Papers

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Papers

This page lists the papers published by the myExperiment team. If you're using myExperiment in your research we would be very pleased if you could mention myExperiment and cite our papers as appropriate. We'd also like to hear from you so we can update our list of your papers that have used or cited myExperiment (so that people can find out about your work and cite you...)

The key myExperiment paper for citation purposes in an e-Science context is:

  • De Roure, D., Goble, C. and Stevens, R. (2009): The Design and Realisation of the myExperiment Virtual Research Environment for Social Sharing of Workflows. Future Generation Computer Systems 25, pp. 561-567. doi:10.1016/j.future.2008.06.010

The key myExperiment paper for citation purposes in a bioinformatics context is:

  • Goble, C.A., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., and De Roure, D. (2010): myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucl. Acids Res. 38 (suppl 2): W677-W682. . http://dx.doi.org/10.1093/nar/gkq429 doi:10.1093/nar/gkq429]

This paper discusses the design principles of Taverna and myExperiment:

  • De Roure, D. and Goble, C. (2009): Software Design for Empowering Scientists. IEEE Software 26 (1) pp. 88-95, January/February 2009. doi:10.1109/MS.2009.22

Citations for myExperiment papers are available in BibTeX and as a compressed EndNote library (myExpEndNote.enlx).

Full List

David De Roure. "Towards Computational Research Objects". To be published in the proceedings of the the DPRMA workshop held in conjunction with JCDL 2013 https://dl.dropboxusercontent.com/u/15772302/ComputationalResearchObjects.pdf

David De Roure, Clare Hooper, Megan Meredith-Lobay, Kevin Page, Ségolène Tarte, Don Cruickshank and Catherine De Roure. "Observing Social Machines Part 1: What to Observe?". Web Observatory Workshop at WWW2013, May 2013 http://users.ox.ac.uk/~oerc0033/preprints/ObservingSocialMachinesPart1.pdf

Jun Zhao, Jose Manuel Gomez-Perezy, Khalid Belhajjame, Graham Klyne, Esteban Garcia-Cuestay, Aleix Garridoy, Kristina Hettne, Marco Roos, David De Roure, Carole Goble, "Why Workflows Break - Understanding and Combating Decay in Taverna Workflows", eScience 2012, Chicago, October 2012 http://users.ox.ac.uk/~oerc0033/preprints/why-decay.pdf

Kevin R. Page, Ben Fields, David De Roure, Tim Crawford, J. Stephen Downie, "Reuse, Remix, Repeat: The Workflows of MIR", MIRrors session at the 13th International Society for Music Information Retrieval Conference (ISMIR 2012) Porto, Portugal, October 8th-12th, 2012 http://ismir2012.ismir.net/event/papers/1008.pdf

Khalid Belhajjame, Oscar Corcho, Daniel Garijo, Jun Zhao, Paolo Missier, David Newman, Raul Palma, Sean Bechhofer, Esteban Garc Cuesta, Jose Manuel Gomez-Perez, Graham Klyne, Kevin Page, Marco, Roos, Jose Enrique Ruiz, Stian Soiland-Reyes, Lourdes Verdes-Montenegro, David De Roure and Carole A. Goble, "Workflow-Centric Research Objects: First Class Citizens in Scholarly Discourse", SePublica2012 at ESWC2012, Greece, May 2012. http://users.ox.ac.uk/~oerc0033/preprints/sepublica2012.pdf

Carole A. Goble, David De Roure and Sean Bechhofer (2012) Accelerating scientists’ knowledge turns. Available as a preprint. The corresponding keynote talk is available in PowerPoint 97-2003 and on myExperiment in Pack 223. Full ref: Knowledge Discovery, Knowledge Engineering and Knowledge Management (Revised Selected Papers of Third International Joint Conference, IC3K 2011, Paris, France, October 26-29, 2011, editors: Ana Fred, Jan L. G. Dietz, Kecheng Liu, Joaquim Filipe). Communications in Computer and Information Science, Volume 348. Springer Berlin Heidelberg, 2013. 3-25. 8 June 2013. doi 10.1007/978-3-642-37186-8_1

David De Roure, Khalid Belhajjam, Paolo Missier, José Manuel Gómez-Pérez, Raúl Palma, José Enrique Ruiz, Kristina Hettne, Marco Roos, Graham Klyne, Carole Goble (2011). "Towards the Preservation of Scientific Workflows". Accepted for 8th International Conference on Preservation of Digital Objects (iPRES 2011). http://users.ox.ac.uk/~oerc0033/preprints/wfpreservev10.pdf

David De Roure, Sean Bechhofer, Carole Goble and David Newman (2011), "Scientific Social Objects". Accepted for 1st International Workshop on Social Object Networks (SocialObjects 2011). http://eprints.ecs.soton.ac.uk/22747/

Sean Bechhofer, Iain Buchan, David De Roure, Paolo Missier, John Ainsworth, Jiten Bhagat, Philip Couch, Don Cruickshank, Mark Delderfield, Ian Dunlop, Matthew Gamble, Danius Michaelides, Stuart Owen, David Newman, Shoaib Sufi and Carole Goble (2011) "Why Linked Data is Not Enough for Scientists". To appear in Future Generation Computer Systems. http://users.ox.ac.uk/~oerc0033/preprints/research-objects.pdf

