[kepler-dev] Re: [SDM-SPA] Latest SPA Release (updated)

[Vouk]

Dan,
I think Bertam would qualify re German
:-)
Mladen

Ilkay Altintas wrote:

>Hi Dan,
>
>This sounds great.
>
>I think we can directly use it with the generic web service actor as it
>is available as a soap service. Developing a wrapper for it might be
>unnecessary.
>
>I will be happy to try it if you could provide me with the operation 
>name and inputs for it.
>
>What I saw from wsdl is that this web service uses almost all soap 
>types. Currently the ws actor handles basic xsd types and some array 
>types. It should be possible to use it as is with the extension to the 
>web service actor for the map array.
>
>Ilkay
>
>
>
>-----Original Message-----
>From: sdm-dev-admin at sdsc.edu [mailto:sdm-dev-admin at sdsc.edu]On Behalf Of
>dcolonn at ncsu.edu
>Sent: Monday, March 08, 2004 10:10 AM
>To: buttler1 at llnl.gov
>Cc: Daniel Colonnese; sdm-dev at sdsc.edu; sdm at renoir.csc.ncsu.edu;
>kepler-dev at ecoinformatics.org; xin2 at llnl.gov
>Subject: Re: [SDM-SPA] Latest SPA Release (updated)
>
>
>
>Soaplab is hosting a WSDL service for tfscan.  The SoapLab developer,
>Martin Senger, just updated the TRANSFAC data on his end.
>
>I was the first on to use this service, so we worked out a few minor
>problems; now it's a working web service.
>
>The tfscan WSDL is at:
>
>http://industry.ebi.ac.uk/soaplab/wsdl/nucleic_transcription__tfscan.wsdl
>
>
>Since you think it is a possible replacement for the old service,  I'll
>get to work on wrapping a ptolemy actor for this tfscan.
>
>And I'll keep my eyes open for a computer scientist who's fluent in German.
>
>
>-Dan
>
>
>  
>
>>Hi Daniel,
>>
>>I believe that this would be a suitable replacement for Transfac.  My
>>understanding is that to use this tool, you need to download the data
>>directly from the transfac site.  Did you have a chance to check that
>>the transfac FTP site is still available?  When I tried, the response
>>just hung.  If we could set up the service locally (either as an
>>executable to include in a distribution, or as a Web service) it would
>>seem to have some value. Perhaps I misunderstood your intent though; did
>>you mean to say that they (the developers of EMBOSS) would be willing to
>>host a WSDL service for the world to access?
>>
>>Many of the services provided by the EMBOSS tool suite that includes
>>tfscan would make useful additions to the bioinformatics side of
>>Kepler.  Once we get the system set up here for Matt, we will explore
>>what would be of value to him.
>>
>>As a side note, it turns out that Matt Coleman has a seat license for
>>genomatix.de, which includes a transfac web interface.  So, it should be
>>possible to develop an actor that uses this information.  Perhaps one of
>>us could contact this company directly to see if they would be willing
>>to make their services available as a Web service for licensed users.
>>This should save us some implementation/screen scraping effort and
>>sounds like a reasonable approach for the company. Any volunteers?
>>
>>Two last pieces of information from my meeting with Matt today:
>>He is going to be on travel for most of March.  We will meet with him
>>again on the 26th to show him the workflow system.
>>Also, in the future, he would be interested in joining our monthly SPA
>>meeting, or perhaps other ad hoc meetings, to discuss the state of the
>>system and what could be done to best meet his needs.
>>
>>Dave
>>
>>Daniel Colonnese wrote:
>>
>>    
>>
>>>Dear All,
>>>
>>>I have found a potential TRANSFAC service. It is a free service offered
>>>by European Bioinformatics Institute.  I have been in touch with the
>>>service author and they are cooperative and willing to work us.
>>>
>>>Before I turn this into a Ptolemy actor, I need some help to determine
>>>whether this service is suitable replacement for the previous transfac
>>>service.
>>>
>>>The service is an interface to the TFSCAN program.  Here is a
>>>description of that program
>>>
>>>http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/tfscan.html
>>>
>>>Let's schedule a meeting for Monday or Tuesday where Matt can help us
>>>decide.
>>>
>>>Please let me know,
>>>
>>>Dan
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>      
>>>
>
>  
>
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