History: Fiction or Science? (Chronology, No. 1)

Book Description

Recorded history is a finely-woven magic fabric of intricate lies about events predating the sixteenth century. There is not a single piece of evidence that can be reliably and independently traced back earlier than the eleventh century. This book details events that are substantiated by hard facts and logic, and validated by new astronomical research and statistical analysis of ancient sources.

Customer Reviews:

Calculations are only as good as your numbers.......2007-08-03

Yes, we can all agree that mainstream history is nearly 100% BS due to politics, economics, ego, problems with dating techniques, and various conspiracies. Agreed. But, I've been researching the distinct possibility that human history (in terms of civilizations) are much more ancient than we've been told, so coming across this book was very interesting to me. I wondered how Fomenko could be wrong (if at all) because he is very persuasive in his presentations. Then it dawned on me. If at previous times in prehistory, due to the various catastrophies that are well documented (comets, asteroids, planetary disruptions, plasma discharge, pole reversals, etc) the Earth was in a different position in relation to the sun, different tilt on its axis, different orbit, different rotation (in terms of velocity and DIRECTION), and the continents were in different positions, then would this not cause the ancients to see the sky (constellations) differently? In other words, is Fomenko making erronious assumptions about the physics of the Earth in pre-history, which then corrupt his data with regards to dating the relevant astrology? The last event to seriously disrupt our planet occured roughly 3500 years ago, according to other good researchers, so is it possible Fomenko has been confused by this? The vastly different physics of our planet in the not so distant past may explain this confusion, which is not to say the "mainstream" version of history is correct; on the contrary. I am not an expert in these fields, but wanted to see if this idea could spark discussion.

Pants on fire?.......2007-07-19

Will people ever read before spamming? Yes, Jesuits could not rewrite world history alone, they had help. Anyway, Dr Prof Acad A.Fomenko does not point to jesuits as the driving force of world wide history manipulation in published volumes 1,2,3;, actually he barely mentions the poor devils. Check it with 'Search inside' feature, please. China is rarely mentioned either, in fact, Dr Fomenko is completely eurocentric. Right, his theory contradicts all mainstream schools of history, because in their actual state they are all built on blatantly erroneus chronology. You don't need a mysterious cabal (conspiracy) to falsify history, the falsification is its modus operandi. It is inherent to history(ians) to falsify (distort) events, as it is inherent to humans to boast as it is inherent to power (authority) to legimize itself by referrring to glorious past made to its own order. Dr Prof Fomenko and team have identified scores of instances of such manipulation in Russian, European, etc.. history, and delivered valid statistical proof thereof. His own 'reconstruction' is completely another story. Forget c14 as a valid method of dating. W.Libby has initially discovered a brilliant method of INDEPENDENT dating. Too bad, c14 method has become a joke after a forced marrige with dendrochronology with consensual chronological scale inbuilt. Radiocarbon method can't stand blind tests, but is so very productive as a rubberstamp.

Accepted History & Chronology Must Be Changed. .......2007-04-09

There is no doubt that history as most know it is a sham, & institution's version of History both University & Church is fradulent & inaccurate. Everything was established with an agenda, The real "Dark Ages" are now when we have access to incredible amounts of information past authorities & more important 'common folk' didn't have but our institutions & educators are slow to evolve because of what has ignorantly & arrogantly been taught for too long. This is on many subjects not just Chronology.

For anyone to question "Why would a Mathematician have anything credible to say of History?" The answer is from Dr. Fomenko's preface in the book: "It would be worthwhile to remind the reader that in the XVI-XVII century Chronology was considered to be a subdivision of Mathematics." These volumes could possibly be some of the most important works to date & should be read by everyone with an interest in History, especially professors & educators who have a duty to the public. I have read both books & must say that 'Chronology 1' has some very eye opening & revolutionary information. Even if these volumes are part true the implications are profound & opens the doors to further investigations & questions which must be done. I speak several different lanquages & must say the logic Dr. Fomenko uses with "inflection" of words & words being read from left to right in one region & right to left in another then written backwards, the removal of vowels & get down to basics of words, or different cities & locations having the same name etc. is correct. Vowel usage has always been optional & varied, actually complicating linquistics & study. The first thing one has to understand is that words never had a fixed spelling in history like we do now, the spelling of words was mutable & regional, as well as names & titles of people were vast, varied & changed, NOTHING WAS FIXED or understood linear. Matters of Life & Death as well as financial profiteering yesterday & today were & are made with ignorant, illogical & conspiratorial views of history & reality, it's time people get closer to the Truth & society collectively grow up.

