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Towards Open Science: The myExperiment approach

De Roure, D., Goble, C., Aleksejevs, S., Bechhofer, S., Bhagat, J., Cruickshank, D., Fisher, P., Hull, D., Michaelides, D., Newman, D., Procter, R., Lin, Y. and Poschen, M. (2009) Towards Open Science: The myExperiment approach. Concurrency and Computation: Practice and Experience . (Submitted)

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Abstract

By making research content more reusable, and providing a social infrastructure which facilitates sharing, the human aspects of the scholarly knowledge cycle may be accelerated and ‘time-to-discovery’ reduced. We propose that the key to this is the sharing of methods and processes. We present myExperiment, a social web site for discovering, sharing and curating Scientific Workflows and experiment plans, and describe how myExperiment facilitates the management and sharing of research workflows, supports a social model for content curation tailored to the researcher and community, and supports Open Science by exposing content and functionality to the users’ tools and applications. Based on this we introduce the notion of the Research Object – the work objects that are built, transformed and published in the course of scientific experiments – and suggest that by encapsulating methods with results we can achieve research that is more reusable and repeatable and hence rapid and robust.

Item Type:Article
Creator/Authors:
David De Roure
Carole Goble
Sergejs Aleksejevs
Sean Bechhofer
Jiten Bhagat
Don Cruickshank
Paul Fisher
Duncan Hull
Danius Michaelides
David Newman
Rob Procter
Yuwei Lin
Meik Poschen
Research Group:Current ECS Groups > Web and Internet Science
Old ECS Groups > Intelligence, Agents, Multimedia
Date:10 April 2009
Information about this record:
Performance Indicator:EZ~13~04~11
Citations:ISI: 2, Google Scholar: 10
Downloads (2010):83
ID Code:17270
Last Modified:23 Sep 2011 10:37
Deposited On:10 Apr 2009 11:39 by De Roure, David

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References in Article

Select the SEEK icon to attempt to find the referenced article. If it does not appear to be in this archive you will be forwarded to the paracite service. Poorly formated references will probably not work.

1. Dirks, L. & Hey, T. (2007) The Coming Revolution in Scholarly Communications & Cyberinfrastructure, CTWatch Quarterly. 3.

2. Seekda http://seekda.com/, visited 8 April 2009

3. Anderson, N., Tarczy-Hornoch, P. & Bumgarner, R. (2006) On the persistence of supplementary resources in biomedical publications, BMC Bioinformatics. 7, 260.

4. Pearson, H. (2006) Online methods share insider tricks, Nature. 441, 678-678.

5. Klimeck, G., McLennan, M., Brophy, S. P., Adams, G. B. & Lundstrom, M. S. (2008) nanoHUB.org: Advancing Education and Research in Nanotechnology, Computing in Science & Engineering. 10, 17-23.

6. Goble, C. & De Roure, D. (2008) Curating Scientific Web Services and Workflow, EDUCAUSE Review. 43.

7. Buckheit, J. B. & Donoho, D. L. (1995) WaveLab and Reproducible Research in Tech. Rep., Dept. of Statistics, Stanford University,

8. Gil, Y., Deelman, E., Ellisman, M., Fahringer, T., Fox, G., Gannon, D., Goble, C., Livny, M., Moreau, L. & Myers, J. (2007) Examining the Challenges of Scientific Workflows, Computer. 40, 24-32.

9. Goderis, A., Sattler, U., Lord, P. & Goble, C. (2005) Seven Bottlenecks to Workflow Reuse and Repurposing in The Semantic Web – ISWC 2005 pp. 323-337.

10. Fisher, P., Hedeler, C., Wolstencroft, K., Hulme, H., Noyes, H., Kemp, S., Stevens, R. & Brass, A. (2007) A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis, Nucleic Acids Res. 35, 5625--5633.

