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

[Bertram Ludaescher]

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>