Biomedical Engineering Reference
In-Depth Information
is easy to use, highly standards-compliant, secure, well supported, easy to
extend with an ecosystem of thousands of plug-ins, and of course it is free
to download, use or distribute.
It therefore seemed a perfectly reasonable request when, at a department
town-hall meeting in 2009, Jim Finkle asked the US Secretary of State,
Hilary Clinton [2] 'Can you please let the staff use an alternative web
browser called Firefox?'. The reply, which came from under-secretary
Kennedy, that '. . It is an expense question . .' was interrupted from the
audience with a shout of 'it's free'. Kennedy continued 'Nothing is free.
It's a question of the resources to manage multiple systems. . . .'. He is, of
course, absolutely right, that in a large organisation, be that governmental,
academic or corporate there are many hidden costs in rolling out,
securing, insuring, maintaining and supporting any software. These costs
are incurred, regardless of whether the software is open or closed source,
free or expensive.
In the following chapter, I will explore some of these costs in more
detail, and analyse a real-world example of how parts of the life sciences
industry have come together to try and fi nd new ways they can use open
source software in the fi ght against disease. Before delving into the
practical use within industry, I will provide an introduction to the
technologies and massive data volumes under consideration by exploring
recent advances in human genetics.
22.2 Background
22.2.1 The Human Genome Project
The Human Genome Project is in many ways one of the wonders of the
modern world. Thousands of scientists from laboratories around the
globe spent a decade and $3 billion to produce what then US President
Bill Clinton described as '. . . without a doubt this is the most important,
most wondrous map, ever produced by humankind' [3]. There was great
excitement and anticipation that its publication would herald a new era
of medical breakthroughs, and it would only be a matter of time until
diseases like cancer would only be heard about in history topics. I do not
intend to go into detail about how the Human Genome Project was
delivered, if you are curious its Wikipedia page [4] is an excellent starting
point. It is, however, worth mentioning that the human genome is
essentially an encyclopaedia written in 46 volumes (known as
chromosomes), and written in the language of DNA. The language of
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