[Pipet Devel] Re: Web interface

Rahul Jain rahul at photino.sid.rice.edu
Thu Jan 21 14:41:01 EST 1999

On Thu, 21 Jan 1999, J.W. Bizzaro wrote:

> Rahul Jain wrote:
> > 
> > I was thinking about the Web interface we are planning to have to TULIP.
> > 
> > We'll need to plan out our design of the other tools very carefully so
> > that we don't have to create messy kludges to get this web interface to
> > work.
> My initial thought regarding the Web interface was not that we could or should
> replicate the GUI loci in a Web browser.  My thought was that Loci can provide
> an HTML interface to _some_ of the _analysis_ loci, considering they are
> command-line, short-lived, output ASCI text, which will be formatted into XML anyway.
> Konrad and I have communicated quite a bit about the limitations of HTML.  In
> fact, when I first mentioned XML, Konrad thought I was speaking of putting
> everything into a Web browser.  Neither he nor I like the static interface of
> HTML browsers, so I will make a point that GUI loci will not look or act like
> one but will be very dynamic.
> In short, I think the Web interface can be a quick-and-dirty way for people
> without the Loci package to access the wealth of analysis loci we may someday amass.

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

> I appreciate that you looked into this.  But I think this plan would be an
> enormous task, and probably best left to some heavy duty Java...which we don't
> want to use for reasons I've expressed before.
> Do you want to take on this Web interface project, as the simpler project I
> envisioned?  I think the biggest part of this would be some sort of XML to
> HTML conversion, which is actually what XSL is all about.  The problem with
> XSL is that browsers don't support it right now, and I don't think there is a
> specification for CML or BSML.  And I think another big thing (providing no
> XSL is used) would be converting diagrams specified by XML into GIF format. 
> You would have to write a program that would generate custom GIF's.  Check out
> NCBI's "graphical view" of nucleotide data:
>     http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?gi=3647232&db=Nucleotide

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.

> Also, the Web interface implementation will work from one server that I will
> have set up.  It will act as a limited version of Loci, and will contact
> certain analysis loci around the Internet.

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.

> This is no small project either.  It will almost parallel Loci itself and use
> many of the same components.  So, we must limit the types of views and
> analysis tools that the Web interface can handle.

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. (Does IE have layers support?)

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