Bioinformatics Computing [Paperback]

Bryan Bergeron (Author)

Book Description

Publication Date: November 29, 2002 | ISBN-10: 0131008250 | ISBN-13: 978-8120322585 | Edition: 1

Bioinformatics Computing is a practical guide to computing in the growing field of Bioinformatics (the study of how information is represented and transmitted in biological systems, starting at the molecular level). This book brings life scientists at every level - from students to research directors - up to speed in computational techniques that apply directly to their work. The life science community needs a practical guide that illustrates the computer science advances that have been made in the past several decades in areas of computer visualization, large database designs, machine learning and other forms of advanced pattern matching, statistical methods, and distributed computing techniques. In addition to exploring general information technology issues, each chapter identifies technologies and approaches on the near horizon that will have a significant impact on bioinformatics, and introduces some of the global, societal issues that will likely define bioinformatics developments in the future.

Editorial Reviews

About the Author

BRYAN BERGERON is a faculty member at both Harvard Medical School and MIT, Editor-in-Chief of e.MD, editorial board member of Healthcare Informatics, and Fellow of the American College of Medical Informatics. He has authored more than 300 publications on topics ranging from AI to computers in medicine.

Product Details

• Paperback: 439 pages
• Publisher: Prentice Hall; 1 edition (November 29, 2002)
• Language: English
• ISBN-10: 0131008250
• ISBN-13: 978-8120322585
• Product Dimensions: 9.5 x 6.8 x 1 inches
• Shipping Weight: 1.9 pounds (View shipping rates and policies)
• Average Customer Review: 4.6 out of 5 stars  See all reviews (5 customer reviews)
• Amazon Best Sellers Rank: #975,877 in Books (See Top 100 in Books)

More About the Author

Discover books, learn about writers, read author blogs, and more.

Customer Reviews

Most Helpful Customer Reviews

18 of 19 people found the following review helpful:

5.0 out of 5 stars A must read!, January 9, 2003

By 

Lukas Cudrigh (Sausalito, CA United States) - See all my reviews

This review is from: Bioinformatics Computing (Paperback)

This book was a pleasant surprise. It's one of the few books on bioinformatics that I've read that doesn't assume the reader has a PhD in biochemistry or mathematics. It's a gentle but thorough introduction to many of the problems faced by life scientists who are trying to get a handle on this thing called bioinformatics. I've been working in the life sciences for years, and this is the first book I've read that explains how I can make use of the various search engines, genomic analysis tools, and the dozens of genomics databases worldwide in my day-to-day life.

I especially appreciate the author's frank analysis of the state of the art at the end of each chapter. He seems to put a balanced spin on the field, pointing out the vast potential of bioinformatics computing in practical medicine and materials synthesis, while grounding the reader in current political and economic realities that are limiting many aspects of the field.

I consider it a must read.

6 of 6 people found the following review helpful:

5.0 out of 5 stars Comprehensive Introduction to the filed of Bioinformatics, December 7, 2004

By 

ART SEDIGHI (Old Bethpage, NY United States) - See all my reviews

This review is from: Bioinformatics Computing (Paperback)

Bergeron wrote this book such that if you have a computer background, you can relate to the topic at hand, and if you have a biology background, you can pick up the material quickly. He uses one to teach the other, and does so rather comprehensively. Major topics and areas of interests in bioinformatics are covered, such as:

* Databases

* Networks and the Internet

* Bioinformatics search engines

* Data mining techniques

* Statistics

* Pattern Matching

* Simulation techniques and modeling

Any of these topics deserve a volume of books dedicated to them, but the author gives the readers enough information that can be useful in determining where to go next. Even though the topics are mostly computing related, the author takes a great care at talking about these topics in the context of Bioinformatics. He even lists the specific applications of each topic at the beginning of each chapter to aid the reader in relating to the topic at hand. For example, after reading the chapter on modeling and simulation, you would know that modeling is used to determine the efficacy of drugs and to determine drug side effects during the drug discovery process.

Databases are probably one of the most important and well known tools in Bioinformatics. The enormous amount of data available for analysis requires large and fast databases. In fact, the amount of data in bioinformatics doubles every eighteen months, so databases and database design is an integral part of bioinformatics computing. In addition to the vast amount of raw data (sequence data and protein data for example) that is stores in databases, the analysis such as pattern matching, simulation and visualization of data requires constant access to databases. The author talks about what are know as primary databases, databases that are used to store raw data, and other value added databases, the one's that store analyzed and/or verified data. One thing that reader gets out databases is the realization of what the data life cycle is in the bioinformatics world, and how it affects all the application areas of bioinformatics.

The databases around the world are either somehow integrated together ease the task of data discovery and data mining. Due to the vast amount of information available, various data mining techniques have been developed over the years to assist in finding the data that a researcher is looking for. Tasks such as data enrichment, missing value analysis for sequence data, data characterization and data distribution analysis mark some of the tasks that data mining techniques needs to accomplish. A number of data mining techniques such as hidden Markov Models, Decision Trees, Neural Networks and Genetic Algorithms are talked about and the pro's and con's of each one is discusses in detail. A bioinformatician needs to be at least aware of the various data mining techniques and should have an overview how they work and why they work in general.

After the data has been discovered, a method of visualization that can get the point across, per se, needs to be used. Visualization and simulation techniques are talked about to show the reader what a bioinformatician needs to do with the information found. There are a number of graphical tools available out there, some free and some not, that are used heavily in this business to aid the understanding of the vast amount of information that is available. Various modeling techniques are being used today to aid with the drug discovery process and figuring out the side effect of newly developed drugs. I would say that this area of bioinformatics will see the most growth in the coming years, and the author, Bryan Bergeron, does a great job discussing this topic.

Statistics is another technique used heavily in bioinformatics computing. Even though most of the statistical tools, Matlab and many others, have been used for a number of years, one must know the theory and reason behind using numerous statistical techniques in Bioinformatics. These techniques are integrated into bioinformatics search engines and the software applications for modeling and simulations, but one still needs to know how they work. Bioinformatics is a new field of study, and not by any means been perfected, so there are still a number research track and advancements that are still untapped, thus making the theory behind how some of the available tools work very important in this field.

Bryn Bergeron in Bioinformatics Computing gives the necessary background for anyone interested in the field of bioinformatics. After reading this book, a reader can get a good idea of which area s/he wants to pursue further. The topics are broken into logical units that can aid the reader in realizing what specific field of bioinformatics is more interesting than others.

Even if you don't decide to pickup one of many advanced books in this topic, you should know about an industry that is growing rapidly, and Bergeron's book can aid you to do just that.

4 of 4 people found the following review helpful:

3.0 out of 5 stars An introduction, but very little computing, October 18, 2005

By 

PAT BAILEY "duluth boy" (Grand Rapids, MI United States) - See all my reviews
(REAL NAME)   

This review is from: Bioinformatics Computing (Paperback)

While the book does an adequate job of explaining the purpose to bioinformatics, it wasn't very technical. I had it as a text for a graduate course, and many of us whose background was in computing found a need to find outside references. It's not a bad book for some high level coverage, but it never seems to get to the meat of a subject in much depth or detail. It is more for someone interested in existing tools and databases, but not for a developer who wants to get started in this field. If you're in that category you may want to look at some other text books such as "Bioinformatics in the Post Genomic Era" by Augen or "Fundamental Concepts of Bioinformatics" by Krane and Raymer. Another potential source is Lesk's "Introduction to Bioinformatics" (a bit older, but it does talk about specific computational skills).