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

Stephane Bortzmeyer bortzmeyer at pasteur.fr
Fri Jul 28 06:26:11 EST 2000


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.

> 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.

>  If we start seeing more funding of
> software development in biosciences, I'd be happy to argue
> that more of it put into the public domain. 

Warning: you mix up "public domain" with "free software". Almost no
software is public domain. Linux is copyrighted, gcc is copyrighted,
TeX/LaTeX is copyrighted, Emboss is copyrighted, etc.
 
> But software isn't sequence data, each code word is the
> product of a single creative intelligence,
               ^^^^^^
               Cooperative work is as common in software as it is in
science. People often do better whan they join. There are even
technical solutions to ease this cooperation (CVS, etc).

> this work.  I think it is appropriate for software authors
> to retain copyright control over work

I 100 % agree. But it has no connection with the fact that the
software is free "free as in free speech, not free as in free beer" or
not.

> that has received
> public funding.   How many scientists who write books
> while on grant funding turn their royalties over to the
> public?

Again, the issue is freedom, not money.

1) Selling free software <http://www.gnu.org/philosophy/selling.html>

2) The long experience of the Cygnus corporation
<http://www.oreilly.com/catalog/opensources/book/tiemans.html>

3) Analysis of several ways to sustain the development of free
software ("The Magic Cauldron")
<http://www.tuxedo.org/~esr/writings/magic-cauldron/>

4) Various licences, public domain vs. copyright
<http://www.gnu.org/philosophy/categories.html>

5) An excellent free (as in beer) service for developers of free (as
in speech) software <http://sourceforge.net/>








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