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RE: [Myexperiment-discuss] Re: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

From: David De Roure <dder@ecs.soton.ac.uk>
Date: Wed, 20 Aug 2008 12:44:46 +0100
To: Matthias Samwald <samwald@gmx.at>
CC: "myexperiment-discuss@nongnu.org" <myexperiment-discuss@nongnu.org>, public-semweb-lifesci <public-semweb-lifesci@w3.org>, "mygrid@listserv.manchester.ac.uk" <mygrid@listserv.manchester.ac.uk>, Marco Roos <M.Roos1@uva.nl>
Message-ID: <C432A473C841FD4A828D556F893891E9152705602D@exchange3.ecs.soton.ac.uk>

Hi Matthias

Just a quick response as director of myExperiment. What you describe - which I see as even more collaborative editing/authoring of workflows - is very interesting and could certainly fit well with myExperiment. We'd be really pleased to work with anyone interested in developing this sort of interface.  A web-based workflow editor (like the one in Galaxy, which we're looking at just now) could certainly be used with it. One thing that's come through clearly in our user engagements is that there's a real demand for a completely web-based workflow authoring and enactment environment, and I know this is something that interests the Taverna, Triana and Kepler teams.

When you look at myExperiment.org you see the social sharing aspects - myExperiment as a social networking site for scientists, where workflows are just one of the things that can be shared.  But it's more than that because it's also a virtual research environment i.e. it directly supports the scientist conducting research, and we've made the myExperiment functionality open so that it can be adapted into the scientist's work environment - we've made it easy to build new interfaces that make use of myExperiment functionality, and to interwork with other tools (e.g. myExperiment data is available in RDF and we're using the emerging Object Reuse and Exchange standard). We have a growing number of people working with us to build new interfaces (including wikis and Facebook).  A case in point is the myExperiment plugin for Taverna, so that people using Taverna to author their workflows have access to myExperiment functionality.

So, volunteers to work with us on web-based workflow editors are welcome. :-)


-- Dave

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

Matthias Samwald
DERI Galway, Ireland // Semantic Web Company, Vienna

Marco Roos
Adaptive Information Disclosure
Faculty of Science
University of Amsterdam
Kruislaan 403, room F1.02
1098 SJ Amsterdam
tel. +31 (0) 20 525 7522
Social communities:
Professional: LinkedIn, myExperiment  and LifeScience@IvI groups on facebook
Personal: Hyves
Received on Wednesday, 20 August 2008 11:46:03 UTC

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