[Biojava-l] BioInformatics toolbox.

[Patrick McConnell]

We (Duke Bioinformatics Shared Resource) are going to make a concerted
effort to create a software package that allows the piping of web services.
We are going to focus on bioinformatics web services, though the project
should be generally applicable to all web services.  We are now in the
process of applying for a grant.

A few questions:

1. We plan for these tools to be open source.  Is there a place for this
under BioJava?  Of some concern: we will be defining some bioinformatics
data types with java interfaces and XML schemas for common bioinformatics
programs.  We will also be providing interfaces for web services, as well
as implementations (implementations will most likely have abstract
functions for returning installation dependent information e.g. path to
blast databases).  Will this sort of thing fit under BioJava?  I believe
the GUI and mechanics of piping would fall under BioJava with no problem
(let me know if I am wrong in this assumption), but I was unsure whether
application-specific code would fit.

2. Is there anyone interested in collaborating on this project?  The level
of collaboration can vary from consulting on ideas to testing beta
applications to actual software coding.  I will be coming up with a list of
sub-projects sometime in the near future (check the link below for the
current ***rough*** list).

3. Assuming their is a place for this in BioJava, should collaboration on
this project continue over this mailing list, or should a new list be
created?

If anyone is interested, they can see
http://mendel.mc.duke.edu:8090/frameworks/webservices/index.html for a more
in-depth description (hopefully it will become progressively more in-depth
as time progresses).

I am pretty excited about this project.  I think it could provide the
impetous for sites adding more flexible services to their arsenal in
addition to the standard (and programmatically clumsy) CGI applications.

-Patrick





"Mario Gianota" <mario.gianota@bookkeeperseye.com>@biojava.org on
04/11/2002 05:09:58 PM

Sent by:  biojava-l-admin@biojava.org


To:   <biojava-l@biojava.org>
cc:

Subject:  Re: [Biojava-l] BioInformatics toolbox.



> This is my first time writing to this list, so I think I should introduce
> myself. My name is Patrick McConnell, and I am a scientific program at
the
[snip]

Wow. These new AI programs are getting _really_ clever !  :-^

Hi Patrick. Your comments and thoughts are pretty much aligned with mine
and
Matt Gundersen's. We're both in favour of a plugin based GUI pipeline
framework. I hadn't thought about the 'service publication and provision'
infrastructure but it is clear that Web Services are one way to solve this
quite neatly.

--Mario

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