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IT-Analysis.com: Open Source in Bioinformatics

Jan 04, 2002, 23:51 (11 Talkback[s])
(Other stories by The Snark)

[ Thanks to Jason Greenwood for this link. ]

"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics â€" gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue â€" an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed.

Nevertheless, Steven Brenner, a bioinformatics researcher at the University of California, Berkeley made it a condition of his post that he be allowed to distribute his software code in an open source manner. The rationale for this is not so much open source idealism, but the fact that source code distribution is important to maintaining software accuracy. If the source is hidden, then bugs have a tendency to persist and when, for example, you are searching large genetic databases, the consequences of software error can be severe - perhaps delaying the discovery of important genetic patterns or the finding of cures.

This open source situation is worth watching, because there are conflicting forces in action. In the US the Bayh-Dole Act allows federally funded universities to make exclusive licensing arrangements with private companies and to profit from any resulting patents accordingly. This they have done, as the $5 billion per annum clearly demonstrates. An open source free for all would threaten this in respect of software. However open source advocates argue that the universities are publicly funded and the public should not be “charged twiceâ€. Both sides of the argument have a point."

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