro photographer would be clueless as to figuring out which filter sizes a specific lens requires (it's printed on the lens) or that a tripod is a must for long exposures. His section on post-processing is limited to telling the reader to purchase expensive Photoshop plug-ins. It gives the impression the author is a shill for the plug-in authors. Don't waste your money on this book.


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Posted in Programming (Friday, July 4, 2008)

Written by Nita Rutkosky. By EMC/Paradigm Publishing. The regular list price is $133.18. Sells new for $26.37. There are some available for $5.99.
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2 comments about Microsoft Word 2003 (Signature Series).
  1. the book is very helpful and has alot of tips in it.


  2. Amazon confirmed a correct order, but the publisher sent the wrong book!! Not only did it take longer than it should have, but they refused to refund my shipping expenses to have it sent back. OPOE books is the worst company I think I have ever dealt with... and I run a multi-million dollar restaurant. They are not friendly, not professional, and need to be put to stake if you ask me. The poorest business practices I have ever witnessed. They claimed that they would have sent a return shipping label, but neglected to mention that prior to my return... besides the fact it shouldn't matter. I'm sure they have an accounting department with a checkbook that could easily mail one payable to me for the expense I incurred do to their wrongdoing.


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Posted in Programming (Friday, July 4, 2008)

Written by Teresa S. Stover. By Microsoft Press. The regular list price is $49.99. Sells new for $4.50. There are some available for $7.00.
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5 comments about Microsoft Office Project 2003 Inside Out.
  1. As an EPM consultant, a good thorough reference book is absolutely essential for me. I have carried my copy of Project 2002 Inside Out all over the country with me and have just about worn it out. I ordered a copy of Project 2003 Inside Out the day it became available, and have recommended it to several clients, all of whom have bought it and thanked me for it.

    The Inside Out books are wonderful, complete references on Project Professional, but they don't go into anywhere near the same level of detail on Project Server or Project Web Access. Granted, if they did, both the 2002 and 2003 versions would have been 10,000 pages long, rather than the current 1,000 or so.

    This book will help you answer pretty much any quesiton you've got about Project Pro, and that tends to be where most of the questions are. As a reference, this is a great tool. The index is thorough, the detailed TOC is very easy to use, and there is a TON on information in here.

    To be fair, I have to say that the 2003 version does cover more of Project Server and PWA than 2002 did. However, it's still just barely scratching the surface. If Ms. Stover would cover only the security model, that would be a huge step forward.

    Bottom line: If you're going to be using Project 2003, either stand alone or in a full-blown Enterprise Project Management scenario, Project 2003 Inside Out is a great tool. I recommend it enthusiasticly.



  2. I needed to learn the ins and out of Microsoft Project in a weekend. The book was the best reference for me to do so. It took me step by step to learnings all the quirks and strategies when working with project.

    I still use it as a reference in my work today and may have to buy another because I am wearing it down so much. It is a very easy book to reference and I would recommend it to any Project user.



  3. I was somewhat disappointed. The things I had questions about weren't covered any more deeply in this book than in the Microsoft Help. Download and read the Microsoft Online books that cover administering and installing Project Server for a free alternative.


  4. Not the best book out there for MS Project. It didn't really seem like the author was a power user. Some of the directions are very superficial and not very useful. Not a good book at all for Project Server administration. Get more bang for your buck with MS Project Special Edition.


  5. I expected better and more advanced information on MS Project. Unfortunately this manual covers only the basics, although it does a very good job doing it.
    Remember when you use to purchase software and it included a Manual?
    Kind of dissapointed of the sustance (or lack of) for advance users.


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Posted in Programming (Friday, July 4, 2008)

Written by Eric Clayberg and Dan Rubel. By Addison-Wesley Professional. The regular list price is $59.99. Sells new for $39.97. There are some available for $39.96.
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5 comments about Eclipse: Building Commercial-Quality Plug-ins (2nd Edition) (The Eclipse Series).
  1. Eclipse: Building Commercial-Quality Plug-ins (2nd Edition) (The Eclipse Series)

    + Provides a good overall picture of plug-ins structure, a lot of details.
    - Contains a lot of methods description that you can find it otherwise in Javadoc, running an eclipse plug-in could have included some more options (in fact for developing I preferred the version from Eclipse help)


  2. I got the book on time and the condition of the book was new as promised. Couldn't ask for more.

    Cheers!


