Bioinformatics, Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice

“…such a helpful and relevant book…I am following [an] MSc distance learning course in Bioinformatics…I would have been at a complete loss without your book!” (Susan Tzotzos MSc, PhD, Vienna, Austria)

We (the authors, Michael Moorhouse and Paul Barry) wrote Bioinformatics Biocomputing and Perl to be a comprehensive, modern and, above all, realistic introduction to the world of Bioinformatics. One author is a Computer Scientist by training; the other has a background in Biochemistry.
Together, we draw on our experience as practising professionals to cover a wide range of Biological and Informatics concepts, practice and ‘traps to be avoided’.

Our aim was not only to transfer a set of skills or programming tricks but also a mindset for how to think as Bioinformaticians. Hence, we included a collection of ‘Maxims’ which offer general guidance on key concepts – imparting the skills useful in judging the approaches to apply and those to avoid.

We wrote this book for three broad categories of readers:

(1) students who are embarking on a formal taught Bioinformatics course and require a good, all-round course text;

(2) Bioscientists whose background is in a non-computationally based research field but who need to use Bioinformatics tools;

and (3) those whose background is in Informatics or Computer Science who need to know something about (computational) Biology.

The book helps readers address two questions often asked by newcomers to the field:

(1) ‘What is possible?’,

and (2) ‘How do I use it to solve my particular problem?’
These are the classic ‘What’ and ‘How’ questions.

Our book also outlines the science underlying the major applications and techniques which Bioinformaticians use and also explains ‘Why’ a particular method is used.

Throughout the book we use well maintained and ‘free to use’ WWW ‘portals’ in preference to propriety software. This, in our opinion, lowers the financial and legal barriers that could otherwise be a deterrent to the reader/researcher.

The use of pre-formed WWW interfaces will only take the reader so far (though in many cases far enough), after which some type of automation of mundane processing operations is required.
To address this need, a large part of the book covers the learning and application of programming skills (we use the Perl programming language in all examples).

Readers are assumed to have little or no prior programming experience. We then progress through more complex topics, such as the design and creation of relational databases for storing information and finally to the automation of sequence manipulation and sequence similarity searching using BioPerl modules. The ability to produce an analysis ‘pipeline’ is an excellent skill set for budding Bioinformaticians.

To help readers transfer between ‘manual intensive’ analyses (using paste & click WWW interfaces) and the more automated pipeline solutions, wherever possible, we describe how to accomplish the same task using both approaches, comparing and contrasting them.

As authors, we have made every effort to write the book in a light and engaging style injecting humour whenever possible. We have also included references to more detailed sources of information (especially for the algorithms of the tools used) and other on-line sources we use and trust. The associated website provides additional material for instructors/readers.