CCPE

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Workspace for CCPE paper from Microsoft eScience Workshop in Indianapolis

Invitation: 

We are very pleased to let you know that your presentation on 
"/Accelerating Time to Experiment - The myExperiment Approach to Open 
Science/" at the 2008 Microsoft eScience was voted to be one of the 
top papers. As such, we'd like to invite you to participate in a 
special issue of* Concurrency and Computation: Practice and
Experience* by submitting a paper for a special issue entitled 
*/Successes in Furthering Scientific Discovery/*/./ It is our hope 
that you will be willing to submit a 10-12 page paper on the topic you 
presented at the workshop for publication in the journal.

Instructions for authors

Deadline is Tuesday 31st March. I have requested a 1 week extension.

Note paper length is 10-12 pages and the instructions say it should be at least 25% new compared to other pubs, the most recent of which is the paper in the IEEE e-Science 2008 conference in Indianapolis (which is 10 pages single column).

Provisional plan is to base the CPPE paper on the e-Science 2008 paper and add:

  • New material on e-Labs based on what Sean is writing for the whitepaper (Sean)
  • 1 page on David Newman's SPARQL endpoint work (David)
  • Evaluation methodology and reports (Rob, Meik, Yuwei)
  • Microsoft work (Jits)
  • Biocatalogue (Jits)
  • Latest stats and analyses (Dan, Don)

Previous material

  • Indianapolis paper in PDF and Word

Strawperson Structure for discussion

Here is the structure of the eScience 2008 paper: 

1. Introduction 
2. The myExperiment VRE
2.1. myExperiment capabilities
2.1.1 myExperiment capabilities
2.1.2 Social model
2.1.3 Open environment
2.1.4 Actioning research
2.2. Related work
3. Software design
3.1. The entities in myExperiment
3.2. Encapsulated myExperiment Objects
4. Implementation
4.1. System Architecture
4.2. Managed REST API
4.3. Deployment
4.4. Evolution
5. Analysis of usage
6. Conclusion

Carole's proposed structure:

  • Section 1 is introduction
  • In section 2 we introduce myExperiment, briefly present our development methodology, highlight the characteristics of workflows and other forms of methods such as plans and standard operating protocols that influence us and compare our work with other method repositories.
  • In section 3 we describe the social model that myExperiment implements and discuss it in practice as identified by a user study that has shadowed and steered the development of the repository. In particular we show that the content is roughly split into a market and a toolbox; and that sharing is desirable and possible but anonymous reuse is difficult. We compare our social content approach to other content services in science and outside science.
  • In section 4 we show how, by exposing the myExperiment functionality, new interfaces have been built and existing interfaces have incorporated myExperiment functionality, including plug-ins to the Taverna workbench, Facebook applications, an iGoogle gadget-based research dashboard and a Silverlight interface, and Chemistry Electronic Lab Notebooks and ‘blogging the lab’ [ref].
  • In section 5 we discuss how myExperiment is a first step towards a general notion of Research Object, which captures aggregations of objects and also encompasses the other forms of data in myExperiment, and is the part of a greater vision of interoperable e-Laboratories.
  • Section 6 is discussion, conclusions, future work

Notes from meeting

  • Don't be afraid to change terminology for sake of paper
  • e-Labs material to go up front rather than at end
  • "What I did on my holidays" is bad
  • Yuwei has doen recent interviews
  • Possible angle - 'the experiment that is myExperiment'
  • Three top-level messages:
    • sharing methods
    • social curation
    • exchanging metadata between apps (social, collaborative, ROs)
  • Current title (Accelerating Time to Experiment - The myExperiment Approach to Open Science) is bad because we have no evidence that we do acceleration. Yuwei suggests Towards Open Science: The myExperiment Approach
  • Need a related work section - everyone to provide references, DDeR to ask Duncan for assistance
  • Other discussion points:
    • how do you measure success
    • need to complete the feedback loop
    • social capital

Contributions

Carole will be working on the paper on Wednesay 25th March

Co-Authors: DDeR, Carole, Sergejs Aleksejevs, Sean Bechhofer, Jiten Bhagat, Don Cruickshank, Paul Fisher, Duncan Hull, Yuwei Lin, Danius Michaelides, David Newman, Rob Procter, Yuwei Lin, Meik Poschen

From Danius:

From Sean

From David Newman

From Jits

To be provided by Duncan - related work, esp pipeline pilot sharing site

From Rob, Meik and Yuwei

Drafts

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