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

[David Buttler]

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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