In article <CMM.0.90.2.710263441.kristoff at genbank.bio.net> kristoff at GENBANK.BIO.NET
(Dave Kristofferson) writes:
> I agree with virtually all of the points that you raise.
Thanks.
>Regarding BLAST, it is a very nice program and we use it on GOS (along
>with IRX which is another NLM production), but the recent introduction
>of BLAZE on GOS demonstrates that, contrary to the opinions of some,
>groups outside of NCBI can also make significant contributions in this
>area.
Of course, this is not an argument that NLM should give up, now that
there are others doing similar work. Indeed, by continuing to compete,
it will keep them on their toes.
> A possible compromise, in
>my opinion, would be for NCBI to continue its database production and
>algorithm research roles, but to stay out of the user interface
>business. They might, of course, outline standards for database
>access interfaces, but general toolkit development seems to me, at
>least, to be overreaching their mandate.
I partially agree. Database and algorithm development seem to be a logical
outcome of who they are and what they are doing. And I agree that fancy user
interfaces are probably not what they should work on, and that the companies
can contribute strongly there. However, database access toolkit development IS
within the scope of what they must do.
A toolkit is not a user interface. It is a set of defined function calls that
manipulate a database. A person using a program need not be aware that it
exists. It is an interface between the program itself and the database, not
between the program and the user.
A robust toolkit would make it possible for people write programs to manipulate
the database. It protects them from changes in the database. It sets
standards for writing code. NCBI must write such things to access the
database, and if done properly, everybody (including the commercial groups) can
benefit. I would like to see such a toolkit so that I can write DelilaII in
it. Companies could use the toolkit as the launching pad for programs to
visually fly through the database.
Tom Schneider
National Cancer Institute
Laboratory of Mathematical Biology
Frederick, Maryland 21702-1201
toms at ncifcrf.gov
