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Re: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

From: Carole Goble <carole.goble@manchester.ac.uk>
Date: Thu, 28 Aug 2008 14:08:56 +0100
Message-ID: <48B6A368.4000305@manchester.ac.uk>
To: Matthias Samwald <samwald@gmx.at>
CC: public-semweb-lifesci <public-semweb-lifesci@w3.org>, carole goble <cag@cs.man.ac.uk>


sorry for the delayed response -- been on a Greek Island for 3 weeks.

er....myExperiment isn't a wiki. Its a Web 2.0 collaborative environment 
built on top of Ruby on Rails.

We have plans to edit workflows through a web interface BUT this is very 
limited -- frankly, workflows are programs, and programs need 
development environments unless you are doing limited and constrained 
editing. Lets not be naive here.

We have entered into discussions with Galaxy, for example, to 
collaborate on such a venture, and we have also promoted work such as 
SeaHawke, which builds Taverna workflows through browsing Moby services.

Moreover myExperiment supports any workflow system - Triana is our next, 
Trident is to be demoed for the e-Science conference, and Kepler, BPEL 
and Pipeline Pilot are in the works. How would you edit all these quite 
different workflows in a general wiki? They are all very different, with 
sophisticated clients to support the workflow design and development.

myExperiment is a piece of the workflow e-Science universe as a sharing 
environment and a repository of many workflows, and also as a platform 
for launching workflows, particularly when set up as an in-house 
enterprise solution.

I did tell Lincoln this :-) 

By the way, I also told Lincoln about HCLS too!!


> Kei Cheung wrote:
>> Also, it's interesting to see scientific workflows can be published 
>> via Wiki (e.g., myExperiment).
> But as far as I know, myExperiment does not allow editing the actual 
> workflows online, you can only upload and visualize workflow files 
> that have been created on the client-side. I guess that still poses a 
> significant hindrance to realizing the 'anyone can edit' philosophy of 
> classic wikis. In this regard, fully server-sided systems such as the 
> well known Yahoo Pipes or the quickly maturing Semantic Web Pipes [1] 
> might be the way to go.
> Regarding the article, it will probably seem a bit puzzling to many 
> people on this mailing list that Lincoln Stein writes
> "To my knowledge, there is currently only one project that aims to 
> bring the pure semantic web to biomedical research. That project is 
> the Simple Semantic Web Architecture and Protocol (SSWAP30)"
> It's nice that Nature allows the community to add descriptions about 
> our various projects on the wiki page associated with the article [2]; 
> unfortunately, though, most readers of the original article will 
> probably not have a look at that wiki.
> [1] http://pipes.deri.org/
> [2] http://nrgwiki.nature.com/cyberinfrastructureforbiology/show/HomePage
> Cheers,
> Matthias Samwald
> DERI Galway, Ireland // Semantic Web Company, Vienna
Received on Thursday, 28 August 2008 13:09:32 UTC

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