alternate mosaic entry to iubio archive

birney at molbiol.ox.ac.uk birney at molbiol.ox.ac.uk
Sat Apr 23 14:01:12 EST 1994

> I still regard gopher and html/www as competitors, and feel
> that gopher in general is as good or better a protocol for
> network information services as html/http/www.  But the pretty
> face of Mosaic has lured away many people from gopher use.
> As people find some of the hypertext linkages, and built-in
> graphics displays, useful for browsing & searching bioscience 
> information, I plan to try adding some of that to my gopher client.
> I don't have the time and resources that NCSA/CERN have for building
> their systems, so my work won't be as fancy.  However,
> it is pretty straight forward to get gopher to do hypertext type
> links, and graphic and rich text displays. 
> If you have a view on gopher+ versus mosaic/http/html/www for use
> in biosciences information services, please feel free to comment here
> or by mail to me.  I'd not like to spend time developing gopher further
> if every one moves away from it to the other side. 

I'm from the other side in that I prefer the http (WWW) way of doing things
and the HTML scripts that you can use. I have only used gopher as an 
information retrevial system, rather than running a database from a 
gopher server

	The benefits that I find are prinicply the hyper-text. I can 'write'
scripts that are automatically crosslinked into the databases in 
NCBI through the web...for example one of my database searching programs
can produce a HTML formatted file in which all the high scores are
automatically linked to WWW server in NCBI...this means that I can open the
file from mosaic and with one click I can pull out the report from  NCBI and
then as that is automatically crosslinked to MEDLINE, look at the references
there. It is quite remarkable how easy this is compared to even having a
window running Networked Entrez beside you to look at the documents. I am
hoping to write even more extensively crosslinked work in the future. I
don't think I could do this using a gopher+ system: or rather if i did I
would perhaps have to run a gopher client from inside the program which may
be concpetually nicer but is a damn sight harder to do. (I would have

	As for the graphical feel to mosaic...there is no compulsion for 
someone who is running a database to pepper their scripts with images. Indeed
most info-servers that are serious use very small icons if at all: it is the 
more flash "fun" servers that go overboard on images. I don't think this
should be an issue for people making serious databases.

	The fact that mosaic has a kitchen sink of protocols wrapped up in
it is not really the fault of the WWW, which is meant to be http protocol.
I have no wish to write or even try to hack any transport protocol: As
higher end programmers I would have thought that the fact that a client
program maintains x number of protocols shouldn't bother us...it is what
sort of servers should we be putting our information on. As for getting
information out automatically, as mentioned above writting html scripts is
very easy...though yes, if you want a program to pick things up from
some server then a) a standard protocol b) this protocol being sane enough
to incorporate into a program are both important features...this is 
something that I would be very scared of trying to do. I'm perfectly happy
to write html scripts to use.

	Mosaic is *incredibly* easy for first time users to understand and
 retreive information...this is very important. There can be no better 
reason to recommend program than this. If you want a info server to be
easily accessibly by *non* informatic/computing people then I think you
have to look at mosaic for the best program that unites many different 
protocols into one interface. A bitch for programmers trying to write 
anything similar but a huge benefit for the vast majority of people.

	The fact that Mosaic is crappy on Macs and that people working over
phones etc might have a problem getting bytes.. this is an important caveat...I
think mac users and stand alone PC users must be a good third of the 
non informatic people mentioned above. I think lynx does have forms
capabilites (at least the latest version). I just hope this situation

	HTML+ promises many improvements: Specifically better forms so that
you can import files into the form and other little pluses. I believe that
the http servers can be quite easy to link up into other programs (one of
them is written in Perl) so that when this happens one could realistically
have a client-server relationship between someone and a big database with
http dealing with transport and mosaic the bare essential GUI interface,
which could give you the richness of say what is now provided by email
servers (BLAST/BLITZ server). I am very excited about this and I'll change
the tiny little mail server I run over to that once it appears.

	Finally, people use mosaic as much more than a information retrieval
system (Web surfing)...people find it easy to use. For this reason and for
the ease of hypertext linking to remote databases, I prefer to write stuff
that is going to use the Web.

I'm a bit of a small-fry in this sort of thing: this a just a humble opinion
(lets not get into a protocol flame war. I hope the above discussion
doesn't sound that way).


ewan birney

birney at molbiol.ox.ac.uk

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