RE: [Myexperiment-discuss] non-taverna workflows

[Linde, A.E.]

I suspect the answer is that, under Workflows, only Taverna workflows can be 
stored since the files are interpreted by the code to extract relevant 
information.

But I'd like to widen this into a suggestion. That is that, instead of 
distinguishing workflows from other types of scientific objects of interest 
that might be stored, that myExp make it possible to store any type of object 
as a distinct named type of entity. I know that non-workflows might be stored 
as Files but my proposal is that myExp remove the specific ability to store 
workflows and abstract that capability to one that permits the storage of any 
type of named entity: those entities to be identified at installation time so 
that myExp can be customised for different scientific enterprises.

The way it might work is that, at deployment time, the site owners would 
identify in some config file, the entities that would be 'named'. Along with 
each entity, would be the fields to be stored relevant to each entity. And then 
plugin code is provided for each entity which takes the uploaded file and 
decodes it to provide the stored fields. This could include the type of stuff 
embedded in each workflow file or generated on the fly. Finally, the config 
supplies a spec (xform?) for the layout of the named entity in each way that it 
might be displayed.

This generic capability could all be provided under the single current workflow 
tab or, maybe better, a separate tab is created for each such named entity.

In the case of Astronomy, we'd stick with Taverna-type workflows, supplemented 
perhaps with more derived information from the global registries, but would add 
another tab for Queries.

I'd been meaning to suggest this for a while but thought this post a good 
opportunity.

Cheers,
Tony.

________________________________________
From: address@hidden address@hidden On Behalf Of Jan Aerts address@hidden
Sent: 23 July 2008 14:40
To: address@hidden
Subject: [Myexperiment-discuss] non-taverna workflows

All,

Is it possible/advised to put non-taverna workflows on MyExperiment?
Michael Barton has blogged about using rakefiles (the ruby equivalent
of makefiles) on
http://www.bioinformaticszen.com/2008/05/organised-bioinformatics-experiments/.
I have used that approach a lot and believe it is a very good
alternative for doing scientific workflows where it is impossible or
not advisable to use webservices for the steps of the process.

Michael has put one of his workflows online on github:
http://github.com/michaelbarton/cost_in_evolution

Or is MyExperiment.org too much tied in with Taverna?

jan. (saaientist.blogspot.com)


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