Very Interesting.......2007-03-07

It is a good proposal and I believe it will mature into something even better in the future. I think it deserves to be read.

History as Science Fiction.......2007-01-10

Anatoly Fomenko has written a very intriguing book, full of pictures, charts, and computer 'proof' of his thesis: backwards of AD900 we don't really know what happened or when. Between AD900 and AD1600 there is more certainty, but there is still a lot of fuzzy ground, and things don't get reliable until we get past the 1600's where the printing press made it very difficult for the perpetrators of this timeline manipulation to change anything that had been committed to print. The Dark Ages did not happen. Books were burned for a reason. One organization has doubled the actual length of its existence by expanding the real chronology. Read why.

I had always wondered why Christ died about AD33 and yet men waited until the 11th century to form the Knights Templar, the Cathars, etc and go after the Holy Land by force. Why the 1000 year gap? Turns out there wasn't more than a 10-12 year gap and he proves it using astronomy. This also implies that the planet is not as old as we have been told, and current Christian and other creationist scientists are already championing that idea without being aware of Fomenko's book. The two groups, creationist scientists and the Russian mathematical analysts corroborate each other. Fascinating.

Of course, all this flies in the face of what we have been told traditionally is the 'proper' chronology of western civilization, and most readers will experience 'cognitive dissonance' in reading this book. It means that our history going backwards from AD1600 becomes progressively more incorrect and unreliable until it cannot be trusted at all... in the space of 700-800 years.

Naturally, the curious, open-minded reader will want to know WHO did this, WHY, and did any of the events we think of as really ancient ever happen?
Dr. Fomenko is a respected scientist/mathematician at Moscow State University who has already answered these questions to the satisfaction of his initially skeptical colleagues. Most of them are now believers, a few still refuse to believe (the usual diehards), and of course the western press has ignored Fomenko's work -- for obvious reasons when you read the book. The ones who perpetrated this chronology ruse have a lot to answer for. They are still with us. That's why this book is a well-kept secret.

I gave the book a 4-star rating because I was unable to check out some of his claims; those I checked were as he said. But if even 1/3 of his claims are true, this punches a big hole in what we think is our history, the meaning of western civilization, our educational process (for repeating the ruse as gospel), and the trustworthiness of the organization that perpetrated this ruse, well-intentioned or not.

This book relates to current research into a Young Earth paradigm, to John Keel's discoveries about our planet, and Fr Malachi Martin's insights (in his now out-of-print books). We are indeed sheep who are manipulated and kept ignorant -- for a reason. While knowing what these men have to say may be the "booby prize" (as in: 'what can you do with this knowledge?'), it will provide interesting reading. Didn't someone say: "...and the Truth will set you free."?? For you to judge if this book contains the truth.

Developing Bioinformatics Computer Skills

Average customer rating:

horrible
Good introduction, somewhat uneven
Useful only for a reference book
Quite good introduction
A Great Book For Exploring the Bioinformatics Field

Developing Bioinformatics Computer Skills
Cynthia Gibas , and Per Jambeck
Manufacturer: O'Reilly Media, Inc.
ProductGroup: Book
Binding: Paperback

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ASIN: 1565926641

Book Description

Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. Genome sequencing projects are producing vast amounts of biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological literature. It's impossible for even the most zealous researcher to stay on top of necessary information in the field without the aid of computer-based tools. Bioinformatics is all about building these tools. Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, as well as for experienced biology researchers who are just starting to use computers to handle their data. 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, and data visualization. Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data.

Customer Reviews:

horrible.......2004-06-11

This book is the worst I've ever purchased. It has been no help whatsoever. It had a couple examples of PERL programming...big deal.

The 5-star ratings are obvious shills (one reviewer wrote a very long review and has never reviewed anything else)

Good introduction, somewhat uneven.......2003-12-18

This book is a good introduction to Bioinformatics and to what it takes to get started in the field. Some reviewers deride it as too superficial or as too Unix-centric, but I think those are two of its strengths. The authors lay no claim to having written the definitive work on the subject of Bioinformatics, and they freely admit that they come in with a certain bias. If you are serious about Bioinformatics this won't be your last book anyway, but it'll get you started.

