[MOBY-dev] Problems with Biomoby services in Taverna 1.2

[mark wilkinson]

I guess it doesn't make you feel any better if I say "yes, we know..."

:-)

M

-----Original Message-----
From: Rebecca Ernst <rebecca.ernst at gsf.de>
Date: Thu, 07 Jul 2005 15:45:35 
To:edward.kawas at gmail.com, markw at illuminae.com,       Martin Senger <senger at ebi.ac.uk>, Dirk Haase <d.haase at gsf.de>,       Heiko Schoof <schoof at mpiz-koeln.mpg.de>
Cc:mobydev <moby-dev at biomoby.org>
Subject: [MOBY-dev] Problems with Biomoby services in Taverna 1.2

Hi Eddie, Mark, Martin, Heiko, etc.!

we recently downloaded Taverna 1.2 and found that basically no workflow 
is functional anymore.
After a look into it we found that there was one major change from 
Taverna 1.1 to Taverna 1.2. which is that obviously Taverna 1.2 passes 
collections on to the next services whereas Taverna 1.1 took a 
collection, splitted it into singles and passed the singles to the next 
service.

There are very many services around that give back collections and very 
few that operate on those.
For the moment this means that most of the Biomoby services are not 
compatible to each other even if they give back the same class of object!
(e.g. using the service getAGILocusCodes you'll receive a collection of 
AGI Codes and if you pass this on to the service 
getArabidopsisProteinSequences it'll fail as this service takes simple 
inputs only )

As far as we see there would only be one solution for that - we would 
need a new moby widget 'splitCollectionsIntoSingles' which still would 
be 'ugly' as you would also need to know what the first service gives 
back and what the next service needs...
Any other ideas / suggestions?


Best,
Rebecca

-- 
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

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--
Mark Wilkinson
...on the road!