Building Bioinformatics Solutions 2nd edition

Second Edition

Conrad Bessant, Darren Oakley, and Ian Shadforth

Platform independent: suitable for readers running Windows, Linux or Mac OS
No commercial software is required as the book is entirely based on open source tools: Perl, R and SQL
Broad coverage of biological applications including sequence analysis, micro array informatics and proteomics
Illustration of key concepts using examples from real biological data and applications
A practical problem-solving focus ensures the book is ideal for graduate courses
Assumes no prior programming experience

Building Bioinformatics Solutions 2nd edition

Second Edition

Conrad Bessant, Darren Oakley, and Ian Shadforth

Description

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. This unique book provides an invaluable introduction to three of the main tools used in the development of bioinformatics software - Perl, R and MySQL - and explains how these can be used together to tackle the complex data-driven challenges that typify modern biology. 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.

Building Bioinformatics Solutions 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.

Building Bioinformatics Solutions 2nd edition

Second Edition

Conrad Bessant, Darren Oakley, and Ian Shadforth

1. Introduction
2. Building Biological Databases with SQL
3. Beginning Programming in Perl
4. Numerical data analysis using R
5. Developing Web Resources
6. Software Engineering for Bioinformatics
Appendix A: Using Command Line Interfaces
Appendix B: Getting started with Apache HTTP Server
Appendix C: Setting up a Linux Virtual Machine in Windows

Building Bioinformatics Solutions 2nd edition

Second Edition

Conrad Bessant, Darren Oakley, and Ian Shadforth

Author Information

Conrad Bessant, Professor of Bioinformatics, The School of Biological and Chemical Sciences, Queen Mary, University of London,Darren Oakley, Software Developer, Nature Publishing Group,Ian Shadforth, Director of Integrated Health, Alere Inc.

Conrad Bessant is Professor of Bioinformatics at Queen Mary, University of London. He is active in both teaching and research, and has been involved in a number of software development projects in the areas of proteomics and metabolomics.

Darren Oakley is a Software Developer at Nature Publishing Group (NPG). During his time at NPG he has been involved in numerous projects for improving the meta-data related to NPG articles. His current role is lead developer on NPG's next-generation online publishing platform.

Ian Shadforth is Director of Integrated Health and Bioinformatics at Alere Inc - a global medical devices and health management company. In this role Ian leads new concept development across technology, analytics and web to better enable individuals to achieve their health goals.