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

[Marco Roos]

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.

Regards,
Marco.

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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Marco Roos
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