That said, I found the material a bit uneven. The authors tend to jump from almost trivial stuff to very complex in a heartbeat, and they sometimes use a concept or command before it can be properly understood One example: Introducing the Unix commands head and tail, then moving on to split and csplit. The introduction to regular expressions as needed by csplit follows a few pages later.

Nevertheless, I plan to use this book as a companion text to my own sequence of computer classes for biologists, and I think it will serve that purpose very well.

Useful only for a reference book.......2003-12-03

We are all well aware that it is impossible to write a book on bioinformatics satisfying all types of readers. That is the reason why we are spending much time on finding a book that we can say "This book is just for me!"

Well, this book is not a self-teaching book by itself. Don't expect that things will become clear to understand after reading this book.

If your expectation is just to taste flavor of bioinformatics and to use it as a reference book, then this book is right for you.

Quite good introduction.......2003-10-03

This is a quite good book for people who have little background in Bioinformatics or Computer Science. I have to say it was pretty good in introducing basic ideas in Bioinformatics, and online resources.

However, I think the authors can do a better job in providing more details in certain areas, for example, in Perl programming, and in sequence alignment. Some parts of the book is so simple that the contents in those parts are not quite useful.

I would recommend this book to people who are new to Bioinformatics. But not to people who have taken one or two
introductory classes.

A Great Book For Exploring the Bioinformatics Field.......2003-04-16

It's no deep secret many Information Technology (IT) professionals today are facing a rough road finding gainful employment. In fact, according to Information Week, nearly 10% of the US IT workforce vanished in the last two months of 2002. More aptly put, some 272,530 American IT professionals in October were unemployed by December. This data is corroborated by the Bureau of Labor Statistics. Where did they all go? Many almost certainly got jobs in other professions and many still could be seeking employment. Employment counselors are encouraging IT professionals to "repurpose" those hard earned tech skills.

Bioinformatics is a ripe apple waiting to be eaten. Bioinformatics simply stated is the computational and analytical methods to biological problems. If this sounds like an open ended explanation, it is. In fact, according to O'Reilly's definitive publication on the topic, "Developing Bioinformatics Computer Skills" by Cynthia Gibas and Per Jambeck, there are several different definitions to Bioinformatics, but suffice to say all revolve around applying IT to the management of biological data.

Chapters one through six delineate the basics including the typical and common software and hardware requirements for Bioinformatics. I will tell you right now if you want to be successful in this fresh field, you must learn Unix. The book points out why. Unix is used extensively in universities and academia where the abundance of software for scientific data analysis is developed. Not to mention in the mid nineties, the only workstations able to visualize protein data structure in real-time were Silicon Graphics and Sun Unix workstations. Linux fans rejoice! As the book points out, "Linux is an excellent platform for developing software, so there's a rich library of tools available for computational biology and research in general."

Sound interesting? At this point you could be overwhelmed and ask yourself, "Where do I start?" Well, you may want to purchase O'Reilly's "Developing Bioinformatics Computer Skills" to see what the fuss is all about, determine whether you have what it takes to succeed in this new field, and most importantly, get an introduction to the software tools for biological applications from the inside out. Bioinformatics is a growing field that will continue for the unforeseeable future.

Book Description

Traditionally an area of study in computer science, string algorithms have, in recent years, become an increasingly important part of biology, particularly genetics. This volume is a comprehensive look at computer algorithms for string processing. In addition to pure computer science, Gusfield adds extensive discussions on biological problems that are cast as string problems and on methods developed to solve them. This text emphasizes the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics.

Customer Reviews:

Very in-depth explanations.......2006-07-27

I bought this book not because I have any interest in computational biology but because at that time I had an interest in (and professional need for) extremely fast and efficient ways to search through massive data stores. In this I was not disappointed, having found thorough treatments of how to do exact pattern matching as well as various types of "closest" match searching though very large data sets in minimal time.

While perhaps overly theoretical for a person like myself who has not had extensive schooling, it certainly matched my expectations.

I would recommend this book to anyone who I thought could benefit from it.

nice intersection of computing and biology.......2006-01-03

The text sits at the intersection of computer science and computational biology. It centres around the observation made by the author and others that often in CS, one has to manipulate strings of text, which are just sequences of text. While in computational biology, a recurrent theme is how to deal with sequences of molecules. These might be in a DNA sample or in a protein.

