[kepler-dev] Re: [SDM-SPA] Latest SPA Release (updated)
Vouk
vouk at ncsu.edu
Tue Mar 9 06:28:39 PST 2004
:-) :-)
ma
Bertram Ludaescher wrote:
>Any translation services anyone?
>
>here is my WSDL (in short syntax)
>
>web service = translation
>operation = german_to_english
>protocol = email
>host = ludaesch at sdsc.edu
>
>
>;-)
>
>Bertram
>
>
>
>>>>>>"V" == Vouk <vouk at ncsu.edu> writes:
>>>>>>
>>>>>>
>V>
>V> Dan,
>V> I think Bertam would qualify re German
>V> :-)
>V> Mladen
>V>
>V> Ilkay Altintas wrote:
>V>
>
>
>>>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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>V> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
>V> <html>
>V> <head>
>V> <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1">
>V> <title></title>
>V> </head>
>V> <body text="#000000" bgcolor="#ffffff">
>V> Dan,<br>
>V> I think Bertam would qualify re German <br>
>V> :-)<br>
>V> Mladen<br>
>V> <br>
>V> Ilkay Altintas wrote:<br>
>V> <blockquote type="cite"
>V> cite="midDLEJICODOMAOLNEPHCLEAENPCAAA.altintas at sdsc.edu">
>V> <pre wrap="">Hi Dan,
>V>
>V> This sounds great.
>V>
>V> I think we can directly use it with the generic web service actor as it
>V> is available as a soap service. Developing a wrapper for it might be
>V> unnecessary.
>V>
>V> I will be happy to try it if you could provide me with the operation
>V> name and inputs for it.
>V>
>V> What I saw from wsdl is that this web service uses almost all soap
>V> types. Currently the ws actor handles basic xsd types and some array
>V> types. It should be possible to use it as is with the extension to the
>V> web service actor for the map array.
>V>
>V> Ilkay
>V>
>V>
>V>
>V> -----Original Message-----
>V> From: <a class="moz-txt-link-abbreviated" href="mailto:sdm-dev-admin at sdsc.edu">sdm-dev-admin at sdsc.edu</a> [<a class="moz-txt-link-freetext" href="mailto:sdm-dev-admin at sdsc.edu">mailto:sdm-dev-admin at sdsc.edu</a>]On Behalf Of
>V> <a class="moz-txt-link-abbreviated" href="mailto:dcolonn at ncsu.edu">dcolonn at ncsu.edu</a>
>V> Sent: Monday, March 08, 2004 10:10 AM
>V> To: <a class="moz-txt-link-abbreviated" href="mailto:buttler1 at llnl.gov">buttler1 at llnl.gov</a>
>V> Cc: Daniel Colonnese; <a class="moz-txt-link-abbreviated" href="mailto:sdm-dev at sdsc.edu">sdm-dev at sdsc.edu</a>; <a class="moz-txt-link-abbreviated" href="mailto:sdm at renoir.csc.ncsu.edu">sdm at renoir.csc.ncsu.edu</a>;
>V> <a class="moz-txt-link-abbreviated" href="mailto:kepler-dev at ecoinformatics.org">kepler-dev at ecoinformatics.org</a>; <a class="moz-txt-link-abbreviated" href="mailto:xin2 at llnl.gov">xin2 at llnl.gov</a>
>V> Subject: Re: [SDM-SPA] Latest SPA Release (updated)
>V>
>V>
>V>
>V> Soaplab is hosting a WSDL service for tfscan. The SoapLab developer,
>V> Martin Senger, just updated the TRANSFAC data on his end.
>V>
>V> I was the first on to use this service, so we worked out a few minor
>V> problems; now it's a working web service.
>V>
>V> The tfscan WSDL is at:
>V>
>V> <a class="moz-txt-link-freetext" href="http://industry.ebi.ac.uk/soaplab/wsdl/nucleic_transcription__tfscan.wsdl">http://industry.ebi.ac.uk/soaplab/wsdl/nucleic_transcription__tfscan.wsdl</a>
>V>
>V>
>V> Since you think it is a possible replacement for the old service, I'll
>V> get to work on wrapping a ptolemy actor for this tfscan.
>V>
>V> And I'll keep my eyes open for a computer scientist who's fluent in German.
>V>
>V>
>V> -Dan
>V>
>V>
>V> </pre>
>V> <blockquote type="cite">
>V> <pre wrap="">Hi Daniel,
>V>
>V> I believe that this would be a suitable replacement for Transfac. My
>V> understanding is that to use this tool, you need to download the data
>V> directly from the transfac site. Did you have a chance to check that
>V> the transfac FTP site is still available? When I tried, the response
>V> just hung. If we could set up the service locally (either as an
>V> executable to include in a distribution, or as a Web service) it would
>V> seem to have some value. Perhaps I misunderstood your intent though; did
>V> you mean to say that they (the developers of EMBOSS) would be willing to
>V> host a WSDL service for the world to access?
>V>
>V> Many of the services provided by the EMBOSS tool suite that includes
>V> tfscan would make useful additions to the bioinformatics side of
>V> Kepler. Once we get the system set up here for Matt, we will explore
>V> what would be of value to him.
>V>
>V> As a side note, it turns out that Matt Coleman has a seat license for
>V> genomatix.de, which includes a transfac web interface. So, it should be
>V> possible to develop an actor that uses this information. Perhaps one of
>V> us could contact this company directly to see if they would be willing
>V> to make their services available as a Web service for licensed users.
>V> This should save us some implementation/screen scraping effort and
>V> sounds like a reasonable approach for the company. Any volunteers?
>V>
>V> Two last pieces of information from my meeting with Matt today:
>V> He is going to be on travel for most of March. We will meet with him
>V> again on the 26th to show him the workflow system.
>V> Also, in the future, he would be interested in joining our monthly SPA
>V> meeting, or perhaps other ad hoc meetings, to discuss the state of the
>V> system and what could be done to best meet his needs.
>V>
>V> Dave
>V>
>V> Daniel Colonnese wrote:
>V>
>V> </pre>
>V> <blockquote type="cite">
>V> <pre wrap="">Dear All,
>V>
>V> I have found a potential TRANSFAC service. It is a free service offered
>V> by European Bioinformatics Institute. I have been in touch with the
>V> service author and they are cooperative and willing to work us.
>V>
>V> Before I turn this into a Ptolemy actor, I need some help to determine
>V> whether this service is suitable replacement for the previous transfac
>V> service.
>V>
>V> The service is an interface to the TFSCAN program. Here is a
>V> description of that program
>V>
>V> <a class="moz-txt-link-freetext" href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/tfscan.html">http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/tfscan.html</a>
>V>
>V> Let's schedule a meeting for Monday or Tuesday where Matt can help us
>V> decide.
>V>
>V> Please let me know,
>V>
>V> Dan
>V>
>V>
>V>
>V>
>V>
>V>
>V>
>V> </pre>
>V> </blockquote>
>V> </blockquote>
>V> <pre wrap=""><!---->
>V> </pre>
>V> </blockquote>
>V> </body>
>V> </html>
>
>
>
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