open-source software for bioinformatics (was Re: Unix vs Linux - the movie.)

James Bonfield jkb at arran.mrc-lmb.cam.ac.uk
Tue Aug 8 08:26:46 EST 2000

In <u9vgxcn7y1.fsf at wol.wustl.edu> eddy at wol.wustl.edu (Sean Eddy) writes:

> a. the ethics of academic science demands disclosure and sharing of resources.
> b. society funds science from taxes and charities
>    with an expectation of getting something back -- namely, accessible
>    basic research results. Society in general does not
>    expect to pay for research twice.
> c. NIH, NSF, and many other agencies have policies *requiring*
>    you to share research resources.

This all makes sense. However there's also a d:

d. Org-'X' requires you to make money if possible.

This is the state of affairs in the UK. The government regularly treats
science as a way of producing spin-offs into industry, or as a way of training 
up people who then go into industry. I know this attitude also exists at some
US univeristies as I recall you speaking about this very matter.

This attitude forces people to be both open and closed, and hardly suprisingly 
that's not easy.

Personally I'd prefer it if 'd' didn't exist, but that's not my choice.
Oddly, bioinformatics is often considered very different in this approach to
benchwork. If someone solves a new structure then it's published and the data
is public - no questions. If someone in that same organisation produces a new 
bit of software then why is it any different? Simply that it's harder to
commercial a structure...

So it's not a matter of "scientists who don't share", but "organisations that
don't let their scientists share". [Note that these are my own personal
opinions and any likeness with particular software or organisations is purely
coincidental :-)]

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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