I've about finished setting up an Internet Gopher server for
biology data at ftp.bio.indiana.edu. It seems to be working well
and biologists look like they are taking to it rapidly and
easily -- I would say it has some of the good features of both
ftp and wais, but is a good bit easier to learn.
New biology file formats for WAIS and Gopher include:
| genbank /* GenBank flatfile format */
| embl /* EMBL flatfile format */
| prositedoc /* Prosite protein doc format */
| prositedat /* Prosite protein dat format */
| biojournal /* Bio journal TOC on bionet.journals */
As I mentioned in a news post last week to bionet.software, this
combination of waisindex with Internet Gopher seems to work
very well as a Genbank biology sequence data server.
The IUBio gopher hole now includes searching of the current
full NCBI-Genbank release, and more recent Genbank + EMBL updates;
searching of the current Prosite protein pattern database;
searching of Bio Journal tables of contents; searching of a compendium
of molecular biology materials & methods protocols. As well
there is access thru Gopher to Drosophila data archives and the IUBio
software and data ftp archive.
This gopher is still experimental -- the computer and disk space
may be required for other projects in the future. I suggest
that other interested biocomputists with a copy of Genbank
or EMBL attached to a computer should think of setting up
a gopher server that can be used at least locally -- your main
cost is about 40mb disk space per 200mb of Genbank/EMBL.
If possible, make your server available to others around the
Internet so that we can have several regional servers to spred
the load. You will find instructions at this server on how to
set your own up. If you have some unix programming ability, and
if my instructions are clear enough, it shouldn't take more
than a few hours.
Modifications to the server software include boolean NOT operator
(I'll eventually add an AND operator if no one else does), and
list files for long match lists. I think the NOT operator will
work with WAIS as well as Gopher, though I've only tested Gopher.
Patch files are available via Internet Gopher to ftp.bio.indiana.edu,
see folder "This Gopher".
Patch files are also available via anonymous ftp to ftp.bio.indiana.edu,
as util/gopher/gopher-bio.patch and util/wais/wais-bio.patch.
The complete IUBio Gopher hole, minus large data and index files,
is available in tar form at this ftp site as
Don Gilbert gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405