  3. This is a good guide for developing Eclipse plugins. Since most online documentation for Eclipse is garbage, this will get you up and running in much less time. It doesn't answer all questions but is a handy reference.


  4. If you're planning to write an eclipse plugin, this is THE book to read. The authors have done a fantastic job. Kudos.
    Now a few suggestions.
    The examples in the book can now be imported in the form of an eclipse plugin. This is great but the examples take a huge leap. For example, chapter 6 introduces you to the concept of views and shows you how to build a simple view with a table and a hard coded set of values. The example in chapter 7 is a huge leap in complexity. It would have been nice to have an example that shows you how to wire events to mouse clicks in the basic "One, Two, Three" view. Instead, the example in chapter 7 tries to do too much. As such, I can only give a limited time to reading the book and going through the examples. The jump in the complexity of the examples from chapter 6 to chapter 7 is like going from "hello world" to socket programming.

    Again, my review is based on the perspective of someone who is writing eclipse plugins as productivity tools for my project, not as commercial products that I plan to sell. I may not be the right audience for your fantastic book but I suspect there are a lot of people like me who want to write plugins as productivity tools. Since your book is THE best book on eclipse plugins, I'm sure they'll be referring to it too.

    Another thing: Part of the examples from chapter 7 don't seem to work. Specifically, the "add to favorites" button on the toolbar doesn't work because the selection object is of the type TextSelection and not IStructuredSelection. Maybe I'm doing something wrong.


  5. I am writing Eclipse plug-ins for almost two years now and owned this book almost from the beginning. Looking back I must say that the book helped me get started and let me believe "it's possible". As probably many others I was a little intimidated at first by the vast possibilities of the framework.
    Now that I am much more experienced I must say that whenever I look into the book it leaves me a little bit disappointed. It only adds little value to the "Platform Plug-in Developer Guide" which is part of the online documentation and already covers a lot.
    The book goes into details and code very quickly without explaining the concepts very well. I still use the book every now and then for finding some nuggets not covered elsewhere and sometimes I get lucky but not too often.
    Shall you buy this book? If you are a beginner and if you like to learn by programming a sample plug-in then yes. The more proficient you get the more the book will lose its value and you will use other sources of information.


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Posted in Programming (Friday, July 4, 2008)

Written by Colin Moock. By O'Reilly Media, Inc.. The regular list price is $39.95. Sells new for $29.78. There are some available for $10.00.
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5 comments about Essential ActionScript 2.0.
  1. I am a beginner, I should understand that. But i wanted to buy it still thinking it would have been good. Its probably great for advance people but i found it personaly very difficult to understand as i am just a low beginner.


  2. My purchase of this book really helps mne a lot. It added up more knowledge and technique on my present expertise with Flash. Highly recommended for all Flash Action Scripters.


  3. As an occasional actionscript programmer, I try to stay to keep myself updated with the language as it evolves, as it has become the standard tools for my digital/artistic works.
    A year ago I dove into "ActionScript for Flash MX : the Definitive Guide" - I must admit I didn't understand some parts of it at first read - and got my poor programming skills to improve themselves at least a few notches up.

    I was a bit discouraged at all this Flash evolutions, thinking I'd be left behind (not to mention Flex 2 and Actionscript 3 right now), when I almost reluctantly bought this book.

    Well, it actually got me excited. Not only I feel way better in Actionscript programming now, seeing and understanding the improvements of the language (I still use the Definitive Guide for its handy and complete language reference while I code), but it also actually taught the principles of Object Oriented Programming.

    It does use some plain metaphors at first like all OOP stuff for dummies I've read here and there, but the author has a way of putting things in a relevent way that makes you actually understand what is what, what goes where, and why. It's clear.

    It's easy, going along his explanations and tutorials, and he also shows you thoroughly the possibilities and limitations of every concepts in the (relative to the Flash environment) he ever talks about, yet remaining accessible even to non-savvy programmers.

    A must have, like all his books I guess.


  4. I took a Java course at the University of Texas @ Austin, which has a well regarded CS program, and I walked out of it knowing what classes, subclasses, and instances were, but no idea how to practically use them. After reading Moock's book, I not only better understand the theory behind object-oriented programming, but how to use it following best practices. I wish I hadn't taken the Java course, because in 500 pages Moock takes you through 3 semesters worth of material.

