Hi folks,
Despite the kerfuffle that surrounded the discussion of VMS and
Unix versions of AUTHORIN a week or two ago on bionet.general, I went
ahead and cut the VMS database submission form program, SUBFORM, from our
system and made it a standalone package. It is a purely VMS based program
written in mainly Pascal with some Fortran, and makes extensive use of
SMG screen handling. It is built around the database submission form as
distributed by the databases. The program was written a couple of years ago
and so uses the form as it was then.
Let me emphasize that this is NOT a VMS version of AUTHORIN. It
produces an ASCII file for mailing to the databases. I am not privy to
the protocol used by AUTHORIN.
The note below describes how to get the program. Also note, that
if you have problems that I will be on leave 4th August through 11th
August off doing a spot of cross-country skiing. So mail responses
to problems might not get answered until after the 11th.
Also I have cross posted this between bionet.general and bionet.
software. As it is software, lets have any further discussion in
bionet.software.
Good Luck, Tony Kyne,
tony at wehi.edu.au
***************************************************************************
THE WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH
POSTAL ADDRESS: POST OFFICE, ROYAL MELBOURNE HOSPITAL,
VICTORIA, 3050, AUSTRALIA
TELEPHONE: International 61-3-345-2555 National (03) 345 2555
TELEX: 30625 Attention ME3659
FACSIMILE: International 61-3-347-0852 National (03) 347 0852
SUBFORM
A PROGRAM TO AID SUBMISSION OF SEQUENCE DATA
TO INTERNATIONAL DATABASES
by
Marina Spaulding
(Ludwig Institute for Cancer Research - Melbourne Branch)
and
Tony Kyne
(The Walter and Eliza Hall Institute for Medical Research)
Correspondence: Tony Kyne,
The Walter and Eliza Hall Institute of Medical Research
Post Office, Royal Melbourne Hospital,
Victoria, 3052
Australia
e-mail: tony at wehi.edu.au
SUBFORM is Copyright (1991) by Dr. Anthony P. Kyne, Computer
Sciences Unit, The Walter and Eliza Hall Institute of Medical
Research, PO Royal Melbourne Hospital, Victoria, 3050, Australia.
This program is made available for public use and must not be sold
for profit. It can be freely distributed, as long the banner section
of this document is included with any distribution.
---- End of Banner ----
The international sequence database submission form program for VMS is
now available. This program uses VMS SMG screens and on screen editing
facilities to assist users in preparing and mailing an entry to the various
database collators. The entry produced by this program closely resembles the
submission form distributed by the databases. The program was built around
the form as it existed a couple of years ago. It is not, repeat not, a VMS
version of AUTHORIN.
The SUBFORM package now is available for ftp from the pub subdirectory at
wehil.wehi.edu.au (128.250.252.13) as a compressed VMS backup saveset.
European and North American users are requested to conserve the precious
satellite bandwith between Australia and the US and try to use ftp or mail
servers at FUNET (nic.funet.fi), UH Gene Server (gene-server at bchs.uh.edu),
IUBIO (ftp.bio.indiana.edu) and EMBL (netserv at embl-heidelberg.de). Hopefully
the package will be available at these sites in a day or so. The package
includes the C version of Don Gilbert's (dogStar Software and Indiana
University biology Department) READSEQ package for reading files in various
popular sequence formats.
(Please note that this SUBFORM package has been pulled from a wider
sequence analysis environment at WEHI/LICR/CSIRO-BME. Hence if you decide to
get into the code to modify the program, and see what appear to be odd bits
of code about, it is some of the support code for local situation.)
Select a home directory for the package and uncompress and unpack the
backup save set. (A decompression executable is also available from
wehil.wehi.edu.au and other sites if you do not have this available.) It will
create a directory subform and subdirectories for sources and documentation
and the READSEQ package.
The top directory, subform, contains all the necessary working files. You
will need to customize a number of files to get the package working. Print
either the Postscript (SUBFORM.PS) or ASCII (SUBFORM.ASCII) versions of the
manual for the rest of the installation process.
SUBFORM has tested OK on VMS 5.2, 5.3-1 and 5.4-2. I suspect that you may
have real difficulties running it on pre VMS 5.0 systems. Major enhancements
occurred with Pascal about then.
Send all comments, bouquets and brickbats to me(tony at wehi.edu.au). Marina
is no longer with us - she has stopped working for the love of science and
now earns lots of filthy money in the commercial world downtown.
Good luck, Tony Kyne.
