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.

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Developing Bioinformatics Computer Skills Review,  August 28 2001
Submitted by Philipp Pagel   [Respond | View]

While I agree that this book is very pleasant to read I really miss substantial information. The authors try to cover a large number of tools and techniques and even the UNIX operating system and Perl in one volume. Unfortunately everything stays very much on the surface. There are plenty of excellent introductory books on UNIX - why not refer to those and talk about algorithms instead? This leads us to the main weakness of the book (in my opinion): Lots of things are touched but none of them are really explained or illustrated by actual code or algorithms.

Of cause a book on applying bioinformatics tools in every day lab-life would also be very usefull. But most tools are presented on extremly limited space so all the reader gets is a rough idea what the tool is for. Many popular and/or important packages are not described or even mentioned at all: e.g. there is just a tiny reference to GCG and EMBOSS is non-existant in the book.

If you are in biology and would like to hear about some of the tools available on the net for free this book is for you: The book will get you curious about many things and give you some keywords to feed the search engine with along with a bunch of URLs. But if you want to learn about computational biology and its foundations and methods you will be disappointed.

For vomputer scientists on the other hand there is not enough real biology in this book - they will probably benefit more from reading books on genetics, molecular biology, or whatever field they encounter.


Developing Bioinformatics Computer Skills Review,  July 09 2001
Submitted by Rodney   [Respond | View]

This is an excellent book. The authors know their audience. I work at a biotech company in Silicon Valley and use this book everyday. It is written in plain English and covers all the skills needed for the bioinformatics environment that I work in. Section II covers the Bioinformatics workstation as well as the tools needed to have a functional system up and running. Bioinformatics Computer Skills is the best and only book on this subject. Whenever a new field in science emerges there needs to be one book that puts it all together for people to get an understanding of what that field is all about, what you need to know to be good in that field (pg 14), what tools you need, what matters and this book does that. This book is not a bible of bioinformatics, but a blueprint of how such systems work and what skills are need as well as where one should seek out further knowledge. O'reilly press, Cynthia Gibas and Per Jambeck have done an excellent job with this first book and I hope there will be other books to follow. They have begun to define this new field. The other reviews (on this web site) that criticize this book do not understand the purpose of the book. It is to shed light on a field that is new and undefined. People who may not have known what bioinformatics is, or what skills one needs to have in order to enter this new field, now have a refrence point. The problem with many scientist today is they really believe they are more important then the people they are trying to save with their great discoveries. Everything having to do with science does not have to be written in the same context of the Journal Of Science etc... Regular people have a right to understand what is being written and how it will affect them in the future. This is a great book on the subject.




Developing Bioinformatics Computer Skills Review,  May 31 2001
Submitted by David Leader   [Respond | View]

I was disapointed in this book. In part that is my own fault as the authors have a different audience and a different approach to the one I was looking for. In part, however, I think O'Reilly has got it wrong by accepting the growing importance of Bioinformatics in the 'post-genomic' era justifies their publishing a book in this area, and then allowing its focus to be on yesterday's paper-and-string-and-Perl culture.

The book makes clear that it is aimed at the experimental biological scientist who wants to do his own bioinformatics on the cheap, and focuses on setting up Linux, finding free software on the web, and using Perl to automate it. There is a wide coverage of topics and programs, but everything except the Linux stuff is ultimately incomprehensible on its own. One would need another book to do anything with Perl, Shell scripting, SQL or to understand the sequence comparison or tree building algorithms, or microarray technology (no colour picture!), to name a few topics that are touched on in an unsatisfactory manner. The range of programs related to protein structure is greater than one finds in other bioinformatics books, but I imagine anyone in that area is au fait with this sort of thing and probably has specific software available.

Although there will be readers for whom this approach is suitable, I think it is important to criticise the philosophy behind the book. Although one can argue that Bioinformatics is part of computational biology, which has been around for a long time, it would be naive to recognize that it is current prominence is solely because of the human and other genome projects, and that its application is to a biological science performed on a different scale than in the past. I doubt that there will be many do-it-yourself biologists glueing together bug-ridden Perl sphaghetti code. The budgets will allow the use of commercial software or the employment of professional bioinformaticians to set up distributed systems using modern robust programming languages (i.e. Java - why are the authors scared of Java? Why does the word 'applet' not figure in the book's index) and proper commercial databases. This will be even more the case in industry.

The biological scientist has a need to understand the theory behind the programs he uses, and this is not provided here. The big audience for a good book on bioinformatics (which I have not yet found) is masters-level university students training in this area. Most of these will be employed by pharma or in supporting big research labs. Certainly they are going to be using Unix, but they will be using sequence software such as GCG, and learning SQL on Oracle databases, and being trained in Java. They need a book that explains the algorithms behind the programs, describes modern techniques such as microarrays properly and provides an introduction to unix and scripting languages that sees them in their appropriate context. Most biological scientists will want to make their bioinformatics queries from their desktop pc or mac in the context of a well designed GUI, even though the bioinformaticist who is concerned with serving these requests will probably be using unix machine.

Sorry to be so negative. The authors wrote about what they believed in, but...


Developing Bioinformatics Computer Skills Review,  February 27 2001
Submitted by Larry Timmins   [Respond | View]

This is a pre-release review

I want to preface this with this disclaimer: I don't have access to the book or its pre-release drafts. However, I'm ready to buy it. After reading many books on the genome and the many false trails and glimpses of promise in genome research -- I want to evaluate this book and determine if it meets my needs (see below). Unlike the ORA legacy of certain books just being a compilation of other ORA books -- I am very happy to see this fresh expansion into an exciting field.

My requirements

I need a transition tool to help create a whole new area of genome related applications. I need a train the trainer vehicle. I don't want to quote theories and research -- I want to be able to provide reference into the extraordinary accomplishments of the toolsmiths and datasmiths (that used Larry Wall's Perl) in the context of bio- and genome-related projects.

Having been around long before the first nutshell guides and books came from O'Reilly & Associates, I have had many opportunities as a specialist in deploying emerging software technology (AKA corporate solutions architect) to work with many individuals and authors associated with O'Reilly. Countless customers involved with applied business solutions on Arpanet and Internet since 1979 would have loved to have the wealth of books today. In the same breath (or series of keystrokes) there is a lot printed that just confused the issue rather than helping. If people had problems placing Internet technology, look out for the new wave of bio- and genome- related developments coming our way. At this moment, I can't tell from the description whether this book will be a boon or a bust. Hope its worth the wait.

Well after investigating many applied aspects of genome research and following the many organizations involved that use Perl to deal with the enormous data analysis requirements, I was looking for a good book to set the stage for the next generation of genome progress: applied usage and applications.

How to get started? Where can I find a resource for a train the trainer type session?

Imagine researching the latest Perl happenings and .NET support on ORA's website to find a title called "Developing Bioinformatics Computer Skills" that opens up the background and tools and starting points for understanding this next market for information technology skills.

Well, I promise to update this review once I read through it and see how close to the real problem domain this book hits.

Regards, LJT ltimmins@optonline.net (Larry Timmins)

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