[MOBY] RE: [MOBY-l] Activity

[Mark Wilkinson]

Hey great!  If you have time/desire it would be wonderful to have a tool
like this.  I was thinking along the lines of the kinds of tools that
visualize protein-protein interactions, since this is a similar type of
problem.... but if you are thinking of another way to visualize the
graphs please suggest it!  

As I say, I wont have time to think about this until at least January,
so it's an open project for anyone with the enthusiasm.

M

On Tue, 2003-08-19 at 09:37, Vijay Narayanasamy wrote:
> Hi,
> 
> Regarding visualization I guess we can use "Graph Visualization" (Nodes and
> Edges). After the database dump we need to have some script that extracts
> all pairs of connected nodes. Once we have this we can feed that data as
> parameter for Graph Visualization Applet. I even guess we can apply
> transitive closure algorithm on this graph to decide the gaps. I have done
> some work using graph visualization in the past.
> 
> Vijay
> 
> -----Original Message-----
> From: Mark Wilkinson [mailto:markw at illuminae.com] 
> Sent: Monday, August 18, 2003 7:15 PM
> To: mobyl
> Subject: [MOBY-l] Activity
> 
> Hi all, 
> 
> NEWS:  The object types text/plain, text/html, text/xml, ... and all
> others that had a '/' character in them have been renamed to text-plain,
> text-html, etc.  I designed the objects in an RDF design tool, and then
> exported stuff to the database, but never considered what would happen
> when these names were serialized into XML ('/' isn't a valid character
> in an element name, for obvious reasons  :-) )  So, I had to go and
> change the names.  Thanks to Vijay for spotting this error.  I know that
> this change wont affect anyone because if anyone had been using these
> objects your services would not have crashed immediately ;-)
> 
> 
> Well, MOBY Central survived the move to mod_perl but my services did
> not.  I just fixed them - the various sequence retrieval, blast, blast
> parsing, and image retrieval services are back up and running.
> 
> Rebecca has asked for a "visualization tool" of sorts that will show the
> possible connections between all extant services so that we can easily
> see the "gaps" that need to be filled and work on those preferentially.
> Does anyone have the time/motivation to work on this?  I certainly wont
> get around to it for a while, and it is a non-trivial problem (beyond
> just making a database dump to the screen and letting the user figure it
> out for themselves...), but I agree that it is worth doing!  I even have
> funding to pay for a student to work on things like this for a few
> months if there are any takers...  :-)  :-)
> 
> Anyway, that's the news for the evening.
> 
> Cheers!
> 
> Mark
-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae