[Biopython-dev] Active projects list? (BOSC Biopython Project Update)

[Peter]

On Tue, Jul 20, 2010 at 4:06 PM, Andrea Pierleoni
<andrea at biocomp.unibo.it> wrote:
>
>
>> I'm not sure we can easily include GPL code in Biopython... it would
>> complicate things. Kyle has also been working on using the JVM DB
>> API for BioSQL under Jython - I'd rather we ended up with a runtime
>> choice of drivers (database specific like mysqldb, and others like the
>> abstractions SQLAlchemy or the web2py DAL) which would all be
>> external to Biopython.
>>
>> Peter
>>
>
> I've checked online and, actually, web2py code comes under:
>
> "GPL2 License with an exception for easier commercialization of
> applications."
>
> and they states:
>
> "Applications built with web2py can be released under any license the
> author wishes as long they do not contain web2py code. In particular they
> can be bytecode compiled and distributed in closed source. The admin
> interface provides a button to byte-code compile.
> It is fine to distribute web2py (source or compiled) with your
> applications as long as you make it clear in the license where your
> application ends and web2py starts."
>
> I don't think this will cause any problem given that the web2py code is
> acknowledged.

I wouldn't want to ship web2py with Biopython - we'd just list it as
another optional package you might want to install for use with BioSQL
(as we do with MySQLdb etc).

> Anyhow, are there any plan in extending the BioSQL interface?
> We could make some methods useful to people not skilled with SQL, that can
> boost their experience with BioSQL. something like selecting all the bioentries
> carrying a given feature type or a qualifier value  or even a dbxref.
> Allowing people to use the BioSQL schema without exactly knowing the
> schema and have to write complex queries could be a big addition.

There are already several query methods, but more wouldn't be a bad
idea. I was thinking we could implement dictionary like access, and
support for iterator over all the records.

Peter