Hello Paul
Just to follow up on Antoon’s comments, the myExperiment
codebase is designed to share any “contributable type”, and
currently we’ve focused on Taverna workflows and on packs. We are
developing support for a variety of other scientific artefacts including, for
example, experimental plans used in the context of electronic lab notebooks in chemistry,
and also statistical models. Kepler is very much part of the myExperiment
picture, and we have enjoyed several fruitful conversations with Bertram about
this. In our workplan we are working now with Triana and will be coming to
Kepler in the period starting this fall.
We follow the Web 2 design principle of cooperation – we’ve
put a lot of work into the myExperiment API so that myExperiment functionality can
be brought through in other interfaces (eg google gadgets, wikis, the Taverna
plugin). It would be great to discuss how we might do some things together.
We’re currently planning some integration work with Galaxy, for example.
Let’s look at some options and see what we can do.
Many thanks
-- Dave
From:
address@hidden
[mailto:address@hidden On
Behalf Of Paul Allen
Sent: 23 July 2008 20:12
To: Antoon Goderis
Cc: address@hidden
Subject: Re: [Myexperiment-discuss] non-taverna workflows
I am happy to hear about
a roadmap that involves support for Kepler workflows in MyExperiment. There are
several efforts already underway or in the planning stages for a web front-end
for dealing with Kepler workflows. I think that Hydrant (https://www.hpc.jcu.edu.au/hydrant/)
is the only one that is public.
I hope that those of us working on Kepler-based web sites can find ways to
collaborate and leverage each other's efforts instead of directly competing.
Antoon Goderis wrote:
Hi Jan,
On Wed, 23 Jul 2008, Jan Aerts wrote:
All,
Is it possible/advised to put non-taverna workflows on MyExperiment?
You can do it by uploading them as a File. You get all the usual goodies
but they don't show up under the workflows tab. At the moment workflows,
when uploaded, have to parse as a valid Taverna workflow, because an
image is rendered and documentation extracted based on the Taverna format.
It's definitely within the remit of the project to have different types
of workflow on myExperiment - so the current situation is temporary and a
matter of resource. Explicit support for Triana workflows and Kepler
workflows (two other environments) are next on the to do list, for
instance.
Antoon
> 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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