[MOBY-dev] [moby] Re: Remora

[Sebastien Carrere]

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
>>
>>     
>
>
>   

-- 
__________________________________________________________

Sebastien CARRERE                        LIPM (INRA-CNRS)
                      B.P.52627 -- 31326 CASTANET TOLOSAN
tel:(33) 5-61-28-53-29
fax:(33) 5-61-28-50-61