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

[David De Roure]

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. :-)

Thanks

-- 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

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


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