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

Michael Schmitz schmitz at biophys.uni-duesseldorf.de
Sat Jul 29 13:33:32 EST 2000

Stephane Bortzmeyer wrote:
> In article <8lqcfb$c02$1 at jetsam.uits.indiana.edu>,
>  gilbertd at bio.indiana.edu (Don Gilbert) writes:
> > Most of the software that I've written and provided
> > to biologists freely has never been funded by any goverment
> > grant or agency.
> Well, I don't write bioinformatics software myself but I assume it is
> the same as any other software: there are several ways to fund
> it. IMHO, none is a reason to choose a licence over the other. Read
> on.

Getting any funding specifically for writing what we now call
bioinformatics software has been notoriously difficult for decades (I
can only talk about the last decade, but considering what the cost for
necessary hardware was before that, it can't have been any better. Don's
memory probably goes back further than mine if you are interested in
details.). As I know it, you had to cover the expenses out of other
grants and could work on some software part time as part of another
project, or in your spare time. I would hope for the funding situation
to improve now, with the hype about bioinformatics, but I'm not holding
my breath (and new funding may even come with mandatory commercial
exploitation of the funded software, now that people got the notion
there's money to be made in bioinformatics. But maybe that's just me
being paranoid).

As long as your funding or contract doesn't come with some strings
attached, there's no intrinsic preference for one type of license over
the other, so why shouldn't Don be free to pick whatever license suits
his purpose? In fact, there's no need to even settle for one license to
cover everything. One license allowing for redistribution including
source code for academic use, plus another one allowing just access to
source code without granting the right for redistribution to commercial
users is perfectly legal. This discussion started out about having
source for peer review purpose, not about having source for the purpose
of freedom. These two issues are near orthogonal. Any license of the
first kind will satisfy the peer review condition. Freedom to
redistribute, as much as I like it, is additional sugar. Important for
you, less important for others. 

> > feeling that all software should be open-source
> > make it hard on the developers who need some kind of income
> > from their work.
> This may be a brand new discussion in the bioinformatics field. But in
> general, this question has long been debated, discussed and solved,
> not only by theory, but also by the experiences of the many companies
> who earn money with free "free as in free speech, not free as in free
> beer" software. I provide some references at the end of this article.

Last time I checked, the discussion was still controversial (I don't
dispute it has been debated for a long time :-). Many of the proposals
involve making money from support or consulting, right? Any sort of
added value, but rarely involving direct license fees. Am I missing
something? And I wouldn't consider it solved. 

I agree the issue isn't about money. It's not about freedom as much as
about peer review either, though. Strictly MNSHO, of course.


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