dbd@THEORY.BCHS.UH.EDU (Dan Davison) (08/03/90)
As I've gotten a couple note indicating confusion about exactly I was referring to: 1) The new feature table is an *excellent* idea. It is essential if important biological information is going to be electronically accessible, i.e. usable. It also represents a lot of hard work by a lot of good people, and I did not intend to denigrate that work or them. 2) Yes, there were announcements about the new feature table and about when it would start appearing. For some very obscure reason I thought the new feature table was going to be INTERNAL to the existing entries, as in an extended "COMMENTS" field or something similar. 3) Lastly, the entire episode is another example of some individuals missing the distinction between being a professional or near-professional programmer (or having one on staff) and *the vast majority of the biological community*. I'm sure the commerical vendors of sw love the change since they now can sell new sw (possibly at "upgrade", instead of "full" cost). But NIH has been wreaking havoc with cutting and not renewing grants that would otherwise have been funded. This means that some folks are not going to be able to hire programmers to fix their software. Therefore, a lot of us will be using GB63 for sw that reads the feature table and ignoring or editing GB Rel. 64 and later. So, I offer a challenge: would someone contribute to the public domain a set of routines that parse the new feature table format? (No, it doesn't have to be distributed from the UH server). C, Fortran, pascal and BASIC seem to be the languges most often used. Summary: no insult intended to the creaters of the feature table; I publically apologize if I have accidentially hurt someone. The release of the new format on the ordinary biologist was just not thought through properly. dan davison
kristoff@genbank.BIO.NET (David Kristofferson) (08/03/90)
Regarding the change in the features table format, Dan writes > I'm sure the commerical vendors of sw > love the change since they now can sell new sw (possibly at "upgrade", > instead of "full" cost). Dan, I love conspiracy theories just as much as the next person (I had my autographed copy of "None Dare Call It Treason" bronzed.) Unfortunately I believe that few if any of the commercial packages actually parse the features table, so this theory will only rate tar and feathers. 8-) Dave -- Sincerely, Dave Kristofferson GenBank On-line Service Manager kristoff@genbank.bio.net
davison@UHNIX2.UH.EDU (Dan Davison) (08/04/90)
> > I'm sure the commerical vendors of sw > > love the change since they now can sell new sw (possibly at "upgrade", > > instead of "full" cost). > Unfortunately I believe that few if any of the commercial packages > actually parse the features table, so this theory... Dave, Mebbe the sw you use doesn't parse the table, but some I use does. besides, *the point of the feature table change was to make the information more accessable and usable*. No consipiracy theory needed nor implied nor meant to be implied. dan -- dr. dan davison/dept. of biochemical and biophysical sciences/univ. of Houston/4800 Calhoun/Houston,TX 77054-5500/davison@uh.edu/DAVISON@UHOU "Without the voice of reason, every faith is its own curse" -- Sting Disclaimer: As always, I speak only for myself, and, usually, only to myself.
JRAMON@ccuam1.uam.es (08/07/90)
Hi Dan,
... and all of you who also are interested.
I am now writing a software package for protein analysis that must read
a protein sequence databank. I wrote a full set of routines in C for accessing
some 11 or so formats, including GenBank, EMBL, NBRF, etc...
In view of the recent postings I fear that I must re-write some of
them. Since the package has been intended to be fully P. D. when finished, I
don't mind to send the new set, as well as 'ye old ones' to the net. I must
say that I'm writing in C. This has some advantages for portability and, YES!,
cleanness of the code. I will try also writing a set in Pascal at the same
time, but then, I won't assure they'll work on ANY Pascal compiler, though
I'll try to make them as general as possible.
More news as soon as I have the new set. I've just got the description
of the new format from EMBL and am now working on them.
By the way, I am also trying to get a ONE package able to be used by
different languages. I now this should be easy using *pascal* calling
convention under MS-DOS and Macs, and that I can build a CDD under VMS. Any
new ideas in this respect? I'll also make it publicly available as soon as
it is finished.
Best wishes for all of you... And don't forget your holidays..
J. R. Valverde
Instituto Investigaciones Biomedicas
C. S. I. C.
and
Dpt. Bioquimica. Facultad de Medicina
U.A.M. - SPAINdavison@UHNIX2.UH.EDU (Dan Davison) (08/09/90)
> I am now writing a software package for protein analysis > that must read a protein sequence databank. I wrote a full set of > routines in C for accessing some 11 or so formats, including > GenBank, EMBL, NBRF, etc... Sounds great, and thanks for offering to submit the code to the public domain. > J. R. Valverde > Instituto Investigaciones Biomedicas > C. S. I. C. And my apologies for rendering your name as "J Ramon" in a previous note...but that's what's on your e-mail address. If I can be of help let me know. 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.