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

From: Marco Roos <M.Roos1@uva.nl>
Date: Wed, 20 Aug 2008 12:11:36 +0200
Message-ID: <48ABEDD8.6090500@uva.nl>
To: Matthias Samwald <samwald@gmx.at>
CC: public-semweb-lifesci <public-semweb-lifesci@w3.org>, mygrid@listserv.manchester.ac.uk, myexperiment-discuss@nongnu.org
Hi Matthias,

Interesting remarks. You'll be interested to know that 'webifying' 
workflows (in various ways) is one of the prime interests of people at 
myGrid and myExperiment. My personal opinion, a bit from a biologist's 
perspective, is that we should be careful not to loose some aspects of 
workflows in our enthusiasm about Web 2.0 and wiki approaches. One of my 
main reasons for liking workflows is that they represent a publishable 
and reproducible 'protocol' similar to a wet laboratory protocol. This 
should not be volatile in any way, which Web2.0 or wiki approaches 
easily can be.

NB Soon, also web services can be published via 'BioCatalogue', which is 
closely associated with myExperiment and with a semantic annotation 
model behind.


Matthias Samwald wrote:
> 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

Marco Roos <http://home.medewerker.uva.nl/m.roos1>
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Received on Thursday, 21 August 2008 02:07:56 UTC

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