Surprisingly, from this simple observation, Gusfield manages to gather together considerable material. Over the decades, computing has accrued many algorithms for text string processing. The book's merit is in presenting those which are also applicable in bioinfomatics. The level of treatment is sophisticated, from the computing vantage. Enough so that perhaps the typical geneticist might not be able to easily follow the narrative. But a researcher with a strong background in both fields might be able to benefit.

What it says, it says best........2003-08-17

If you haven't read this book, you don't know biological string matching. The book's focus is clearly on string algorithms, but the author gives good biological significance to the problems that each technique solves. I came away from this book understanding the algorithms, but also knowing why the algorithms were valuable.

No, there isn't any real source code here. That should not be a problem - this book aims above the cut&paste programmer. The book in meant for readers who can not only understand the algorithms, but apply them to unique solutions in unique ways.

String matching is far too broad a topic for any one book to cover. The study can include formal language theory, Gibbs sampling and other non-deterministic optimizations, and probability-based techniques like Markov models. The author chose a well bounded region of that huge territory, and covers the region expertly. The reader will soon realize, though, that algorithms from this book work well as pieces of larger computations. The book's chosen limits certainly do not limit its applicability.

By the way, don't let the biological orientation put you off. DNA analysis is just one place where string-matching problems occur. The author motivates algorithms with problems in biology, but the techniques are applicable by anyone that analyzes strings.

Definitive String Algorithms Text.......2003-01-05

If you like definition-theorem-proof-example and exercise books, Gusfield's book is the definitive text for string algorithms. The algorithms are abstracted from their biological applications, and the book would make sense without reading a single page of the biological motivations. Gusfield aims his book at readers who are fluent in basic algorithms and data structures (at the level of Cormen, Leisersohn and Rivest's excellent text). The exercises are wonderfully illustrative, being neither trivial nor impossible.

All of the major exact string algorithms are covered, including Knuth-Morris-Pratt, Boyer-Moore, Aho-Corasick and the focus of the book, suffix trees for the much harder probem of finding all repeated substrings of a given string in linear time. In addition to exact string matching, there are extensive discussions of inexact matching. Even the discussions of widely known topics like dynamic programming for edit distance are insightful; for instance, we find how to easily cut space requirements from quadratic to linear. There is also a short chapter on semi-numerical matching methods, which are also of use in information retrieval applications. Inexact matching is extended to the threshold all-against-all problem, which finds all substrings of a string that match up to a given edit distance threshold. The theoretical development concludes with the much more difficult problem of aligning multiple sequences with ultrametric trees, with applications to phylogenetic alignment for evolutionary trees (an approach that has also been applied to the evolution of natural languages).

Note that there is no discussion of statistical string matching. For that, Durbin, Eddy, Krogh and Mitchison's "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acides" is a good choice, or for those more interested in language than biology, Manning and Schuetze's "Statistical Natural Language Processing". There is also no information on more structured string matching models such as context-free grammars, as are commonly used to analyze RNA folding or natural language syntax. Luckily, Durbin et al. and Manning and Schuetze also provide excellent coverage of these higher-order models in their books.

This book is not about efficient implementation. If you need to build these algorithms, you'll also need to know how to write efficient code and tune it for your needs. This is an algorithms book, pure and simple.

As a computer scientist, I found the discussions of computational biology to be more enlightening than in other textbooks on similar topics such as Durbin et al., because Gusfield does not assume the reader has any background in cellular biology. Instead, he provides his own clear and gentle introductions illustrated with algorithms, applications, open problems and extensive references. Like most Cambridge University Press books, this one is beautifully typeset and edited.

All about suffix trees.......2001-11-05

Excellent book on String Algorithms. A lot of material. This is not an easy read, though, relatively not difficult for an algorithms and data-structures book.

This is the most complete resource i could find about suffix trees, how to implement them, usages, and algorithms. Actually, when I took this book, I was interested in suffix arrays. Well - this book explains those better than the original paper do.

Many applications to suffix trees are listed, along with comparisons to other algorithms applied to those problems.

If you need to get into string algorithms from computer science perspective - this is a good book to start. If you want to "feel" of the biologists side of the story, than this is not a good choice.

I use this book as a textbook on the subject, and I'm sure I'll be using it as a reference later on.