11. Neylon, C. Science in the Open http://blog.openwetware.org/scienceintheopen/, visited April 8 2009

12. Bradley, J.-C. UsefulChem http://usefulchem.blogspot.com/, visited April 8 2009

13. Tapscott, D. & Williams, A. D. (2008) Wikinomics: How Mass Collaboration Changes Everything, Penguin Group (USA) Incorporated.

14. Shneiderman, B. (2008) Science 2.0, Science. 319, 1349-1350.

15. De Roure, D. & Goble, C. (2009) Software Design for Empowering Scientists, Software, IEEE. 26, 88-95.

16. De Roure, D., Goble, C. & Stevens, R. (2009) The design and realisation of the Virtual Research Environment for social sharing of workflows, Future Generation Computer Systems. 25, 561-567.

17. Oinn, T., Greenwood, M., Addis, M., Alpdemir, N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D., Li, P., Lord, P., Pocock, M., Senger, M., Stevens, R., Wipat, A. & Wroe, C. (2006) Taverna: lessons in creating a workflow environment for the life sciences: Research Articles, Concurr. Comput. : Pract. Exper. 18, 1067--1100.

18. McPhillips, T., Bowers, S., Zinn, D. & Ludäscher, B. (2009) Scientific workflow design for mere mortals, Future Generation Computer Systems. 25, 541-551.

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20. Trident: Scientific Workflow Workbench for Oceanography http://www.microsoft.com/mscorp/tc/trident.mspx, visited April 8 2009

21. Lin, Y., Poschen, M., Procter, R., Voss, A., Goble, C., Bhagat, J., De Roure, D., Cruickshank, D. & Rouncefield, M. (2008) Lessons from Developing a Social Networking Site for Scientists in e-Social Science '08 Manchester, UK.

22. De Roure, D., Goble, C., Bhagat, J., Cruickshank, D., Goderis, A., Michaelides, D. & Newman, D. (2008). myExperiment: Defining the Social Virtual Research Environment. Paper presented at the IEEE Fourth International Conference on eScience (eScience '08).

23. Williams, A. J. (2008) Internet-based tools for communication and collaboration in chemistry, Drug Discovery Today. 13, 502-506.

24. Lin, Y., Poschen, M., Procter, R., Voss, A., Goble, C., Bhagat, J., De Roure, D., Cruickshank, D. & Rouncefield, M. (2008) Agile Management: Strategies for Developing a Social Networking Site for Scientists in 4th International Conference on e-Social Science Manchester, UK.

25. Bradley, J.-C. (2007) Open Notebook Science Using Blogs and Wikis in Nature Precedings

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27. Nielsen, J. (2006) Participation Inequality: Encouraging More Users to Contribute in

28. Groth, P. T. & Gil, Y. (2009) A scientific workflow construction command line in Proceedings of the 13th international conference on Intelligent user interfaces, ACM, Sanibel Island, Florida, USA.

29. Biton, O., Davidson, S. B., Khanna, S. & Roy, S. (2009) Optimizing user views for workflows in Proceedings of the 12th International Conference on Database Theory, ACM, St. Petersburg, Russia.

30. Goderis, A., Fisher, P., Gibson, A., Tanoh, F., Wolstencroft, K., De Roure, D. & Goble, C. (2009) Benchmarking Workflow Discovery: A Case Study From Bioinformatics, Concurrency and Computation: Practice and Experience. Accepted for publication.

31. Mons, B. (2005) Which gene did you mean? BMC Bioinformatics. 6, 142.

32. Miller, E. (1998) An Introduction to the Resource Description Framework, D-Lib Magazine.

33. Williams, R., Stewart, J. & Slack, R. (2005) Social Learning In Technological Innovation: Experimenting With Information And Communication Technologies, Edward Elgar Publishing, Incorporated.

34. Glaser, H., Millard, I., Jaffri, A., Lewy, T. & Dowling, B. (2008) On Coreference and The Semantic Web in 7th International Semantic Web Conference, (submitted), Karlsruhe, Germany.

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