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Kelly P. Vincent (State College, PA USA)

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SQL Pocket Guide (Pocket Reference)
SQL Pocket Guide (Pocket Reference)
by Jonathan Gennick
Edition: Paperback

18 of 19 people found the following review helpful
3.0 out of 5 stars Not quite there, 6 July 2004
I expected a bit more from this book. Although naturally a small book "pocket guide" can't include everything you want, I think that this guide is a bit inconsistent in the things that it does include. I am still learning SQL, and basically needed something that would remind me of the syntax to use. I know what I need to do (like create a table, work with dates, and so on), and I just need help phrasing it right. Often this book does come through for me, but other times it does not. For instance, I found good information about updating and inserting rows. But the only explanation of creating a table is not very general - it specifically touches on how to handle field names with spaces and other unusual characters when creating tables. So it may be that this book is more useful for someone who already knows quite a bit about SQl, and just needs something to jog their mind. But if that is the case, it seems strange that so many very basic things really are included. I'm not sure who the intended audience really is, as this book is not successful in trying to be all things to all readers...
One of the nice things about the book is that it includes MySQL in this edition. Apparently, previous editions did not. It does seem to do a good job of addressing the different versions of SQL that people might be using. For instance, in an example where they were discussing the use of double quotes on field names, they mention that this doesn't work in MySQl. Some sections of the book are further broken down in subsections like "Oracle", "MySQL", and so on. The other two platforms that are dealt with are microsoft SQL Server and IBM DB2.
Clearly, this book is better than nothing. And in my case, since I didn't want to spend the money or have to lug around another heavy book, it is also better than some of the bigger, genuinely better books. It certainly is relatively inexpensive, so there's a good chance you still might find it useful. Just don't expect it to answer all your SQL needs, however basic they seem.

Beginning Perl for Bioinformatics
Beginning Perl for Bioinformatics
by James Tisdall
Edition: Paperback
Price: £26.50

10 of 11 people found the following review helpful
5.0 out of 5 stars A great way to get started in bioinformatics programming, 26 Jun. 2004
I think this is a really good introduction to both Perl and Bioinformatics programming. I already know several other languages, and have been meaning to pick up Perl for a while. So I thought this book might be too basic for me, but because I was new to the field of Bioinformatics, I did not find it terribly basic. I also do believe that it would be very good for someone with a biology background wanting to learn perl for bioinformatics (this is the audience the book claims to be targeting). Perl is a very powerful language, and I do think that it could be hard for programming beginner to learn. However, I think this book does a very good job of introducing several important topics in Perl gently. The best thing about it is the extremely numerous examples, which can all be downloaded from the book's website, so you don't have to waste time typing them in. This provides a great source of learning and experimenting with the code, but it also provides a platform for developing more advanced programs. You can just build new programs on top of much of the code from the book, which is very convenient, and is also what programming efficiently is all about.
There are 13 chapters in the book, and I'll give a quick summary and insight into each below:
Chapter 1 Biology and computer science: This gives a quick and gentle introduction to the goals of the field of bioinformatics, and how the two fields of biology and computer science contribute to it. It sets the context of the book.
Chapter 2 Getting started with Perl: This is a good chapter which details how to set up Perl on your computer, and get started using it.
Chapter 3 The art of programming: This chapter discusses the common approaches that people take to programming, and open source programming. Design, pseudocode, algorithms, and implementation are all discussed.
Chapter 4 Sequences and strings: This provides a dual introduction to the string variable type in Perl and basic sequence analysis in bioinformatics. The general basics of Perl are covered as well, but the focus is on working with strings (actually scalars, and also arrays), which are very important in bioinformatics.
Chapter 5 Motifs and loops: This chapter covers further topics in Perl (such as control structures (conditional stetments and loops), and searching DNA and proteins for sequences (motifs).
Chapter 6 Subroutines and bugs: This chapter covers the important topic of subroutines, or breaking your code into small, reusable chunks. This is quite important in programming. The chapter also introduces debuggin, which is also (unfortunately) a very important part of programming.
Chapter 7 Mutations and randomization: This chapter introduces the concept of mutation in bioinformatics, and how to model that with a computer, via a random number generator. It does a good job of explaining the (sort of strange) way that random number generators work, and the importance of using them correctly in order to get genuinely random numbers (which you obviously want!).
Chapter 8 The genetic code: This chapter talks more about the genetic code in terms of translating DNA into protein. It also introduces hashes, which are another important variable type in Perl. It provides some good examples, and also deals with reading files in the FASTA data format, which is commonly used.
Chapter 9 Restriction maps and regular expressions: Regular expressions were introduced and used in earlier chapters, but are covered more deeply here. It also introduces restriction enzymes and restriction maps, which are important for designing effective and efficient laboratory experiments. The chapter explains the process of developing a program for computing restriction maps, and provides some good example code.
Chapter 10 GenBank: This chapter basically covers the methods you need to go through in order to extract information from GenBank, one of the most important databanks of genetic sequence information.
Chapter 11 Protein data bank: This chapter is similar to the last, except that it deals with the Protein Data Bank instead of GenBank.
Chapter 12 BLAST: This is another specific chapter, dealing with the Basic Local Alignment Search Tool (BLAST), a pervasive tool in bioinformatics.
Chapter 13 Further Topics: Gives a cursory discussion of several "advanced" topics, like DNA computing, graphics pogramming and relational databases.
You can see from the above chapters how the book proceeds, covering both aspects of Perl and tasks in bioinformatics one step at a time, which means that it's good for beginners with any background, really. All of the chapters (except the very early ones) have lots of sample code. Obviously this book isn't intended to be the only book you own on bioinformatics or Perl. It doesn't provide a thorough discussion of either, and you will especially need another book on bioinformatics if you are new to the biological sciences. You will need a more solid reference for the Perl language, which you can get from Programming Perl, or you can use the online documentation. If you are new to programming, you would also possibly benefit from using another beginning book, like Learning Perl, but I still believe that having a targeted book like this is invaluable to the starting bioinformatician.