    Of course, Essential ActionScript 3.0 is coming out soon, so you might want to wait for it, but make sure you buy at least one of them.


  5. This one felt more like work >.> And halfway through the book my copy had an extra duplicate chapter and that confused me for a little bit. This was a necessity for me though because I had to learn the syntax differences between how AS2 does it compared to what I'm familiar with (C++, etc.). I really didn't enjoy reading this book though as it felt more like work than any of the other Flash/AS books I've read so far.

    I'd recommend it only if you HAVE to learn about AS2 classes syntax ;-) Or want to punish yourself.


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Posted in Programming (Friday, July 4, 2008)

Written by William R. Stanek. By Microsoft Press. The regular list price is $29.99. Sells new for $9.69. There are some available for $5.45.
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5 comments about Microsoft Exchange Server 2003 Administrator's Pocket Consultant.
  1. Buy it only if you haven't installed Exchange server help yet. If you have than read the help first and save money.

    (Bought it in Russian and checked in English to make sure that translation is correct. Well it's a copy of English book, unfortunately)


  2. This book has been very helpful with building a new server, migrating from MS Exchange 2000.


  3. I spend most of my time working with SQL Server, but recently I had to take over and rebuild our Exchange. As I've had good success with Stanek's other books, I picked this one up the week before to help me get up to speed on Exchange, and it did an excellent job. I successfully upgraded, had all our servers up and running by Monday morning and we have an extensive multiple server configuraiton with OWA, wireless, and X.400 MTAs. Exchange Administrator Pocket Consultant is by far the one Exchange book I can't recommend highly enough. Get it, you'll be glad to have it on hand. I refer to this book constantly.


  4. There have been several of these types of books published by MS Press. Several years ago I purchased the Exchange Pocket Consultant. These books, and the information provided by William Stanek, are great.

    I traveled quite a bit doing Exchange migrations and clustering. The ability to toss something light, but dense with great information, into a backpack was awesome. It was also fun to pull it out and go over some of the principles with admins starting to operate their new Exchange 2003 infrastructures.

    This book goes over the basic principles of configuring and administering an Exchange 2003 infrastructure. The information is presented in an easy to understand format and helps to facilitate learning about Exchange operations.


  5. As with most MS support material, this one is heavy on geek speak and too light on real-world examples and "most-common" scenarios and solutions. The issue is the amount of time it takes to wade through the explanations in order to find the simple setting or solution that is needed to solve the problem. But overall I would recommend this book for MS Exchange Server administrators - it does save some time over looking things up on Microsoft's absurdly complex "support" pages.


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Posted in Programming (Friday, July 4, 2008)

Written by David Carlson. By Addison-Wesley Professional. The regular list price is $34.99. Sells new for $22.34. There are some available for $15.05.
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5 comments about Eclipse Distilled (The Eclipse Series).
  1. With Eclipse becoming extremely popular as an integrated development environment, there have been a number of books published to help you learn the tool. I recently received a copy of Eclipse Distilled by David Carlson, and it's a pretty good addition to the collection...

    Contents:
    Part 1 - Getting Started: A Java IDE and So Much More!; Hello Eclipse; Managing Your Projects; Customizing Your Workbench; Rapid Development; Java Project Configuration; Debugging Your Code
    Part 2 - Getting Agile: Characteristics of Agile Development; Updating the Eclipse IDE; Continuous Testing with JUnit; Refactoring Your Code; Continuous Integration with Ant; Team Ownership with CVS; Coding Standards; Index

    If you're looking for a book that covers a large number of the features of the Eclipse IDE, this book will be a good choice. In addition to covering all the technical details for installation, options, and "how to" things like refactoring, the author also covers how Eclipse works with various other common programming tools like JUnit and CVS. It's not a definitive guide on these other software packages, but you'll get a good grounding on how they integrate.

    What this book *isn't* is a tutorial guide to learning Eclipse. There are a number of Eclipse books that will walk you through a number of examples of how the package works and how to write code with it. This book really doesn't do that. You'll find out a lot about all the different options, but it's not like a "step 1, step 2, step 3" presentation. I really don't consider this a detriment to the book. If I wanted a tutorial, I could find one. But if I want a book that shows me all the mechanics and let's me figure out how to apply them to my needs, the "Distilled" approach works great.

