[Biopython-dev] Developmental policies

Peter Cock p.j.a.cock at googlemail.com
Tue Jan 13 12:54:57 UTC 2009

> So, the very pertinent question are:
> 1. Can biopython command-line interact with applications with no license?

I think so, yes.  If there was a license then it may try and impose
rules which could prevent this (possible in some legal
jurisdictions?).  Even "viral" licences like the GPL should be fine in
this context.

However, for the Population Genetics software you are talking about,
trying to get the authors to make their licence explicit would be
worthwhile (even if they just say its given freely to the public
domain or whatever the terminology is).

> 2. Is biopython interacting with applications (command-line or web)
> for which the license is not clear regarding interaction with
> software?

For command line tools (e.g. ClustalW, BLAST) calling them from a
script is common practice.  In fact, by the nature command line tools
are generally expected to be used in this way.  I think we are OK

For web tools, in some cases the provider provides clear instructions
(e.g. NCBI and BLAST and Entrez).  Another example is Bio.PDB can
fetch files from the FTP site - which is by its nature provided as a
public server.  In other cases things are perhaps a little less clear
cut.  Speaking generally, many websites do have conditions imposed in
their terms of service (e.g. TV listing sites don't want people
"screen scraping" with a script to "steal" the schedule information),
although these may not be legally enforeable.  However, this is
unlikely to be a problem in the academic setting applicable to most
websites Biopython may interact with.


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