[Pipet Devel] Re: Web interface

J.W. Bizzaro bizzaro at bc.edu
Thu Jan 21 15:30:04 EST 1999

Rahul Jain wrote:
> Since we are limiting the interface to many loci to GTK/GNOME, we are
> limiting the people able to use Loci to those with Linux. GTK/GNOME may
> compile on other Unices, but I don't think GNOME does,

Both GTK and the entire GNOME desktop have been ported to just about every
platform that can run X-Windows.  So, we really have all Unices covered.

> and I'm sure that
> it'll probably take quite a bit of tweaking to get it to compile on any
> other system.

Probably.  Especially if we use UNIX utilities.  Portability is a huge issue
that we aren't about to conquer just yet.  You can see Sun tearing their hair
out over this issue and Java.  *But* by using Python, we are in a much better
position to port Loci than EMBOSS would be.

***It's a tradeoff guys!  We are sticking with one platform for development so
that we don't limit ourselves to the intersection of all UNIX, Windows, and
Mac GUI, which is relatively small.  *And* we get to use native UNIX
implementations, not everything running through a virtual machine.  Besides, I
have confidence that GTK/GNOME will find its way to those other platforms
without any effort of our own.  If not, we'll see about porting to native
Windows and Mac API...It's been done.

> Our main concern should be getting it to work under Windows,
> since those who use any other Unix won't have any trouble with Linux if
> they need to run it. Windows users, on the other hand are often either
> unable to understand Linux or not allowed by superiors to use Linux.
> That's where we really need to target the Web interface.

Yes, that is exactly what the Web interface is targeting :-)  But can we put
all of the bells and whistles in the Web interface that we have available with
GTK?  There is just no way right now.  As I said in my last e-mail to Carlos,
we want Loci to be as dynamic as Word and Excel.  If Microsoft can't put those
in a Web browser, I certainly doubt we could put Loci.  The Web interface will
simply have to work with the limitations imposed on that type of interface.

> I think this is where Perl really can be useful. It's designed to process
> and manipulate text, and there are modules for XML and HTML. Also, there's
> GD for creating GIFs. OTOH, Perl and Python running at the same time would
> probably wear out all but the best servers, so I think we may have to rely
> on Python alone. Then again, mod_perl would make the system much more
> responsive. If there's a GD module for Python, then it shouldn't be too
> tough to do the whole thing in Python and have it integrate much more
> cleanly with the other parts of Loci.

I am not really anti-Perl, but Python can handle much of what Perl can, and I
think we should not try to mix Perl and Python.  I don't know if there is a GD
module for Python.  We'll have to look (Konrad, do you know of one?).  There
is an XML parser being developed by the Python developers.  Of course, Python
can handle text as well as Perl can.

> Oh, the way I envisioned it, the Web interface would be a package that
> could be installed on any Loci server as a Loci client and it would use
> CGI to handle the requests from other computers.

Yes it would be a client in the way it would substitute for all (nearly) of
the client side loci.  But it would act as a Web server (really, work with a
Web server) that can be tapped into by anyone using a Web browser.  Where
should it go?  I think we may just need one at the main Loci URL (which
doesn't exist yet).  Why do you think it should be portable?  It can be, but I
don't think it has to be, as long as one Web server can handle the requests.

> I think I'll do this project, as I haven't taken any molbio/genetics
> courses yet. Considering the situation of the people who would use the Web
> interface, they probably have a JavaScript capable browser, so I can
> implement most of the widgets.

Great!  But let's see what we can do using standard CGI over JavaScript (see
my last message).  If we have to use it, then we have to.

> (Does IE have layers support?)

You've got me there.  I haven't used IE much at all.

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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