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Bioinformatics Software Engineering

Bioinformatics Software Engineering

Delivering Effective Applications

by Paul Weston

Paperback / softback Publication Date: 08/10/2004

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Bioinformatics Software Engineering: Delivering Effective
Applications will be useful to anyone who wants to understand
how successful software can be developed in a rapidly changing
A handbook, not a textbook, it is not tied to any particular
operating system, platform, language, or methodology. Instead it
focuses on principles and practices that have been proven in the
real world. It is pragmatic, emphasizing the importance of
what the author calls Adaptive Programming - doing what works in
your situation, and it is concise, covering the whole software
development lifecycle in one slim volume.

At each stage, it describes common pitfalls, explains how these
can be avoided, and suggests simple techniques which make it easier
to deliver better solutions.

"Well thought-out ... addresses many of the key issues facing
developers of bioinformatics software." (Simon Dear,
Director, UK Technology and Development, Bioinformatics Engineering
and Integration, Genetics Research, GlaxoSmithKline)

Here are some examples from the book itself.

On software development:

?Writing software properly involves talking to people
? often lots of people ? and plenty of non-coding work
on your part. It requires the ability to dream up new
solutions to problems so complicated that they are hard to

From description to specification:

?Look for verbs ? action words, such as
?does?, ?is? and ?views?.
Identify nouns ? naming words, like
?user?, ?home? and
?sequence?. List the adjectives ?
describing words, for example ?quick?,
?simple? or ?precise?.

The verbs are the functions that must be provided by your
application. The nouns define the parameters to those
functions, and the adjectives specify the constraint conditions
under which your program must operate.?

On how to start writing software:

?Handle errors. Take in data. Show
output. Get going!?

On testing:

?It may not be physically possible to test every potential
combination of situations that could occur as users interact with a
program. But one thing that can be done is to test an
application at the agreed extremes of its capability: the maximum
number of simultaneous users it has to support, the minimum system
configuration it must run on, the lowest communication speed it
must cope with, and the most complex operations it must

If your program can cope with conditions at the edge of its
performance envelope, it is less likely to encounter difficulties
in dealing with less challenging situations.?

On showing early versions of software to users:

?It can be hard explaining the software development
process to people who are unfamiliar with it. Code that to
you is nearly finished is simply not working to them, and seeing
their dream in bits on the workbench can be disappointing to
customers, especially when they were expecting to be able to take
it for a test drive.?

On bugs:

?If your users find a genuinely reproducible bug in
production code, apologize, fix it fast, and then fix the system
that allowed it through. And tell your customers what you are
doing, and why, so they will be confident that it will not happen
again. Everybody makes mistakes. Don?t make the
same ones twice.?

And one last thought on successful software

"You have to be a detective, following up clues and examining
evidence to discover what has gone wrong and why. And you have to
be a politician, understanding what people want, both in public and
in private, and how this is likely to affect what you are trying to
do. This book cannot teach you how to do all of that, but it
can help."
Software Engineering
Paperback / softback
Publication Date:
John Wiley & Sons Inc
Country of origin:
United States
Dimensions (mm):

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