[MOBY-dev] [moby] Re: Remora
Mark Wilkinson
markw at illuminae.com
Thu Aug 3 16:31:44 UTC 2006
"The language itself should be considered volatile, any users of it
should join the taverna developers list and monitor it, we do not
support this language for use outside of Taverna."
LOL! Well, Tom, when you build something this useful, you can't expect
people not to use it!
M
On Thu, 2006-08-03 at 18:12 +0200, Sebastien Carrere wrote:
> Hi Mark and Eddie,
>
> I flip this discussion onto the mailing list :-[
>
> The lack of XSCUFL specifications is a real problem for us.
> The only one I have been able to find is a 2 years old one
> (http://www.ebi.ac.uk/~tmo/mygrid/XScuflSpecification.html)
>
> Nevertheless, I can start to develop a Remora/XSCUFL adapter at this
> time, using the template sent by Eddie to deal with secondaryArticles.
>
> By this way, we could provide Remora user the possibility to
> download/upload their workflow in "current" XSCUFL format.
>
> Cordialement,
>
> Sebastien
>
> Ed Kawas a écrit :
> > Hi,
> >
> > I represent secondarys like the following:
> > <s:Parameter s:name="parameterName">parameterValue</s:Parameter>
> >
> > Where 'parameterName' is the articlename for the secondary parameter and the
> > 'parameterValue' is the value.
> >
> > For example:
> > <s:processor name="getUniprotIdentifierByGeneName" workers="10">
> > <s:description>some description</s:description>
> > <s:biomobywsdl>
> >
> > <s:mobyEndpoint>http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl
> > </s:mobyEndpoint>
> > <s:serviceName>getUniprotIdentifierByGeneName</s:serviceName>
> > <s:authorityName>bioinfo.icapture.ubc.ca</s:authorityName>
> > <s:Parameter s:name="genome">human</s:Parameter>
> > </s:biomobywsdl>
> > </s:processor>
> >
> >
> > This is how it is done in Taverna.
> >
> > Eddie
> >
> >> -----Original Message-----
> >> From: Mark Wilkinson [mailto:markw at illuminae.com]
> >> Sent: Wednesday, August 02, 2006 3:36 PM
> >> To: Sebastien Carrere
> >> Cc: GOUZY Jérome; Eddie Kawas
> >> Subject: Re: [moby] Re: [MOBY-dev] Remora
> >>
> >> Hi Sebastien,
> >>
> >> I've spoken with Eddie and he is able to represent
> >> SecondaryArticles in SCUFL, at least for Taverna. By the
> >> sounds of it, SCUFL is relatively undefined (I can't find any
> >> documentation for the language anywhere) and in Taverna
> >> apparently you are allowed to specify your own SCUFL tags,
> >> and declare how they should be parsed, so it's more or less
> >> wide-open to be extended.
> >>
> >> So... we represent Secondary parameters in SCUFL, and they
> >> can be interpreted by Taverna; however since there is no
> >> definition of the SCUFL language anywhere that we can find,
> >> we are certain that (at the
> >> moment) only Taverna can handle these new secondary parameter
> >> tags. My feeling is that, from the perspective of Taverna,
> >> all inputs are identical, so they haven't created different
> >> port types for secondaries vs. primaries as we require for MOBY.
> >>
> >> Eddie will tell you more - I have c.c.'d him this message.
> >>
> >> It's probably a good idea to flip this conversation onto the
> >> mailing list, but I don't want to send your message to the
> >> list without your permission :-) If you want to c.c. the
> >> list with your response that would be great!
> >>
> >> Cheers!
> >>
> >> Mark
> >>
> >>
> >>
> >>
> >> On Wed, 2006-08-02 at 10:21 +0200, Sebastien Carrere wrote:
> >>
> >>> Bonjour Mark,
> >>>
> >>> Remora is not yet SCUFLized.
> >>> When we started our project, the problem with SCUFL is that
> >>>
> >> it did not
> >>
> >>> deal with SecondaryArticles ...
> >>> For us it was a critic.
> >>>
> >>> So, my question is : " is SCUFL deals with
> >>>
> >> moby:SecondaryArticles now ?".
> >>
> >>> If th answer is yes, I can write a parser SCUFL <->
> >>> RemoraWorkflowsDescription.
> >>> If no, maybe I can also write it but with loss of information ...
> >>>
> >>> Sincerely,
> >>>
> >>> Sebastien.
> >>>
> >>> mark wilkinson a écrit :
> >>>
> >>>> Hi Remora developers!
> >>>>
> >>>> I have a quick question for you - before I say this in my
> >>>>
> >> manuscript can you confirm that you are using SCUFL "under
> >> the hood" in Remora? I'm guessing, but I don't know...
> >>
> >>>> The next iteration of gbrowse-moby (available tomorrow!)
> >>>>
> >> generates a SCUFL document while you browse, and I want to
> >> say that this document can then be loaded to Taverna AND
> >> Remora... But I'm not certain of that.
> >>
> >>>> Are any of the other clients using XSCUFL?
> >>>>
> >>>> Cheers!
> >>>>
> >>>> M
> >>>>
> >>>>
> >>>> --
> >>>> Mark Wilkinson
> >>>> ...on the road!
> >>>> _______________________________________________
> >>>> MOBY-dev mailing list
> >>>> MOBY-dev at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>>>
> >>>>
> >>>>
> >> --
> >> Mark Wilkinson
> >> Asst. Professor, Dept. of Medical Genetics University of
> >> British Columbia PI in Bioinformatics, iCAPTURE Centre St.
> >> Paul's Hospital, Rm. 166, 1081 Burrard St.
> >> Vancouver, BC, V6Z 1Y6
> >> tel: 604 682 2344 x62129
> >> fax: 604 806 9274
> >>
> >> "Since the point of a definition is to explain the meaning of
> >> a term to
> >> someone who is unfamiliar with its proper application, the
> >> use of language that doesn't help such a person learn how to
> >> apply the term is pointless. Thus, "happiness is a warm
> >> puppy" may be a lovely thought,
> >> but it is a lousy definition."
> >>
> >> Köhler et al, 2006
> >>
> >>
> >
> >
> >
>
--
Mark Wilkinson
Asst. Professor, Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics, iCAPTURE Centre
St. Paul's Hospital, Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274
"Since the point of a definition is to explain the meaning of a term to
someone who is unfamiliar with its proper application, the use of
language that doesn't help such a person learn how to apply the term is
pointless. Thus, "happiness is a warm puppy" may be a lovely thought,
but it is a lousy definition."
Köhler et al, 2006
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