Amazon.com

Biology, it seems, is a good showcase for the talents of Perl. Newcomers to Perl who understand biological information will find James Tisdall's Beginning Perl for Bioinformatics to be an excellent compendium of examples. Teachers of Perl will likewise find the text to be filled with fresh programming illustrations of growing scientific importance. Seasoned Perlmongers who want to learn biology, however, should search elsewhere, as Tisdall's emphasis is on Perl's logic rather than Mother Nature's.

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

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

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

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

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

Book Description

With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems. Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference. The book covers:

Programming basics and working with DNA sequences and strings
Debugging your code
Simulating gene mutations using random number generators
Regular expressions and finding motifs in data
Arrays, hashes, and relational databases
Regular expressions and restriction maps
Using Perl to parse PDB records, annotations in GenBank, and BLAST output

Customer Reviews:

A practical introduction to programming for biologists.......2006-12-31

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.

Reasonable book for learning Perl.......2006-11-11

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

Mostly for the Biologist.......2006-09-20

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.

Beginning Perl for BioInformatics.......2006-01-17

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.

excellent introduction..........2005-12-31

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.

System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

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System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Manufacturer: The MIT Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0262195488

Book Description

Research in systems biology requires the collaboration of researchers from diverse backgrounds, including biology, computer science, mathematics, statistics, physics, and biochemistry. These collaborations, necessary because of the enormous breadth of background needed for research in this field, can be hindered by differing understandings of the limitations and applicability of techniques and concerns from different disciplines. This comprehensive introduction and overview of system modeling in biology makes the relevant background material from all pertinent fields accessible to researchers with different backgrounds.

The emerging area of systems level modeling in cellular biology has lacked a critical and thorough overview. This book fills that gap. It is the first to provide the necessary critical comparison of concepts and approaches, with an emphasis on their possible applications. It presents key concepts and their theoretical background, including the concepts of robustness and modularity and their exploitation to study biological systems; the best-known modeling approaches, and their advantages and disadvantages; lessons from the application of mathematical models to the study of cellular biology; and available modeling tools and datasets, along with their computational limitations.

Average customer rating:

Very nice book
Very Practical & Useful Users Guide
Blast User's Bible
useful for comparative sequence alignment tasks
How does sequence alignment actually work?

Blast
Ian Korf , Mark Yandell , and Joseph Bedell
Manufacturer: O'Reilly Media, Inc.
ProductGroup: Book
Binding: Paperback

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ASIN: 0596002998

Book Description

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

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

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

Customer Reviews:

Very nice book.......2006-11-08

This is a very good book. It goes into the gory details of all the BLAST features. There is a very nice introduction (Part II of the book) that explores the theoretical background that is at the foundation of BLAST before diving into the practical use of this powerful tool. Moreover, you can find some useful tips on how to handle the setup and administration of locally installed BLAST databases. It's worth having it on your bookshelf.

Very Practical & Useful Users Guide.......2006-07-12

From a users-perspective this book serves its purpose well - it explains what it is that BLAST is doing "under-the-hood" so that one may better customize Blast's search behavior. All I know is that I really learned a lot of basic fundamental core concepts here that I previously just took for granted.

The book discusses the biology, statistics, algorithms, and computer science issues involved in explaining blast. I liked this approach because it does not head super far into any one core area but rather sticks to a strong fundamental overview of each topic. The other strong aspect of this book is that the author thoroughly compares NCBI and WU Blast throughout, characterizing instances where one may choose one over the other and/or how to tweak the parameters for both in those situations.

I orginally bought the book b/c I wanted an overview on PAM and BLOSUM matrices and to understand how Blast Statistics work. It really served as an informative contextual tutorial that has definitely raised my overall understanding on not only Blast, but to better grasp the very interdisciplinary nature concerning sequence alignment for in-silico biological research.

Blast User's Bible.......2006-01-29

This is the place to start for anyone using NCBI BLAST. It's a thorough description of the various BLAST programs for nucleotides, amino acids, and codons.

The book offers a biology refresher early on, but this is aimed mainly at people with serious interest in BLAST - people who normally won't need that. Next, it discusses traditional dynamic programming alsorithms for local and global alignment. Then, in just a few pages, it summarizes the mathematical meanings and derivations of the various BLAST scores (raw scores, P-values, ane E-values). The discussion just skims the theory, but will help the reader make sense of the programs' output.

