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Building Bioinformatics Solutions$
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Conrad Bessant, Darren Oakley, and Ian Shadforth

Print publication date: 2014

Print ISBN-13: 9780199658558

Published to Oxford Scholarship Online: April 2014

DOI: 10.1093/acprof:oso/9780199658558.001.0001

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Software engineering for bioinformatics

Software engineering for bioinformatics

(p.265) Chapter 6 Software engineering for bioinformatics
Building Bioinformatics Solutions

Conrad Bessant

Darren Oakley

Ian Shadforth

Oxford University Press

This chapter provides a practical introduction to key software engineering practices that can be used to facilitate the efficient production of readable, flexible, and reliable program code even in complex multi-developer projects. These practices include unit testing, version control, in-code documentation, and user-centred design. The chapter also provides information on getting started with three languages that are popular in bioinformatics — Python, Ruby, and Java — and compares the capabilities of these languages with each other and with Perl.

Keywords:   software engineering, unit testing, version control, user-centred design, documentation, Perl, programming languages, bioinformatics

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