ODONNELL@arcb.afrc.ac.uk (08/04/90)
A faint echo of Dan Davisons remarks here. I understood what he meant first time, and I sympathise. New NAQ? -------- How about some super-duper s/w to allow VAXes to cope with the vast increase in Dbase size? NAQ is getting old, and is very slow in coping. Dbases in bits -------------- I know I am supposed to use Genbank and EMBL divided up into chunks, but that means the average user has to do the same search several times on several different bits of the dbase. And I just KNOW someone (the average biologist user) will moan at me that the PRIMATE data is not in the VERTEBRATE data - and why not? Fast indexing ------------- Yes - I would like something like the OWL database - Index files larger than the database itself. But I don't have the disk space, and I'm asking for more disk space than Administration has (what!!!!! you CAN'T need that much!) Shopping list ------------- I would like a means of processing my own original dbases to work in conjunction with some new s/w ie:Faster indices. An NAQ with the ACCESSION number feature in instead of having to create something for PSQ. You're doing a good job ----------------------- And how many of you out there are tinkering with the old PIR programs with each release of Genbank and EMBL, everytime the format changes. Be brave - we are the unsung heros! Anyone else suffer EMBL23's entry XLRN01 which had > 25 lines before the DE line? This is where the computer-literate biologists end up: computing support! I am not complaining - I enjoy the challenge, but I can think of other things to do. ***************************************************************************** Cary O'Donnell Tel: (+44) 582 762271 ext 226 AFRC Computing Centre Fax: (+44) 582 761710 West Common email: ODONNELL@UK.AC.AFRC.ARCB Harpenden (Molecular biology support at AFRCCC) Herts AL5 2JE U.K. (AFRC = Agricultural & Food Research Council) Disclaimer: You can please some of the people all of the time .....
JRAMON@ccuam1.uam.es (08/07/90)
Something more...
I would also like to know of your needs. My programs only take care of
the sequence, hence I've not thought too much about other accesses. Any
suggestions?
Oh! Isn't it nice to go back to the metaliguistics of the list? It is
all fine to discuss about witches and other theories about database formats,
but... Why not better touch a positive solution? I mean, you change the format,
and tell this is better. No doubt! But, why?
I suppose you had something in mind before doing this. Why not share it
so that we can design our sw not only for our punctual specific purpose but
also in such a way that it could be useful for other guys. Enginnering a sw
project is more easy if you know in advance all the reasons for changes, all
the needs expected and the uses it is intended for.
My apologies for the english, I've just re-read this and sounds
horrible. (Just some more meta-linguistics).
J. R. Valverde
Instituto Investigaciones Biomedicas, CSIC
&
Dpt. Bioquimica, Facultad de Medicina, UAM
(Both in Madrid. Spain, of course).
Disclaimer: Que bonitos ojos tienes,
debajo de esas dos cejas.
(not in point, but sound well, and I also like silly senetences)kristoff@genbank.BIO.NET (David Kristofferson) (08/08/90)
> Why not share it > so that we can design our sw not only for our punctual specific purpose but > also in such a way that it could be useful for other guys. Enginnering a sw > project is more easy if you know in advance all the reasons for changes, all > the needs expected and the uses it is intended for. As Dave Benton mentioned in an earlier message, GenBank, EMBL, and DDBJ have been circulating this info for some time. There was nothing secret about this process. I would recommend that anyone who develops software that utilizes any of the sequence databanks become a regular reader of the various release notes and also get on any databank mailing lists that are available. The databanks can not hope to reach everyone personally with an interest in these matters, but, if one wishes to do things "by the book" and avoid wasting time, a certain amount of effort to stay informed must also be made on the part of the software developer. -- Sincerely, Dave Kristofferson GenBank On-line Service Manager kristoff@genbank.bio.net
davison@UHNIX2.UH.EDU (Dan Davison) (08/09/90)
> As Dave Benton mentioned in an earlier message, GenBank, EMBL, and > DDBJ have been circulating this info for some time. There was nothing > secret about this process. Even Dave K. misses my point. Sigh. SO WHAT? What I keep trying to emphasize is responsibility to the community that has come to depend on software. All concerned in this venture did not think about the consequences on users NOW. dan -- dr. dan davison/dept. of biochemical and biophysical sciences/univ. of Houston/4800 Calhoun/Houston,TX 77054-5500/davison@uh.edu/DAVISON@UHOU Disclaimer: As always, I speak only for myself, and, usually, only to myself.