[MOBY-dev] moby grapgs updated

[Rebecca Ernst]

Hi Martin!

that's another nice feature!
the problem I have at the moment is that I can't squeeze any graph out 
of the tool- I always get Apache errors.
(I tried all graphs and none worked. the new one is timing out)

cheers,
rebecca

Martin Senger wrote:

>Hi all,
>   I have updated moby graphs (and also few other things in jMoby - see
>docs/ChangeLog if you wish).
>   The main change is that now there is a possibility to draw a path 
>between two selected data types, and that the result can be expressed as a 
>workflow definition that can be consequently loaded to Taverna and 
>hopefully run.
>   I expect (at least) two things to happen soon:
>
>   * You will/may find that the caching in graph servlet is not yet
>perfect. I need some time to make it more robust, but I will be travelling 
>now - so if you find problems, just try the same again, and blame me...
>
>   * Having now generated workflow definitions, more people will try it in 
>Taverna. This is perfect, it's an ultimate goal. But I again need more 
>time to improve moby stuf in Taverna, again make it more robust. And I 
>will - so again try to send your comments, suggestion and bug reports, and 
>blame me...
>
>   Also I hope that I fixed few things that Frank was reporting:
>  
>
>>1. MOBY allows multiple whitespace-separated words in the object
>>ontology, but when they are graphed, they show up as separate nodes.
>>This is probably just a matter of enclosing the node names in double
>>quotes for GraphViz.
>>    
>>
>
>  
>
>>2. The first time I try to draw the object ontology, after reloading the
>>registry, I get an error from Tomcat like this:
>>    
>>
>
>   Finally, here is the URL of the new moby graphs (actually it is the 
>same as before, you can still get there from the main BioMoby page):
>
>http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs
>
>   With regards,
>   Martin
>
>  
>

-- 
Rebecca Ernst
MIPS, Inst. for Bioinformatics
GSF Research Center for Environment and Health
Ingolstaedter Landstr. 1
85764 Neuherberg
fon: +49 89 3187 3583
email: Rebecca.Ernst at gsf.de