    I like the book, but I can see how some people might not be enamored with the lack of sample code. If you're going in with your eyes open, you should be fine...


  2. In his forward, David Carlson writes: "This is the book I wanted to read when I started using Eclipse three years ago." Wow! And this is the book I wanted to read too!

    Like husbands and wives, wrenches and nuts, hands and gloves, some things were meant to fit together, while others repel like oil and water. When I learn a new programming language, IDE, API, software program, etc. I want the basics, the practical, the stuff I really need to get going. In any of these endeavors, there is simply too much to learn to sit reading detailed information on features that just never come up for me. Give me a good grounding in the basics, and I will pick up the details on the fly when I need them.

    Carlson's book will get you up to speed fast. Furthermore, it gives you the basics on several of the latest development methods with which Eclipse is compatible. He provides excellent basic discussions of Agile Development, JUnit testing, Ant, refactoring and the Concurrent Version System. He easily fits all this information into less than 300 pages.

    If this approach fits you like it fits me: Quick! Buy this book and get started.


  3. I manage multiple developers spread around the globe building product relying on the Eclipse Web Standard Tools (WST) and other parts of Eclipse. Getting each team member's IDE configured and updated was sucking up time.

    Chapter 9, "Updating the Eclipse IDE," saved us time equivalent to purchasing boxes of the book. Now we have flexible, consistent, repeatable configurations that make upgrading to new versions of WST and other features easy.

    We have adjusted our team's practices based on info in other chapters too.

    Carlson has provided excellent information for developers who want to work more effectively in the Eclipse environment. I'm delighted with the purchase.


  4. I read this book end to end but didnt find even a single startling fact about eclipse that i didnt know already.It was more like feature round up ( which you can discover going through the menu items in eclipse IDE)
    I would recommend this book for people who are absolutly new to eclipse .


  5. This is an excellent book and I recommend it highly to start with Eclipse.
    It saved me an incredible amount of time by providing the right level of information on virtually all important features of Eclipse.
    This book is for people with a background in development, but new to Eclipse.


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Posted in Programming (Friday, July 4, 2008)

Written by Rafael C. Gonzalez and Richard E. Woods and Steven L. Eddins. By Prentice Hall. The regular list price is $149.33. Sells new for $82.28. There are some available for $84.00.
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5 comments about Digital Image Processing Using MATLAB(R).
  1. If you want to get up to speed on Matlab and plan to use it for image processing, this book is a must.

    I have lots of experience in computer graphics and in programming languages like C++ and C#, but prior to reading this book I had never really used Matlab nor implemented complicated image processing algorithms. This book is a great introduction to both.

    The book is divided in twelve chapters touching both low-level image processing (e.g. spatial filtering) and higher-level concepts required for computer vision, like image registration and segmentation. Gonzalez et al are talented writers, explaining relatively complicated concepts clearly and concisely, without getting lost in the mathematical details. People interested in the more theoretical aspects should (and probably already have) check their other book.

    The only potential downside of this book is that it's definitely designed to be read sequentially, one chapter at a time. The matlab concepts are introduced piece by piece. For example, if you skip Chapter 5 (on image restoration, i.e. getting rid of noise) you may not realize that you missed the introduction to the image registration functions. Personally I liked this style (it added variety to a potentially dry subject), but a reader with less time to cover all of the matter may find this to be a problem.


  2. This book educates the reader in image processing and MATLAB. While I am experienced in both, I found the book to be an extrememly useful reference book for projects involving image compression and image representation. The book offered practical descriptions and useful code for computing the fast wavelet transform. It was especially useful in describing how the edges should treated. This is a big issue that other textbooks gloss over. I had never seen it described in a textbook, and it was described so well.

    The color image processing chapter is excellent, and the image processing chapter is pretty good. Lots of explanation and code.

    While the book stands alone, it can also be seen as a useful companion book to the more theoretical "Digital Imaging Processing" by Gonzalez and Woods (2nd edition). This is a different book even though it has close to the same name.


  3. I bought this book for two reasons (a) I needed an overview of IP and (b) I wanted to examine different pattern analysis algorithms with a practical twist. On both counts, as an non-IP researcher, I was very satisfied. The book is very well laid out, so well in fact that it would put to shame many of its rivals. It served my needs. I can't comment on whether it will meet the needs of a broader community. I would certainly recommend it based on my experience.


