[Biopython-dev] Structure and LDNe

Bruce Southey bsouthey at gmail.com
Tue Jan 6 12:41:29 EST 2009


Tiago Antão wrote:
> Hi all,
>
> Jason Eshleman (he subscribes to this list also) has made available
> code to interact with Structure (a widely used application in
> population genetics - the 2 papers related to it have around 3000
> citations acording to Google scholar). We will try to convert his code
> to the Bio.PopGen namespace, create documentation and test cases.
> To this adds the exsiting LDNe code (mine). This all should be ready
> in a reasonably fast time frame (I suppose before the next release).
>
> The all important statistics part is still due, I am afraid (I don't
> know if anybody has looked at the beta code on git). But at least this
> LDNe and Structure code will be ready to go soon.
>
> Tiago
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>   
Hi,
What are the licenses for LDNe and Structure?
Saying just 'free' is insufficient because it is not clear in which 
definition is being used.

Also, please ensure that none of the code that is included into 
Biopython is not a deriviative of LDNe and Structure unless these have 
explicit license that is compatible with Biopython.  For example, 
'copying' an existing function into Python would be considered a 
derivative. Obviously reading a documented output is probably not 
considered a derivative.

I prefer to be proactive with licenses so these don't bite back like has 
happened in some formally open sources projects or use of unclean code 
sources. A current example of this is that the current release of scipy 
0.7 has been significantly delayed due to some major effort to check 
various functions that reference the Numerical Recipes book (which has 
an incompatible license).

Anyhow, this sounds good!

Bruce


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