Introduction to Bioinformatics
Introduction to Bioinformatics
by Arthur M. Lesk
Edition: Paperback

26 of 27 people found the following review helpful
5.0 out of 5 stars A great introductory book, 25 Jun. 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.
The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.
One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

Corpus Linguistics: An Introduction (Edinburgh Textbooks in Empirical Linguistics)
Corpus Linguistics: An Introduction (Edinburgh Textbooks in Empirical Linguistics)
by Tony McEnery
Edition: Paperback
Price: £23.99

7 of 7 people found the following review helpful
5.0 out of 5 stars a wonderful introduction, 8 Mar. 2003
This is quite a good introduction to a rather enigmatic and interdisciplinary field. Corpus linguistics has been around for a while, but the appearance of computers a couple decades ago made genuinely large corpora a very real possibility for the first time. Despite this, there are very few books out there that deal with the topic, especially at an introductory level. It seems to be a field for experts on the move--linguists who develop an interest in statistics, or computer scientists who develop an interest in natural language. This book attempts to remedy this, and get new people interested corpus linguistics from an early stage.
The book is organised into seven chapters, each with a summary or conclusion, study questions and a further reading section. The first chapter, "Early Corpus Linguistics and the Chomskyan Revolution", deals with the pre-computer corpora that were used to study language. Then it goes on to defend corpus linguistics against Chomsky's strong opposition to the use of corpora in language study. The second chapter deals with the basics of what a corpus really is, and "What is in It?". This covers such topics as corpora versus general machine-readable text, encoding and annotation, and even the feasibility of multilingual corpora. Chapter 3, "Quantitative Data", discusses the fact that corpora open up the possibility of real quantitative analysis on language, but does not necessarily rule out qualitative analysis. The fourth chapter is my favourite: it is called "The Use of Corpora in Language Studies", and list the surprising variety of ways in which corpora have been and can be used. The next chapter covers corpora and natural language processing, with topics such as part-of-speech analysis, parsing and automated lexicography. Chapter 6 is a case study: the authors detail an analysis (using corpora, of course) of the hypothesis that some genres of writing represent a sublanguage (a closed set of a natural language). This chapter is interesting, and illustrates how corpora can be used, as well as introducing the reader to some real corpora. The final chapter is a view of what the authors foresee for the future of corpus linguistics. There are also a small glossary, two reference appendices (corpora mentioned in the text and software for corpus research), suggested answers to the problems, and good bibliography.
This book would be great as a text for a course in corpus linguistics, but it's also extremely accessible to any interested reader. The authors do not assume much knowledge of any type, but at the same time they do not condescend and over-explain. I highly recommend this book to anyone wanting to find out more about this cool field, and anyone who wants a general (but introductory) reference to it.

