[Biopython-dev] Code review request for phyloxml branch

[Brad Chapman]

Hi all;
Hilmar -- thanks for writing up a nice summary of the license
details. Jaime, I think it's a shame we would let these issues
prevent working together. It sounds like you and Eric have some
shared goals and it would be great to see that evolve into some
useful functionality in Biopython.

Generally, the BSD-like license which Biopython uses encourages
cooperation and keeps people at both academia and industry happy. As
scientists, our goal should be to avoid letting these types of issues
preventing collaboration. Truthfully, there is very little opportunity
for exploitation of bioinformatics software; the economics are just not
there for companies to sell code.

> (It is a common misconception that GPL is unconditionally viral. I can  
> take GPL code and link to it and keep my code closed source for as  
> long as I please if I never redistribute it. GPL was written with  
> software vendors in mind, whose business consists of distributing  
> software for commercial gain. GPL has therefore sometimes been called  
> anti-commercial. This is wrong, too, but I won't go into the details  
> here.)

I agree 100%, but in practical terms it is very difficult to have this
argument at a company. Speaking from experience, GPL creates all kinds
of nasty thoughts in people's heads which prevents adoption of code in
corporate environments. For Biopython and other bioinformatics projects,
we should be actively encouraging contributions from companies as
well as academia.

> Biopython can freely utilize GPL-licensed (or closed source, for that  
> matter) software if it doesn't link to it. IANAL but I think it can  
> also redistribute GPL-licensed code along with Biopython so long as  
> Biopython doesn't link to it, and it is made clear that some of the  
> distribution falls under a different license than BSD. (Linux  
> distributions mix BSD and GPL software, too.)

Yes, but this complication is bad. Let's keep it simple,
Brad