Building Bioinformatics Solutions With Perl, R and MySQL

About this book

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 select the appropriate analytical tools and databases, how to use 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.

Contents

1. Introduction
2. Building Biological Databases with MySQL
3. Automating Processes Using Perl
4. Numerical data analysis using R
5. Programming for the Web

Appendix: Using Command Line Interfaces
Index

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