[Pipet Devel] An apology, Loci, gnome, and CORBA

Alan J. Williams Alan at TheWilliamsFamily.org
Wed Jun 23 20:08:13 EDT 1999

On Wed, 23 Jun 1999, Justin Bradford wrote:
 > I'm currently at Genentech in the Biocomputing department, and that's
 > basically where things are now (except with a web front-end and a sprinkle
 > of Java). I'd like Loci to be a next generation kind of project, but
 > really, I think we have more complicated interfaces, but not a whole lot
 > more programming than doing it the old way.

I've toyed with using bioperl and writing an apache mod_perl system for
doing bioinformatics, but you can only do so much through that medium.
Non-the-less, it would be great if the underlying infrastructure of loci
could be utilized through a mod_perl or cgi interface should someone
decide to implement a web interface down the road. 

 > As we are making use of GNOME, I would agree that it makes sense to use
 > their technology for these things. It makes all of the tools more
 > flexible in the GNOME environment.

 > However, there has to be some flexibility in the interface (to the data in
 > particular). What if I want to make a tool that uses data in a unique way
 > (which we don't have an interface for)?
This is why the data access/storage needs to have good/general

 > I guess, fundamentally, I'm interested in Loci from a data storage,
 > management, and interface issue. I'm thinking of a system which can pull
 > data from various sources in a very flexible way and then combine and
 > present that data in an equally flexible way to any arbitrary program.
One of my frustrations as a researcher is all the bits of sequence data,
blast reports, restriction maps, structure predictions, etc.. that are
strewn over many directories and accross five computers.  Furthermore,
what sequence did this blast report come from? GDE does a decent job of
providing an interface to the many programs (if you go to all the trouble
of putting together the gdemenus and writing glue scripts) but it does a
horrible job at managing data.  If Loci is going to be the next generation
bioinformatics package, it is going to have to have good (and
flexible) data management. 

But hey, you already knew that.  Just adding my support to Justin's

Alan Williams           
University of California, Riverside   "Where observation is concerned,
Dept. of Botany and Plant Sciences     chance favors the prepared mind."  
Alan at TheWilliamsFamily.org                         -- Louis Pasteur

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