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

Michael Schmitz schmitz at biophys.uni-duesseldorf.de
Tue Aug 1 15:28:36 EST 2000

Don Gilbert wrote:
> Open source/freely available source for bioinformatics works is
> a great idea, which I fully support, for various reasons, but not
> at the expense of forcing authors to agree to diminish their
> copyrights on the basis of peer or ageny pressures.
> The point I want to make is that it is not reasonable to hit
> bioinformatics software developers over the head with blunt
> analogies such as 'source code [an individual's creation] is like
> the human genome code [nature's creation]', or 'source code
> [copyright is automatic] is like patented works [an involved
> legal process]', or arguments like 'open source developers can
> easily recoup their investments [by providing extra value added
> support and effort] and are protected by their copyright [in a
> world where they can trust all competitors or have money & time
> to fight legal battles]'.

I can't really see where I hit you over the head with any analogy. I
pointed out the added value model as the only workable one (to my
knowledge) because Stephane presented the open source issue a bit too
cut-and-dried for my taste. 

On the issue of trust: at least we have clear rules on copyright (which
is automatic though by no means a natural right BTW). Other than that,
it's really no different from what I'm asked to do when publishing a
paper. I'm forced to deposit sequence or coordinates, and depositing
constraint information or equivalent experimental detail is strongly
suggested beyond that. Why not hold papers on software to the same
standards? And sometimes it would even be nice for the referee to have a
look at detail information such as source code or a precise description
of some algorithm. 

With molecular modelling software, you really picked the worst case
example I can possibly think of. I don't want that to happen to
bioinformatics now. 


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