  4. Great text for learning image processing and using it with MATLAB. Hopefully the instructor also uses its mathematical insight as well.


  5. This book has been really helpful to write my own tools for image analysis, such as leaf area index estimations from digital images and microscopy imaging analysis.

    I think that for people involved in image processing and analyisis, this book is a must.


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Posted in Programming (Friday, July 4, 2008)

Written by Alfred V. Aho and Jeffrey D. Ullman and John E. Hopcroft. By Addison Wesley. The regular list price is $70.80. Sells new for $44.98. There are some available for $22.95.
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5 comments about Data Structures and Algorithms (Addison-Wesley Series in Computer Science and Information Pr).
  1. I believe two books make a classic collection in data structures - one was the data structures book by sartaj sahni (his first edition book many years ago - I haven't looked at his recent books). That was the book I had to study when I was an undergrad student. Now I was entrusted with the task of teaching Data Structures and after looking at several books, this is the one I chose (may be because it comes most close to the style of teaching using psuedo-pascal that I grew up with).

    I believe psuedo languages are the best way to learn concepts of any computer science area without getting bogged down in the nitty gritty of a language's syntax and semantics. I found the problems at the end of the chapters to be thoughtful and not extremely hard for undergraduate students. This book also goes into brief mathematical aspects of analysing the complexity of algorithms where necessary. The mathematical analysis is usually the part that most undergrad students moan and groan about, but they better get used to it IMO, if they wish to elevate themselves from the ranks of "a programmer" to an software / algorithm designer.

    I have to agree that this book can be extremely hard for the weaker students in the class who have never had any programming or basic college algebra exposure. For all others, this book should be great.


  2. Perfect book. Nice and small. You can buy it cheap too, it's old. But it's full of the meat and potatoes, no fluffy Java source code. Sure, it uses Pascal, but it's not that hard to understand Pascal code even if you never programmed in Pascal (me neither). What matters is the discussions behind the scenes. It covers the whole range of what you should know and it's concise. They don't write books like this anymore.


  3. This book explains very clearly the subjects of data structures and algorithms. Its in-depth coverage is very intuitive and easy to follow unlike other literature that is often tedious or esoteric.
    The only complaint I have is the choice of the programming language. Pascal is a language of the past. A new edition using C will make this book simply a gem.


  4. It is just an okay book, not extraordinary in any way. Especially, this is certainly not for the novice in this topic, i.e., it is certainly not a good introductory book. So if you are new to data structures and algorithms, stay away from this book, go for some good introductory book.

    For the advanced readers, it is an okay book. Better books are available, e.g., books by Cormen et al. and Robert Sedgewick.

    The book is written in a way not very intersting or engaging. The algorithms are not explained in detail. Often things are left unexplained or assumed that the reader already knows it. Algorithms are presented in pseudocode, which causes problems especially for the readers familiar to some particular programming language.


  5. Hyperbolic remarks about this book will mislead you into thinking that this book is absolutely unique, when it's not. The material here is standard and present on many, many algorithms and data structures book.

    Furthermore, this book is dated, as it uses Pascal. It has very little relevance for today's world of collections of data structures made by experts (on Java, C#, Eiffel, Smalltlak, etc.) which are resources you need to know how to tap into to be more productive.

    And as a last point, algorithm analysis is not the strong point of this book either, as it is just a late chapeter in the book and gets nowhere near advanced (i.e., real) algorithmic analysis (for which you will need higher math, such as calculus and probability).

    Nevertheless, it's a good book but I don't know if you should buy it instead of that other, nice and new book using Java 5.0 using generics.


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Posted in Programming (Friday, July 4, 2008)

Written by James Tisdall. By O'Reilly Media, Inc.. The regular list price is $39.95. Sells new for $18.00. There are some available for $15.54.
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5 comments about Beginning Perl for Bioinformatics.
  1. i find this book is an excellent intoudction for one of the most intersting topic..The book is so easy to read if you know the elementary of molecular biology and begining introudction about perl. I do recommed this book to start with if you interested about programming for bioinformatics. You will be able to build simple bioinformatics programmes after reading this book as well as you will be able to understand easily how the commerically avaliable bioinformatics programs are working.


  2. Excellent book. The perl programming language is the most versitile and powerful software tool available today. This book was written for Biologists to learn this incredible programming language. Examples are pulled from real problems Biologists face and explained in terms they can understand. The book is clearly written.


