[Biojava-l] BioInformatics toolbox.

[Chris Mungall]

On Fri, 12 Apr 2002 "Patrick McConnell" <MCCon012@mc.duke.edu> wrote:

> 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
> Duke Bioinformatics Shared Resource.  We work on a variety of things, but I
> am currently working on a flexible java framework for high-throughput batch
> computing.
>
> In reference to the Bioinforamtics toolbox thread, I do not see complex
> data types as an issue.  I have (for some time now), toyed with the idea of
> setting up a GUI pipeline like this for bioinformatics web-services. The
> way I see it is that one should be able to view the the complex format of
> the output of one node (i.e. nested java interfaces or in my case an XML
> schema), and draw pipes from particular parts of the data (like hsp
> sequence in the blast example) to another node.  You could also install
> filters between 'actions' that sort data based on a particular field and
> criteria.  In addition to actions and data (actions and pipes), there needs
> to be a special action that is an end-point that knows how to do something
> intelligent with the data like display it or save it to a file.
>
> Personally, I see web-services as an ideal environment for this sort of
> toolbox because web services have well defined inputs and outputs (via a
> WSDL file).  Has anyone heard of an application of this sort as applied to
> web-services?  Assuming no one has (and I am able to find some free time),
> I plan to pursue this idea.  Would defining java interfaces for
> web-services fall under the biojava project?  What about implementations?
> Has anyone attempted to define interfaces for complex data such as blast or
> (even worse) Medline articles?

There's a tool called Magik which seems to be pretty good at doing this
kind of thing, you can get the beta from:

http://www.tekadence.com

It makes things like wrapping XEMBL in a GUI or piping data between
webservices pretty easy. You have full control via scripting so you can do
any kind of filtering and complex piping you like, at the same time it's
simple enough to use that someone's who's never coded before could easily
knock up a user interface.

> -Patrick