Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice [Kindle Edition]

"...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)

"...such a helpful and relevant book...I would have been at a complete loss without your book!" (Susan Tzotzos MSc, PhD, Vienna, Austria)

Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today’s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material.

Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease.

Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples.

Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet.

Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.

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.

Bioinformatics, Biocomputing and Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease.

Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS–PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples.

Working with the Web presents a discussion of the Web–based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet.

Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal–W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.

Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. Source code, related links, errata and presentation materials are provided at glasnost.itcarlow.ie/∼biobook/index.html (in PowerPoint format).

Michael Moorhouse works as a Bioinformatics Researcher for Erasmus MC in Rotterdam, The Netherlands. He holds a B.Sc. from UMIST and an M.Sc. from The University of Manchester. Michael recently completed a Ph.D. from The University of Birmingham in the UK. He has been involved in numerous bioinformatics courses throughout the UK and Netherlands. This is Michael’s first book.

Paul Barry works as a Lecturer in Computing Science at The Institute of Technology, Carlow in Ireland. He holds a B.Sc. from The University of Ulster in Jordanstown, Northern Ireland and recently completed an M.Sc. from The Institute of Technology, Sligo in Ireland. He is the author of Programming the Network with Perl (Wiley, 2002).