[Biojava-l] library for running blast and formatdb]

[Tom Oinn]

Patrick McConnell wrote:

> Forwarded below is another stab at the problem that EBI has made.  After
> just glancing at the docs, it looks pretty good.  And, the developer on the
> project (Martin Senger) appears dedicated to moving his code to BioPerl and
> BioJava.  So, that sounds good to me.  Martin: please take a look at my
> implementation and see if there is anything that you like : - )

Following up from that, I have code in my interface builder that talks 
to Martin's soaplab system, anyone curious could take a look at 
http://www.ebi.ac.uk/collab/mygrid/service1/talisman and click on the 
'emboss tutorial workflow' demo application. Soaplab has turned out to 
be remarkably easy to use, generally about five or six lines of code on 
the client side (admittedly Talisman's soaplab client code is longer, 
see 
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/talisman/talisman1.4/src/org/embl/ebi/escience/talisman/action/CallSoapLab.java?rev=1.5&content-type=text/vnd.viewcvs-markup) 
, obviously we're pushing it pretty heavily as part of this MyGrid 
project. It's maybe worth pointing out that although we're using Soaplab 
to access the EMBOSS toolset, it can (and is) accessing other systems.

Ciao!

Tom