[Biopython-dev] pySRS (was Re: ANN: mindy-0.1)

Andrew Dalke dalke at acm.org
Mon Mar 26 05:05:11 EST 2001

> IMHO a biopython approach would include e.g. gdbm
> for a light version

Any reason for gdbm over Sleepycat's Berkeley DBM?
I admit to personal preference since an old boss of
mine is now at Sleepycat.  I also think it is more
powerful and has more development than gdbm.  For
example, bsddb can support multiple simultaneous
readers and writers, can do transactions, and allows
b-tree storage for ranged searches.

> (gdbm is present on almost all unixes and can be used
> [similar to cpickles] for FAST storage and retrieval
> of simple key-value data)

My background was mostly on SGIs which didn't have
gdbm installed.  I don't know about Solaris boxes
or other non-Linux/*BSD OSes.  Robin Dunn's interface
to bsddb includes a library for automatic pickling
to the database.  As I recall, part of Robin's work
is funded by Digital Creations so Zope can use bsddb
for its object database.


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