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

John S. J. Anderson jacobs+usenet at genehack.org
Thu Jul 27 23:44:01 EST 2000

>>>>> "Don" == Don Gilbert <gilbertd at bio.indiana.edu> writes:

Don> Most of the software that I've written and provided to biologists
Don> freely has never been funded by any goverment grant or agency. In
Don> cases of no or partial public funding for software development,
Don> which I think are far more common than most non-developers
Don> realize, those with the feeling that all software should be
Don> open-source make it hard on the developers who need some kind of
Don> income from their work.  If we start seeing more funding of
Don> software development in biosciences, I'd be happy to argue that
Don> more of it put into the public domain.

Public domain != (Open Source|Free Software)

I haven't seen anyone argue that bioinformatics software should be put
into the public domain (certainly not in this thread). I also don't
think that it's a reasonable argument that Open Sourcing some
bioinformatics software would put programmers out of work.

As an example, let's consider Affymatrix and their microarray analysis
software. Do you really think they make money off the sale of the
software? I would wager that the majority of their revenue comes from
selling chips, chip readers, and reagents -- without those, the
software is of zero value. Also, when you consider that most of their
customers probably lack the sophistication to build the software
themselves, and would prefer to just buy a binary (maybe with a
support contract thrown in for good measure), I don't see how opening
their source would have a negative impact on their bottom line at all.

In fact, I would hope it would have an opposite effect -- people would
be more likely to buy Affymatrix chips and chip readers because
trusted authorities would be able to review the software and verify
that it was bug-free.

Don> I think it is appropriate for software authors to retain
Don> copyright control over work that has received public funding.

Again, there are several licenses in common use that allow software
authors to retain full, legally enforceable copy-write control over
their software, while still providing open source code access.

Don> How many scientists who write books while on grant funding turn
Don> their royalties over to the public?

I don't think this is a valid analogy. A book is a expression of not
only the author's knowledge about a particular subject, but also his
opinion concerning different viewpoints about that knowledge.

Software, on the other hand, is a tool -- it's written to _do_
something. Knowledge and opinion do come into play, but it's not
really the same thing.

What are the rules concerning money made from patents on knowledge
gained by public funding? That seems to be the appropriate comparison


           [ John S Jacobs Anderson ]------><URL:mailto:jacobs at genehack.org>
[ Genehack: Not your daddy's weblog ]------><URL:http://genehack.org>

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