Those 75 pages set the background; the next 250 contain the real meat of the book. They cover the various BLAST programs, options, and outputs. More than that, these sections discuss setting up experiments based on BLAST, and how to deal with the problems you're likely to encounter. This could be a bit more explicit about how PSI_BLAST works (and why it sometimes doesn't), but coverage is generally strong.

A few things are weak, like emphasis on the fact that experiments aren't strictly repeatable. For example, if you exactly replicate today's test next week, even if all of the other output is identical, you might still get different (and worse) E values, since they depend on the size of the database. PSSMs get little if any discussion. Also, details about internals are weak - but this is a user's book, not an implementor's, so that's a matter of scope rather than suffiency.

Most of the book's points are illustrated with actual output or with Perl code - the lingua franca of bioinformatics, for some reason. If you're serious about using BLAST and about understanding what it's really telling you, this is the book to own.

//wiredweird

useful for comparative sequence alignment tasks.......2004-01-20

BLAST is a well-known tool for bioinformatics (biological sciences+computer sciences). In this book contains a concepts of central dogma of molecular biology, sequence aligment, sequece similarity, practical BLAST programs (divide into 5 programs), and how to install and use BLAST tool. Moreover, it also offers enough tips to improve my BLAST searches usage. I think this book's content is well-writing and well-organizing for comparative sequeces alignment tasks. I use this book to begin in bioinformatics and it can help me to learn about this. But this book does not contain all of things that I want to known on bioinformatics or computational biology.

How does sequence alignment actually work?.......2003-11-24

If you want to understand the nuts and bolts of how sequence alignment works, then this is the book for you. It will be especially useful for BLAST users who want to understand how it actually works and also for developers who don't know much biology, struggle with the math, but have no problem reading a perl script.

The book is basically divided into:
0. A Foreword by Stephen Altschul (the co-creator of BLAST)
1. A quick web intro to a BLAST search
2. Sequence alignment and how the algorithms work
3. Blast and how the Blast statistics are calculated
4. The different types of Blast e.g. WU-Blast
5. Approaches to Performance speedup
6. Reference sections on BLAST parameters

The real key is that this book neatly splits the difference between academic texts and papers which are quite often too difficult to read without sufficient background (and they are not precise about the implementation anyway) and the user-manual type texts which don't discuss the theory at all.

One of the best chapters (in my view) is chapter three, where they explain and illustrate the workings of the Needleman-Wunsch and Smith-Waterman algorithms for global and local alignment. If you read the text, then study and run the included perl code, you WILL understand how they work, but be prepared to spend several hours trying different examples. The real advantage of this approach is that you get a deep, practical understanding of how alignment actually works, that you just can't get from reading a mathematical treatment of the subject. Once you understand this chapter, you are actually sufficiently expert to get inside alignment code and modify it for your own purposes.

Ian Korf does continually emphasize that the algorithms may look clever, but they are, in the end, robotic in that they will quite happily align complete rubbish if you are not careful about controlling the algorithm and thinking carefully about the results you get.

There are a couple of mistakes in the diagrams (chap 3), that are addressed in the errata, but the perl code is correct.

Book Description

Bioinformatics – the process of searching biological databases, comparing sequences, examining protein structures, and researching biological questions with a computer – is one of the marvels of modern technology that can save you months of lab work. And the most amazing part is that, if you know how, you can use highly sophisticated programs over the Internet without paying a dime and sometimes, without installing anything new on your own computer. All you need to know is how to use these technological miracles.

That's where Bioinformatics For Dummies comes in. If you want to know what bioinformatics is all about and how to use it without wading through pages of computer gibberish or taking a course full of theory, this book has the answers in plain English. You'll find out how to

Use Internet resources
Understand bioinformatics jargon
Research biological databases
Locate the sequences you need
Perform specific tasks, step by step

Written by two experts who helped develop the science, Bioinformatics For Dummies is all about getting things done. If you're just getting your feet wet, start at the beginning with a quick review of those necessary parts of microbiology and an overview of the tools available. If you already know what you want to do, you can go directly to a chapter that shows you how. Get the lowdown on

Researching and analyzing DNA and protein sequences
Gathering information from all published sources
Searching databases for similar sequences and acquiring information about gene functions through sequence comparisons
Producing and editing multiple sequence comparisons for presentation
Predicting protein structures and RNA structures
Doing phylogenetic analysis

With an Internet connection and Bioinformatics For Dummies, you'll discover how to peruse databases that contain virtually everything known about human biology. It's like having access to the world's largest lab, right from your desk. This book is your lab assistant – one that never takes a day off, never argues when you ask it for help, and won't demand a benefits package.

