IUBio Gopher+ server adds sequence search and analysis

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Thu Aug 19 16:12:49 EST 1993

Gopher+ now does gene sequence search and analysis

I'm pleased to announce new biocomputing services at IUBio
Gopher hole, and a new GopherApp release for Macintoshes.
Gopher+ users can now use biosequence search services thru
IUBio Gopher, with the same ease that has made the original
Internet Gopher such a success.

Gopher+ will eventually be able to provide easy-to-use,
widely accessible user interfaces to many biocomputing
analysis services.  The example at IUBio now provides a few
such links to NCBI's BLAST search and Fred Hutchinson
Center's BLOCKS search as a proof of this concept.

Here is gopher link information to these examples
Name=Gopher+ Test at IUBio

This folder currently contains:
  Gopher+ Mol. Biology services/
     -- gopher+ dialogs for entering your sequence data and
    related options to use search services at NCBI, FHCRC and 
    later others.
     -- client programs for Mac (GopherApp++, TurboGopher),
    MS Win (HGopher), and Unix.
     -- some examples and documents from the U.Minn. gopher team

NOTE: The only gopher+ clients that I am aware of which can
properly use the Mol. Biology services are GopherApp++ and
TurboGopher for Macintosh.  The MS Windows program HGopher
*may* work, but I haven't the computer to test it on.  The
Unix curses client does *not* work properly for these

Eventually I and others may well find this is a good way to
simplify the use of local biocomputing services such as GCG,
Phylip and similar command-line type of programs. Adding a
new service thru Gopher+ involves simple steps: design a
dialog screen, and write a small shell script to pass the
user's choices on to a program for analysis.  Results can be
e-mailed to the user, or returned immediately if the process
is quick enough.

Now Gopher+ can provide essentially the same simple front-
end as my prior works with Mac Hypercard (HyperGCG and
Genbank Search), but with certain great improvements.  Since
the inception of biogophers, I had hopes that we could shoe-
horn more complex dialogs, with sending data from client to
server, into gopher.  With the Gopher+ protocol, that became
feasible, but implementing it took longer than I'd thought
(I changed languages *and* program libraries *and* revised
for gopher+ ... the gopher+ part wasn't the big time

This material is still quite experimental, and has bugs and
gotchas. You should plan on 6 months or so until it matures.  
Please send feed back and bug reports, and be patient in waiting
for replies and updates.

I wish to thank Indiana University Biology department and
the Flybase genome project for not getting too upset at my
long programming weekends while their paying work piled up.

- Don Gilbert

        = = = = = = GopherApp update = = = = = =

GopherApp is an Internet information service program for
Macintosh computers.  It provides a Finder-like link to the
range  of Internet Gopher services.

++ This release of version 2.0 has several known and
suspected bugs.  Users are warned IT WILL LIKELY FAIL AND
CRASH, causing you to loose work and restart your Macintosh.
It is made available for those who wish to help the author
debug it and to test its new features.

To use GopherApp, your Mac must have a network connection to
the  Internet, and it must have MacTCP installed and
operating (as  with NCSA Telnet, Eudora, network news and
similar MacTCP-based  Internet programs).  You may obtain
GopherApp thru anonymous ftp to ftp.bio.indiana.edu, in
folder /util/gopher, as gopherapp++.hqx. You may also obtain
updates using Gopher to this same IUBio archive
(ftp.bio.indiana.edu). Look for a folder called "IUBio

GopherApp is written by Don Gilbert, using the MacApp
extensible Macintosh programming framework from Apple
Computer. It was derived from a subset of a biosequence
analysis program called SeqApp.
++ GopherApp 2 beta does not yet work with Mac System 6.

Comments, bug reports and suggestions for new features may
be addressed via e-mail to         Software at Bio.Indiana.Edu

                                             -- Don Gilbert


19 Aug 93, v 2.0b3    Major revision, now called
GopherApp++.  Translated from Object Pascal to C++, and from
Macapp version 2 to version 3 (the later was harder than the
former).  Added many Gopher+ features, including ASK dialogs
and alternate views.  Added multitreaded execution of TCP
transactions (thanks Peter Speck for Nuntius's example).
There are still several known and suspected bugs in this

Don Gilbert                                     gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405

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