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0 954 52320 2
Horizon Bioscience
GBP40
The Internet for Cell and Molecular Biologists
Andrea Cabibbo (Editor), Richard Grant (Editor), Manuela Helmer Citterich (Editor)
The obvious criticism to make of a book with this title is that the Internet is far too fluid a medium to be covered in print form. It is inevitable that somewhere between the authors writing the book and it arriving on your shelf that links will become updated, website designs will be changed and new resources will become available. Yet the authors have gone some way to meet this criticism and the book has much to recommend it. Their book is far more than just a list of websites and recipes for carrying out BLAST searches.
The book begins with a quick overview of what the Internet is, how it works, how to get connected and how to search it. Seasoned users might find this section superfluous and skip straight to the chapters on DNA and protein sequence alignment. It is these chapters which are the real strength of the book. In addition to describing the commonly available packages for carrying out these tasks there are accounts of how sequence alignment software actually works. These sections are to be recommended to anyone who wishes to use BLAST as more than just a black box into which sequences are dropped and alignments appear, as if by magic, at the other end. There are descriptions of the computation of alignments and explanations of those mysterious numbers which appear alongside them. If everyone who did a BLAST search read these sections before drawing inferences from their results fewer daft conclusions might be published. As with all the sections, these chapters are well referenced.
The chapters on sequence alignments are followed by a description of protein structure modelling. This is a vast area which it is difficult to do justice to in a single chapter and the authors wisely restrict themselves to relatively simple tools which are freely available online. In this chapter and those on sequence alignments, the authors give appropriate health warnings about divining too much biological relevance from computational methods in the absence of supporting experimental evidence. It is refreshing to see a group of authors who are clearly very enthusiastic about the application of computational methods in biology retaining a healthy scepticism about them.
The next two chapters deal with genomic and bioinformatic methods. As before an attempt is made to describe the underlying biological principles before diving into describing the available Internet resources. The treatment is quite rigorous, but inevitably brief. As the technology and the conventions for data archiving are still evolving in these fields it is probably these chapters which have the greatest risk of being out of date in a short space of time. The book finishes with a mixed bag of chapters: an account of newsgroups, a description of how to access email from any location and finally a list of useful Internet bookmarks. Newsgroups are an acquired taste with many, perhaps most, biologists rarely if ever making use of them. This chapter is written with sufficient enthusiasm for the topic to tempt more people to have a look and see what is on offer.
The list of Internet bookmarks is a bit of a disappointment and brings us back to the initial criticism. Although the book was published in 2004, some of the links are already out of date. Furthermore the book gives detailed instructions for the use of resources like PubMed or BLAST. These instructions are supplemented with plenty of screenshots. The risk is that changes in the format of sites would render large parts of the book obsolete. It is a pity there is not an accompanying website where links and screenshots could be kept up to date. Nevertheless, this book would be a welcome addition to university libraries and anyone who wants to know the science behind some of the commonly used resources would be well advised to consult it.
David J Timson, Queen's University, Belfast
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