Meetings & Conferences

Integrative Bioinformatics 2007, Day 2: myExperiment, Goble Keynote

Other than where specified, these are my notes from the IB07 Conference, and not expressions of opinion. Any errors are probably just due to my
own misunderstanding. 🙂

Carole compares it to mySpace. First, an introduction to workflows, where all of the standard bioinformatics statements are made: workflows are fantastic, but laborious, this is the era of Service Oriented Architecture, trying to make repetitive & mundane stuff easier. This leads nicely into a mention of Taverna, a "workflow workbench". Taverna 2 is being built now. They are getting 15,000 downloads per month, when in a good month. Then Carole spent a slide talking about the phrase "In the Cloud", which is a descriptor for independent third-party applications, tools and software. Taverna was designed for people who have little access to resources. She then described a few good examples of how Taverna could be used. Carole suggests to do more in Taverna rather than just workflows, for example SBML models or lab protocols. Then she gave some reasons why using experimental data standards are a good idea. Carole also mentioned that workflows (rather than just data) could be included in peer-reviewed articles.

myExperiment is meant to make it easy for scientists to pool information and data, and is meant to look like a social networking site. This includes collaborative social bookmarking and content sharing. They want to leverage and serve the long tail end of the "cloud". They'll use it as a gateway to other publishing environments and a platform for launching workflows. it is an "Open Archives" Initiative. Want to be able to launch and run workflows via Taverna via myExperiment. Also wants to encourage workflow "mashup" and publishing.

Here's where my opinion goes: By halfway through the talk, she hadn't said what she meant by myExperiment, other than that it is meant to be the mySpace for bioinformatics. However, she did spend at least the last 15 minutes discussing it. Further, while she talks about the usefulness of experimental data standards in relation to adding lab protocols to Taverna, she mentioned it without ever relating to FuGE. As FuGE is being published in Nature Biotech and is being touted as a possible standard experimental data exchange format, it seems an odd omission. (Especially as one of the main developers of FuGE, until recently, also worked at University of Manchester.) In conclusion, while very interesting, not as "meaty" as I'd like. A good talk overall, and I think I'll sign up for myExperiment!

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By Allyson Lister

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