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Building Bioinformatics Solutions: with Perl, R and MySQL (Paperback)

by Conrad Bessant (Author), Ian Shadforth (Author), Darren Oakley (Author)

4.5 out of 5 stars See all reviews (2 customer reviews)

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Product details

Paperback: 224 pages
Publisher: OUP Oxford (27 Nov 2008)
Language English
ISBN-10: 0199230234
ISBN-13: 978-0199230235
Product Dimensions: 24.4 x 18.8 x 1.5 cm

Average Customer Review: 4.5 out of 5 stars See all reviews (2 customer reviews)

Amazon.co.uk Sales Rank: 128,616 in Books (See Bestsellers in Books)

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#8 in	Books > Computing & Internet > Computer Science > Algorithms > Genetic
#18 in	Books > Computing & Internet > Databases > Databases & the Web
#19 in	Books > Computing & Internet > Programming > Languages > Perl

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Product Description

Modern bioinformatics encompasses a broad and ever-changing range of activities involved with the management and analysis of data from molecular biology experiments. Despite the diversity of activities and applications, the basic methodology and core tools needed to tackle bioinformatics problems is common to many projects. Building Bioinformatics Solutions provides a comprehensive introduction to this methodology, explaining how to acquire and use the most popular development tools, how to apply them to build processing pipelines, and how to make the results available through visualisations and web-based services for deployment either locally or via the Internet. The main development tools covered in this book are the MySQL database management system, the Perl programming language, and the R language for statistical computing. These industry standard open source tools form the core of many bioinformatics projects, both in academia and industry. The methodologies introduced are platform independent, and all the examples that feature have been tested on Windows, Linux and Mac OS. This advanced textbook is suitable for graduate students and researchers in the life sciences who wish to automate analyses or create their own databases and web-based tools. No prior knowledge of software development is assumed. Having worked through the book, the reader should have the necessary core skills to develop computational solutions for their specific research programmes. The book will also help the reader overcome the inertia associated with penetrating this field, and provide them with the confidence and understanding required to go on to develop more advanced bioinformatics skills.

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	7% buy Bioinformatics for Dummies 4.7 out of 5 stars (3) �12.54

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2 of 2 people found the following review helpful:

5.0 out of 5 stars Just what I was looking for ..., 22 Mar 2009

By	vinos - See all my reviews

This is a great little book. OK, there are plenty of other places to get information about using Perl, R and MySQL for bioinformatics, but this is the book that gets you started on that road and shows you how everything fits together. You can actually write useful bioinformatics tools after working through this book.

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2 of 2 people found the following review helpful:

4.0 out of 5 stars Good companion guide to learning Bioinformatics, 28 Jan 2009

By	Mr. T. Tubbs (UK) - See all my reviews (REAL NAME)

I'm a student currently on the Masters Applied Bioinformatics course at Cranfield, so have a student's guide to both the book, and also knowledge of the course content. I'm happily not a schill, and have probably given more than my fair share of feedback both good and bad and seen it acted on.

Some books you get from the library, some you get a copy of, this book is one to buy and use as a companion guide to your studies, and/or alongside a bioinformatics course.

In wanting to learn about bioinformatics, students can come from different backgrouns. So there can be a large range of knowledge on actual usage of computers and programming. By being able to cater from the absolute beginner, who only knows basic PC skills, through to more technically advanced areas and subjects, the beginners can catch up, and the pros can get the lowdown on new information.

I would recommend buying this book as a companion guide as mentioned (like Lesk Introduction to Bioinformatics or Understanding Bioinformatics both worthy of buying a copy)

In areas of bioinformatic learning like Java, Linux, it's probably best to initially get a copy of books for the relevant areas like the recommendations below from the library as you'll know the information fairly quickly. With a taster of Linux, you'll be more prepared for working on the command line, and understanding that you'll be a typist as much as a programmer at the start! Recommendations would be:

General
Introduction to Bioinformatics, Bioinformatics: The Machine Learning Approach (Adaptive Computation and Machine Learning)Developing Bioinformatics Computer Skills
Developing Bioinformatics Computer Skills

Java
Java - the 9 in 1 Java guide Java All-in-one Desk Reference for Dummies, Sams Teach Yourself Java 6 in 21 Days, Head First Java, Head First Java: Your Brain on Java - A Learner's Guide, Effective Java: Second Edition, Beginning Programming for Dummies

Like other languages, you can bolt on knowledge, and get reminders through the "in a nutshell", "cookbook" style books.

Perl
Probably best to start with is Beginning Perl for BioinformaticsBeginning Perl for Bioinformatics and at a higher level, Mastering Perl for Bioinformatics
Tisdall's work has been built on. Use Google, with decent search words will help a lot.
Perl for Dummies (For Dummies (Computers))
Sams Teach Yourself Perl in 24 Hours
Sams Teach Yourself Perl in 21 Days
Perl: A Beginner's Guide (Beginner's Guides (Osborne))

Perl in a Nutshell (In a Nutshell (O'Reilly))
Bioinformatics, Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice
Perl Programming for Biologists

With all of these, it's well worth going through the various books on Amazon and checking out the comments to see what level the books are, and what style, ratings etc.

R
If you've previous programming knowledge, some people say
* Gentleman, R., (2009) R Programming for Bioinformatics (Chapman & Hall/CRC Computer Science & Data Analysis),
chocolate teapot in my opinion - not a starter book if you don't know programming a fair bit & R a little beforehand. Much better off with Building Bioinformatics Solutions information on R, and asking helpful folk.

I know a few coursemates who packed the shelves with R books. Seemed a waste of money (on not so great books - R doesn't have anything like Dummies' guides of Head First out there).

You can't learn Bioinformatics solely from a reading a book, as you might Biology with textbooks and papers. It's a skill set that needs learning to reinforce, so having a go, making mistakes, learning from those mistakes and linking concepts is needed.
The book helps with this, and the http://bixsolutions.net/ site should help you here - use the resource! The book has a nice pace and learning curve, and you can easily use the book in parallel with coding at a computer.
You really need this support, and help, so i'd suggest having a look (i'm sure there will be Cranfield students/staff/others there to help).

In Summary
Pros:
- Covers the concepts, fundamentals, key areas well
- A book actually able to make R more palatable for a beginner was a welcome surprise. Very handy chapter - wish i'd got the book earlier just for this!
- Decent print quality and binding (won't smudge, decent paper))
- Well explained, logical run through of information, good writing style.

Cons:
- bixsolutions.net was of time of writing, last updated on the front page November 25th 2008.
- Lack of extra web based content currently (e.g. screencasts, or test case examples gone through step by step) Show us the 21st century teaching tech!
- Lack of colour photos. (Much cheaper to show them on the web than print i'll admit!)

Reading doesn't get you out of learning by having a go, but this book will certainly help you learn!

(Amazon only allows 10 linked book recommendations, so i'll make a "Bioinformatics for Cranfield students" list on Amazon)

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