Customer Reviews:

Using the free software on internet sites to help your research.......2007-03-14

The first chapter is a short review of DNA and RNA sequences, amino acids, and protein. The other chapters teach you to use the free software found on the Internet to work with your research. Information is also given which helps explain some biochemicals. My skills are in Software Development using C++ language, and I need more information on biochemicals to understand the problems and to develop algorithms to solve them.
My only criticism is that I would like the book to give more biochemical theory before taking up the subject of Internet software.
Overall, this is a good beginner's book on biochemistry.

Good.......2007-02-16

I am a couple years into a PhD in bioinformatics, but this is the book I started with. I knew some biology and some computer science, but I still found a lot of the databases, etc. confusing and the field has a decided lack of simplified documentation (though it is getting better).

Of course, bioinformatics is a pretty broad topic and no book could possibly cover everything.

If you do not know any biology at all you probably should also get a basic text on genetics/molecular biology (or read thema at the NCBI web site books section for free). You don't need anything in depth to read the dummies book, just at the level of an introductory biology book. Hint: DNA to RNA, RNA to Protein. And you want to know why proteins are similar because proteins with similar amino acid sequences often have similar chemical properties and therefore similar functions, so if you know what one protein does you can guess what a protein like it probably does.
:-)

And despite the name of the book the authors are REAL bioinformaticists (T-Coffee rocks!)

Yes, It's Really Written at the For Dummies Level........2007-01-18

This book kind of blew me away. Bioinformatics is such a big word.

Then in the second chapter they tell you 'How Most People Use Bioinformatics.' And all of a sudden they have you on line to the National Library of Medicine at the National Institute of Health. They have you looking at protein sequences, and you even understand what they are saying.

This is a 'For Dummies' book. It is written in their traditional style, assuming that you know very little -- well to be sure they say they are making the assumption that 'You likely have a background in molecular biology. If you don't - or if you need to brush up on your molecular biology - Chapter 1 gives you a brief overview of the basics.'

I found that the first few chapters went down pretty easily. By part IV it had gone further than I wanted to go, and I quit reading.

BUT if I were going to be taking a course in bioinformatics, or even thinking about taking such a course, or just looking at a degree in biology, I'd spend a week or two getting around this book. It's written a hell of a lot better than any text you're likely to get assigned, and at its price it's quite a deal.

Great introductory text.......2006-09-20

This is an excellent introduction to Bioinformatics. It does assume some very basic knowledge of biology- perhaps a couple of paragraphs could help the total newbies.

Have you noticed that reviews of bioinformatics books tend to follow certain patterns? The Computer Scientists and mathematicians complain that there is not enough detail about the algorithms, the biologists complain that they could not get through the math, and everyone complains that there is not enough detail about their favorite programs! Let us face the fact that this is a very broad field, and most people that want to learn about it will never design algorithms.

great beginner.......2005-12-16

In spite of the title (I don't know many dummies interested in multiple sequence alignments) this reference is written by experts in the field of bioinformatics and is very accessable for the beginner. I purchased this book as a beginning graduate student so that I could learn which programs to use to compare amino acid and nucleic acid sequences as well as prepare them for publication and this book was perfect for this end. This text doesn't delve into the algorithms or much theory (which is learned through practice and other sources), nevertheless, I recommend this for the researcher for a crash course or quick reference. This book really helped me get my feet wet in this area (and recently publish a nice alignment) and will certainly reduce my workload next semester for my bioinformatics course!