Hindi Made Easy: Bk. 1 (GCSE Series)
Hindi Made Easy: Bk. 1 (GCSE Series)
by J. S. Nagra
Edition: Paperback
Price: £2.75

59 of 60 people found the following review helpful
5.0 out of 5 stars simple but solid introduction, 19 Jan. 2003
This is an incredibly slim and quite basic introduction to the study in Hindi. It doesn't cover a lot of ground, but it is very inexpensive and I think potentially very useful for younger learners (such as teenagers, for whom the book is written), and even adults who are not experienced in studying other languages.
The book includes a section on vowels, telling you how to pronounce them and showing you the full character in the Hindi script. These are not too difficult so the section is quite short. It then includes a section on consonants and on consonant pronunciation. Hindi consonants are much more difficult for native English speakers, since there are many sounds that we don't have in English. Fortunately this section includes diagrams of the vocal tract (i.e. the mouth and tongue) to show you exactly what to do with your tongue so you can make these crazy sounds! This quite good. Then it jumps right into vocabulary: there are several words per page, each introducing a letter of the alphabet and including a picture, the English meaning, the word in the Hindi script, and the Hindi pronunciation in the (modified) Roman script (i.e. with the same letters as English). This is the first third of the book.
Then the book gets a bit more difficult, as it gets into detail about how to write Hindi. Many more words are introduced, and then some short reading passages are included. This part of the book is organised by sound. Most of these are vowel sounds, because vowels are written differently when they are at the start of the words than when they are elsewhere, so they can be difficult to learn to write and read. At the end of the book are a few more short reading passages and finally a glossary containing the words used in the book.
In short, this is a good introduction to Hindi, but it probably would be too simple for experienced language learners. But if you are not ready for something serious like the Teach Yourself Hindi book, or if you aren't sure if you want to invest that kind of money yet, this is a great way to get a feel for learning Hindi.

Psycholinguistics (Oxford Introduction to Language Study)
Psycholinguistics (Oxford Introduction to Language Study)
by Thomas Scovel
Edition: Paperback
Price: £19.00

2 of 2 people found the following review helpful
4.0 out of 5 stars very introductory, 19 Jan. 2003
This is a slim book introducing the interesting field of psycholinguistics. Its size and style make it very accessible to beginners to psycholinguistics, though those already well-acquainted with linguistics in general might find it a bit simplistic. It will not provide a good enough introduction for an class in psycholinguistics, but will be useful for a topic on psycholinguistics in a general linguistics class, for instance. One thing that drives me crazy about this entire series of introductory linguistics texts is that there is no index! Clearly, it is not intended as a reference, but rather as a genuine introduction and jumping-off point.
The book is organised into 5 chapters, including one an introduction to the field, and then four which each focus on an important area of psycholinguistics: acquisition, production, comprehension (recognition) and finally dissolution. The last chapter, on dissolution, includes some information on the distinct but related field of neurolinguistics. There is then a section of relevant reading selections, organised by chapter topic. There is also a short appendix on references, which would provide a good place to start building a bibliography or doing some more in-depth exploratory reading. Finally there is a glossary defining important terms used throughout the book.

Research Methods and Statistics in Psychology
Research Methods and Statistics in Psychology
by Hugh Coolican
Edition: Paperback

