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

[dcolonn@ncsu.edu]

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
>>
>>
>>
>>
>>
>>
>>
>