  3. People come to Bioinformatics from either the bio side or the CS side, with a few from various other disciplines. This book is best for the bio person who is getting into programming, not the programmer who is getting into bio.

    For you CS types, I attended a tutorial by Tisdall on this material some years ago. One of the attendees asked why you needed an editor to code in Perl. That is the level that we are dealing with here!

    It is a crime that biology and biochem students are not taught any perl- this is a very useful tool that will be more important as time goes on.

    Perhaps someone could write a book on bioinformatics Perl for programmers someday, but that is not the goal of this book.


  4. For the students of molecular biology and genetics, and also other bioinformatics-related departments, this book is an above-average supply to study Perl.


  5. Although this book was written for biologists with no previous programming experience who have decided they need to learn to program in PERL, it is also useful for programmers entering the field of bioinformatics who need to learn the language. However, you should have some background in biology or else you'll be lost as to the purpose of the examples. That's because almost all of the examples and exercises are based on real biological problems, and this book will give you a good introduction to the most common bioinformatics programming problems and the most common computer-based biological data. This book is over five years old, but it still stands alone in that what it does it does better than any other book I've run across. The follow-on to this book is "Mastering Perl for Bioinformatics", and I recommend that book for both CS and biologist types that want to get into the more advanced parts of PERL and yet stay in the realm of learning the language via real biological problems. The following is a short run down of each chapter:

    1. Biology and Computer Science - Covers some key concepts in molecular biology, as well as how biology and computer science fit together.

    2. Getting Started with Perl - Shows you how to get Perl running on your computer and also talks about Perl's benefits.

    3. The Art of Programming - Provides an overview as to how programmers accomplish their jobs. Some of the most important practical strategies good programmers use are explained, and where to find answers to questions that arise while you are programming is carefully laid out. These ideas are made concrete by brief narrative case studies that show how programmers, given a problem, find its solution.

    4. Sequences and Strings - You start writing Perl programs with DNA and proteins. The programs transcribe DNA to RNA, concatenate sequences, make the reverse complement of DNA, and read sequence data from files. This is the first chapter to conclude with exercises.

    5. Motifs and Loops - Continues demonstrating the basics of the Perl language with programs that search for motifs in DNA or protein, interact with users at the keyboard, write data to files, use loops and conditional tests, use regular expressions, and operate on strings and arrays.

    6. Subroutines and Bugs -Extends the basic knowledge of Perl in two main directions: subroutines, which are an important way to structure programs, and the use of the Perl debugger, which can examine in detail a running Perl program.

    7. Mutations and Randomizations - Genetic mutations, fundamental to biology, are modelled as random events using the random number generator in Perl. This chapter uses random numbers to generate DNA sequence data sets, and to repeatedly mutate DNA sequence. Loops, subroutines, and lexical scoping are also discussed.

    8. The Genetic Code - How to translate DNA to proteins, using the genetic code. It also covers a good bit more of the Perl programming language, such as the hash data type, sorted and unsorted arrays, binary search, relational databases, and DBM, and how to handle FASTA formatted sequence data.

    9. Restriction Maps and Regular Expressions - An introduction to Perl regular expressions. The main focus of the chapter is the development of a program to calculate a restriction map for a DNA sequence.

    10. GenBank - The Genetic Sequence Data Bank (GenBank) is central to modern biology and bioinformatics. In this chapter, you learn how to write programs to extract information from GenBank files and libraries. You will also make a database to create your own rapid access lookups on a GenBank library.

    11. Protein Data Bank - Develops a program that can parse Protein Data Bank (PDB) files. Some interesting Perl techniques are encountered while doing so, such as finding and iterating over lots of files and controlling other bioinformatics programs from a Perl program.

    12. BLAST - Develops some code to parse a BLAST output file. Also mentioned are the Bioperl project and its BLAST parser, and some additional ways to format output in Perl.

    13. Further Topics - Looks at topics beyond the scope of this book. These topics include sequence alignment methods like the Smith-Waterman algorithm and microarray techniques that enable the measurement of the relative levels of thousands of gene transcripts at a time. These topics are only briefly mentioned, and you are shown places outside of the book to get further information.

    Appendix A - Resources for Perl and for bioinformatics programming, such as books and Internet sites.

    Appendix B - Summary of those parts of the Perl language that will be most useful as you read this book.


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