Building Bioinformatics Solutions: with Perl, R and MySQL [Paperback]

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.

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)

This book covers MYSQL, PERL, and R. It introduces each theme, and uses relevant bioinformatic examples. In the final chapters, it ties together all three softwares, and teaches to combine them. The book is a nice primer, and a great place to start if you have little experience in bioinformatics. The book doesn't really go in depth, and do not cover very advanced topics (but this is not the point of the book, and it points you to very nice resources). The authors use good examples from working with databases, and manipulating sequence.

I guess it would be perfect for an introductory course in Bioinformatics.