Discovering Knowledge in Data: An Introduction to Data Mining

Average customer rating:

conveys basic ideas

Discovering Knowledge in Data: An Introduction to Data Mining
Daniel T. Larose
Manufacturer: John Wiley & Sons, Inc.
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471666572

Book Description

Learn Data Mining by doing data mining
Data mining can be revolutionary-but only when it's done right. The powerful black box data mining software now available can produce disastrously misleading results unless applied by a skilled and knowledgeable analyst. Discovering Knowledge in Data: An Introduction to Data Mining provides both the practical experience and the theoretical insight needed to reveal valuable information hidden in large data sets.
Employing a "white box" methodology and with real-world case studies, this step-by-step guide walks readers through the various algorithms and statistical structures that underlie the software and presents examples of their operation on actual large data sets. Principal topics include:
* Data preprocessing and classification
* Exploratory analysis
* Decision trees
* Neural and Kohonen networks
* Hierarchical and k-means clustering
* Association rules
* Model evaluation techniques
Complete with scores of screenshots and diagrams to encourage graphical learning, Discovering Knowledge in Data: An Introduction to Data Mining gives students in Business, Computer Science, and Statistics as well as professionals in the field the power to turn any data warehouse into actionable knowledge.

An Instructor's Manual presenting detailed solutions to all the problems in the book is available online.

Download Description

Customer Reviews:

conveys basic ideas.......2006-08-25

The book gives a good introduction to data mining. Larose manages to cover the important techniques used to analyse data and turn it into knowledge. These include neural networks, various types of clustering. Most importantly, perhaps, he discusses how to try various models and how to evaluate the effectiveness of each model.

The book's length is insufficient for many readers to actually get enough information to apply several of the methods. The details of using neural networks, for example, can be quite voluminous. But the value of the book is in conveying the basic qualitative ideas of the methods.

Average customer rating:

Data Mining Methods and Models
Daniel T. Larose
Manufacturer: Wiley-IEEE Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471666564

Book Description

Apply powerful Data Mining Methods and Models to Leverage your Data for Actionable Results

Data Mining Methods and Models provides:
* The latest techniques for uncovering hidden nuggets of information
* The insight into how the data mining algorithms actually work
* The hands-on experience of performing data mining on large data sets

Data Mining Methods and Models:
* Applies a "white box" methodology, emphasizing an understanding of the model structures underlying the softwareWalks the reader through the various algorithms and provides examples of the operation of the algorithms on actual large data sets, including a detailed case study, "Modeling Response to Direct-Mail Marketing"
* Tests the reader's level of understanding of the concepts and methodologies, with over 110 chapter exercises
* Demonstrates the Clementine data mining software suite, WEKA open source data mining software, SPSS statistical software, and Minitab statistical software
* Includes a companion Web site, www.dataminingconsultant.com, where the data sets used in the book may be downloaded, along with a comprehensive set of data mining resources. Faculty adopters of the book have access to an array of helpful resources, including solutions to all exercises, a PowerPoint(r) presentation of each chapter, sample data mining course projects and accompanying data sets, and multiple-choice chapter quizzes.

With its emphasis on learning by doing, this is an excellent textbook for students in business, computer science, and statistics, as well as a problem-solving reference for data analysts and professionals in the field.

An Instructor's Manual presenting detailed solutions to all the problems in the book is available onlne.

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Provides an introduction into data mining methods and models, including association rules, clustering, K-nearest neighbor, statistical inference, neural networks, linear and logistic regression, and multivariate analysis Presents a unified approach based on CRISP methodology, which involves Strategic Risk Assessment based on Organizational Mode A companion Web site features downloads of large data sets used in the chapter projects, with a discussion area and message board, where readers are encouraged to exchange ideas

Genomic Perl: From Bioinformatics Basics to Working Code

Average customer rating:

Not a good perl programming book period!
Develops effective genomic toolkits for UNIX, Windows & Mac

Genomic Perl: From Bioinformatics Basics to Working Code
Rex A. Dwyer
Manufacturer: Cambridge University Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 052180177X

Book Description

In this introduction to computational molecular biology, Rex Dwyer explains many basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, he covers the biological background for each problem, develops a model for the solution, and then introduces the Perl concepts needed to implement the solution. The chapters discuss pairwise and multiple sequence alignment, fast database searches for homologous sequences, protein motif identification, genome rearrangement, physical mapping, phylogeny reconstruction, satellite identification, sequence assembly, gene finding, and RNA secondary structure. Concrete examples and a step-by-step approach enable readers to grasp the computational and statistical methods.

Customer Reviews:

Not a good perl programming book period!.......2003-12-18

This books tries to combine and explain both bioinformatics and perl programming yet fails miserably at both. Though I have taken a class on learning perl this code is difficult to read and poorly explained. The bioinformatics is useless because the examples are simply stupid. For example instead of using free energy to determi