42 of 45 people found the following review helpful
4.0 out of 5 stars Extensive, but a little annoying at times, 18 Jan. 2003
This is a pretty good introduction to statistics, especially for complete beginners. I had to buy it for a course, and at first wasn't too impressed with it, primarily because of the writing style. The author keeps the tone very light and says many jokes and funny things, which never bothered me. What did irritate me was that he also has a tendency to really "dumb-down" everything, to the point where you feel like it has been written for younger students, rather than university students (which I gather it sort of was).
However, I figured out after working my way through the course that the text is actually pretty good: it covers several statistical tests that other texts skip. Tests detailed include: binomial sign test, Chi-square, Wilcoxon matched pairs signed ranks, Mann-Whitney U, Wilcoxon rank sum, t test, Pearson's correlation, Spearman's rho, regression (including multiple), Kruskal-Wallis, Jonkheere trend, Friedman, Page trend, ANOVA (one-way, two-way, more-than-two-way, unrelated and related), MANOVA, ANCOVA. It also covers the design of experiments in detail. And the author really does make an effort to explain everything fully, for readers who have neither a statistical background nor even a strong maths background. It serves as a really good reference, even if reading it is a bit painful.
In short, I doubt this is the best statistics book out there, but it is the best statistics reference book I've seen yet. So I would recommend it if you are starting from scratch. But if you are comfortable with maths or even basic statistics, I wouldn't bother this book, as I'm sure you'll find it as irritating to read as I did.
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Speech and Language Processing
Speech and Language Processing
by Daniel Jurafsky
Edition: Library Binding

8 of 8 people found the following review helpful
5.0 out of 5 stars the best introduction to the field, 30 Dec. 2002
This is the basic text for my master's course in Speech and Language Processing. It is used in several classes, though as the only text in the natural language processing class, which is clearly its strength. We also use it in the speech processing class, but it does need supplemental material here. If you are looking for a introduction to speech and language processing, you can't find a better book, and with a reasonable price at that.
Specifically, the book covers natural language processing, computational linguistics and speech recognition. There is also a chapter dealing with speech synthesis, and another on machine translation. As a reminder of the important of linguistics in this field, even though it largely transcends it, the book is organised into four topical sections with several chapters each: Words, Syntax, Semantics and Pragmatics.
The Words section includes chapters which introduce regular expressions, finite-state transducers, (computational) phonology, text-to-speech synthesis, probabilistic models of pronunciation and spelling, n-grams, and finally hidden Markov models (HMMs) and speech recognition. The Syntax section introduces word classes and part-of-speech tagging, context-free grammars, parsing, features and unification. The Semantics section has chapters on meaning representation, semantic analysis, lexical semantics, word sense disambiguation and information retrieval. Finally, the Pragmatics section covers discourse, dialogue, conversational agents, natural language generation and machine translation.

Sociolinguistics (Oxford Introduction to Language Study ELT)
Sociolinguistics (Oxford Introduction to Language Study ELT)
by Bernard Spolsky
Edition: Paperback
Price: £19.00

3 of 3 people found the following review helpful
4.0 out of 5 stars very introductory, 24 Dec. 2002
This is a decent introduction to the topic of sociolinguistics, though I think there are other better introductory texts. It's quite a slim volume, with seven chapters. First the author discusses the study of language from a social perspective, including the approaches and methodologies used in sociolingustics. Then he moves on to the ethnography of speaking and converstation structure, including a section on the roles of politeness and terms of address. He then deals with variation, then style, gender and social class. The next two chapters discuss bilingualism and multilingualism. Finally, the last chapter covers the more general topic of "applied linguistics", which deals with the various aspects of language planning and policy.
Although the book often discusses English, it is by no means limited to Western examples. One major disadvantage of this book is that it does not contain an index. On the other hand, the last third of the book is dedicated to readings related to each of the chapter topics. These readings are generally very small snippets from "real" people in the field. While these might be nice, I think they are too short to be of any real use, as they remind me of things you see in high school textbooks. What they do is make it clear that this book is really intended for the reader early in their academic career: even those new to linguistics might find the book to simplistic if they are beyond first year or so.

Maid of the Mist
Maid of the Mist
by Colin Bateman
Edition: Paperback

1 of 2 people found the following review helpful
3.0 out of 5 stars I've read worse, 20 Dec. 2002
This review is from: Maid of the Mist (Paperback)
This book was okay. The plot was far-fetched (actually, it was almost completely unbelievable) and violence was all over the place, but that's okay in this kind of fiction, as long as it makes up for it in cleverness. I'm not completely convinced that it did so, though admittedly it couldn't have been that bad, since I did finish the book. I suppose it had its moments. If you like violent crime fiction with little witticism bombs throughout (and an occasional surprise mixed in for good measure), you'll probably enjoy this book, as long as you don't mind putting up with a fair amount of silliness.

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