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SeqPup, a new easy-to-use client for GCG/other biocompute services

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Tue Jul 2 08:22:30 EST 1996



For GCG software users, and especially those who would like
to use such software but have been intimidated by the learning
curve, you may now find some help with the new version
of SeqPup, a biosequence editor for most computer systems.

This new SeqPup provides Internet client-server connections to
computers that run GCG and other command-line (or weak user interfaced) 
biocomputing programs (Clustal, FastA, BLAST, Phylip, etc.).  

The main drawback w/ the current SeqPup for GCG usage is that
GCG graphics are not displayed in SeqPup.  I hope to add support
for this in a later revision.   

Those who want to try out this SeqPup as a client for GCG or other
software are encouraged to do so.  Biocomputing service providers
will need to install a fairly simple program, bopper (see below),
on a server.  If you have 'popper' installed for e-mail reading,
it is quite similar.  There is also a trial server running for
a short time at IU.


SeqPup, version 0.6 development release, June/July 1996

New in this release:
	Easily use GCG and other command-line software over network
	Bare-bones autosequencer (ABI,SCF) base calling, editing, assembly
	Expanded sequence size limits (now can open 1.9MB H.flu genome)
	Numerous bug fixes and improvements
	
[-- see bionet.software or the iubio server for some more details --]

You can obtain this release thru anonymous ftp, gopher or
http to iubio.bio.indiana.edu, in folder /molbio/seqpup.
Versions are available for Macintosh (PowerMac and 68K), 
MS Windows (Win95, WinNT and Win3), and Unix/XWindows systems
including Sun Solaris, SGI Irix, DEC Unix, Linux.   The Internet 
locators to this software are

  <ftp://iubio.bio.indiana.edu/molbio/seqpup/>
  <gopher://iubio.bio.indiana.edu/11/IUBio-Software+Data/molbio/seqpup/>
  <http://iubio.bio.indiana.edu/1/IUBio-Software%2bData/molbio/seqpup/>

Source code for this software is at
  <ftp://iubio.bio.indiana.edu/util/dclap/source/>.
  
The bopper source for installed a server for SeqPup Internet BOP
functions is in this same folder as
  <ftp://iubio.bio.indiana.edu/util/dclap/source/bopper.tar.gz>


Background:

It has been a goal of mine for some time to provide client-server
interfaces to biocomputing software, to make some typical command-line
programs or those w/ weak user interfaces easier for the
average biologist.   The GCG suite is a good example of this -
while it is very powerful in terms of all the biosequence analyses
that can be done, it is also very intimidating to the average
biologist (many at IU avoid it due to that). 

A few years back I was about ready to develop a network protocol
for interfacing client software like SeqPup with
server programs.  With the arrival of gopher then http protocols,
those initially looked like a solution, but turned out to be time
consuming sidetracks.   Rather than waste more time,
I took an existing protocol, POP for mail reading, and its
server software.  This I modified to provide the details that seemed
needed for biocomputing data analyses.  The result is called
BOP (biocomputing office protocol, an acronym that named itself),
and bopper is the server software to enable this.  The first client
software to use this is the new release of SeqPup.  It is a fairly
simple protocol, and other biocomputing client software may wish to 
look at it.

On the SeqPup side, this protocol is implemented in a manner similar
to the use of local external programs that SeqPup already handles.
One writes an HTML form to describe a dialog for selecting program
options, and use sequence data as selected from the SeqPup editor windows.
A few special variables for data inputs and outputs, server host, etc.
are used.

At this stage, there are some bugs in the cli/server implementation.
Sometimes handshaking fails.  Many improvements may be made.
But at the basic level it works.

I look forward to hearing from biologists, and esp. biocomputing
service providers, on problems and suggestions for improving this.

- Don

-- 
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu



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