[moby] Re: [MOBY-l] Taverna & MOBY services

[Mark Wilkinson]

yeah, Taverna rocks!  You do need to create an input object, as you
suggest.  There's a "local Java Widget" called "create moby data" in the
available widgets/services panel that will do that for you.  you
similarly need to unpack it at the end using the "parse moby data"
widget.

Just this morning I was chatting with Martin about creating a more
intelligent set of MOBY widgets in Taverna that could fully unpack a
MOBY object into its sub-objects, and/or into plain text to pass into
other services.  We're going to start working on this shortly!

M


On Thu, 2005-01-20 at 14:42, Twigger Simon wrote:
> Michael,
> 
> I hadnt seen those, I also didnt read further into the taverna docs and 
> there does seem to be a bunch of MOBY info and examples so I think I 
> need to RTFM some more and that will certainly help!
> 
> Thanks for pointing out the examples.
> 
> Simon.
> 
> 
> On Jan 20, 2005, at 4:36 PM, Michael Jensen wrote:
> 
> > Did you try the Dragon DB Annotated Images example workflow that comes
> > with the Taverna examples? That one works well and can be used to help
> > you figure out others.
> >
> > -Michael
> >
> >
> > On Thu, 20 Jan 2005 16:30:51 -0600, Twigger Simon <simont at mcw.edu> 
> > wrote:
> >> Hi there,
> >>
> >> Im trying to get a quick MOBY service up and running using Taverna and
> >> its not working quite as I would like.
> >>
> >> I deregistered my old keywordToGene service, moved it to a new 
> >> machine,
> >> updated the MOBY code to 0.8 and reregistered the service. Ive checked
> >> it out using the gbrowse client and it seems to behave appropriately.
> >> Querying with a global_keyword seed text of A2m brings back the 
> >> correct
> >> information. However, if I set something up in Taverna to send the 
> >> same
> >> text to the service it always fails, the stack trace in the terminal
> >> seems to indicate a perl problem with an error thrown by XML::Parser
> >>
> >> I noticed from Mark's last presentation that the taverna workflow 
> >> shown
> >> there seems to have two input objects (blue triangles) - presumably a
> >> namespace and an ID that are going into a create_moby_data 'box'. Im
> >> wondering if there is more to using MOBY via Taverna than a simple 
> >> text
> >> input object and that is my problem, or if its a more fundamental
> >> service problem.
> >>
> >> I would love to get things working with Taverna so any thoughts would
> >> be most appreciated!
> >>
> >> Cheers,
> >>
> >>        Simon.
> >>
> >> --
> >>
> >> Simon N. Twigger, Ph.D.
> >> Assistant Professor, Department of Physiology
> >> Medical College of Wisconsin
> >> 8701 Watertown Plank Road,
> >> Milwaukee, WI, USA
> >> tel: 414-456-8802
> >> fax: 414-456-6595
> >> AIM/iChat: simontatmcw
> >>
> >> _______________________________________________
> >> moby-l mailing list
> >> moby-l at biomoby.org
> >> http://biomoby.org/mailman/listinfo/moby-l
> >>
> >>
> >
> >
> --
> 
> Simon N. Twigger, Ph.D.
> Assistant Professor, Department of Physiology
> Medical College of Wisconsin
> 8701 Watertown Plank Road,
> Milwaukee, WI, USA
> tel: 414-456-8802
> fax: 414-456-6595
> AIM/iChat: simontatmcw
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 
Mark Wilkinson
Assistant Professor (Bioinformatics)
Dept. Medical Genetics, UBC, Canada