David De Roure ; Kevin R. Page ; Benjamin Fields ; Tim Crawford ; J. Stephen Downie ; Ichiro Fujinaga , (2011). An e-Research approach to web-scale music analysis. Preprint http://rsta.royalsocietypublishing.org/content/369/1949/3300.full

De Roure, D., Goble, C., Aleksejevs, S., Bechhofer, S., Bhagat, J., Cruickshank, D., Fisher, P., Kollara, N., Michaelides, D., Missier, P., Newman, D., Ramsden, M., Roos, M., Wolstencroft, K., Zaluska, E. and Zhao, J. (2010) The Evolution of myExperiment. In: Sixth IEEE e–Science conference (e-Science 2010), December 2010, Brisbane, Australia. http://eprints.ecs.soton.ac.uk/21458/

Bechhofer, S., Ainsworth, J., Bhagat, J., Buchan, I., Couch, P., Cruickshank, D., Delderfield, M., Dunlop, I., Gamble, M., Goble, C., Michaelides, D., Missier, P., Owen, S., Newman, D., De Roure, D. and Sufi, S. (2010) Why Linked Data is Not Enough for Scientists. In: Sixth IEEE e–Science conference (e-Science 2010), December 2010, Brisbane, Australia. http://eprints.ecs.soton.ac.uk/21587/

Page, K., De Roure, D., O'Neill, G., Nagel, B., Crawford, T. and Fields, B. (2010) Semantics for music analysis through linked data: How country is my country? In: Sixth IEEE e–Science conference (e-Science 2010), December 2010, Brisbane, Australia. (Accepted) http://eprints.ecs.soton.ac.uk/21595/

Roos, M., Bechhofer, S., Zhao, J., Missier, P., Newman, D., De Roure, D. and Marshall, M. S. (2010) A Linked Data Approach to Sharing Workflows and Workflow Results. Lecture Notes in Computer Science (Tools in Scientific Workflow Composition at 4th International Symposium on Leveraging Applications, ISoLA 2010), 6415 . pp. 340-354 http://eprints.ecs.soton.ac.uk/21749/

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.: Towards open science: the myExperiment approach, Concurrency and Computation: Practice and Experience, Volume 22, Issue 17, pages 2335–2353, 10 December 2010, DOI 10.1002/cpe.1601. Published Online: July 7 2010. http://www3.interscience.wiley.com/journal/123573352/abstract

Goble, C.A., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., and De Roure, D.: myExperiment: a repository and social network for the sharing of bioinformatics workflows, Nucl. Acids Res., 2010. doi:10.1093/nar/gkq429 http://nar.oxfordjournals.org/cgi/content/abstract/gkq429

De Roure, D. and Goble, C. (2010) Anchors in Shifting Sand: the Primacy of Method in the Web of Data. In: Web Science Conference 2010, 26-27 April, 2010, Raleigh, NC, USA. http://eprints.ecs.soton.ac.uk/20817/

Bechhofer, S., De Roure, D., Gamble, M., Goble, C. and Buchan, I. (2010) Research Objects: Towards Exchange and Reuse of Digital Knowledge. In: The Future of the Web for Collaborative Science (FWCS 2010), April 2010, Raleigh, NC, USA. http://precedings.nature.com/documents/4626/version/1 and http://eprints.ecs.soton.ac.uk/18555/

De Roure, D., and Goble, C. (2009, November 18). Scholarly Communication and the Web. In: Research In a Connected World, Alex Voss, Elizabeth Vander Meer, David Fergusson (eds.) Retrieved from the Connexions Web site: http://cnx.org/content/m32860/1.3/

Wolstencroft, K., Fisher, P., De Roure, D. and Goble, C.(2009, November 26). Scientific Workflows. In: Research In a Connected World, Alex Voss, Elizabeth Vander Meer, David Fergusson (eds.) Retrieved from the Connexions Web site: http://cnx.org/content/m32861/1.3/

Newman, D., Bechhofer, S. and De Roure, D. (2009) myExperiment: An ontology for e-Research. In: Workshop on Semantic Web Applications in Scientific Discourse in conjunction with the International Semantic Web Conference, October 2009, Washington DC, US. http://eprints.ecs.soton.ac.uk/17787/

De Roure, D. (2009) e-Science and the Web. IEEE Computer. http://eprints.ecs.soton.ac.uk/17765/

Goble, C. and De Roure, D. (2009) The impact of workflow tools on data-centric research. In: Data Intensive Computing: The Fourth Paradigm of Scientific Discovery, Tony Hey, Stewart Tansley and Kristin Tolle (eds). Pages 137-145. http://eprints.ecs.soton.ac.uk/17336/

De Roure, D. and Goble, C. (2009) Lessons from myExperiment: Research Objects for Data Intensive Research. In: eScience Workshop 2009, October 15-17, 2009, Pittsburgh, US. http://eprints.ecs.soton.ac.uk/17744/

Pickering, A., Gutteridge, C. and De Roure, D. (2009) A networked registration scheme to support open science. In: UK e-Science All Hands Meeting 2009, Oxford, UK. http://eprints.ecs.soton.ac.uk/17680/

De Roure, D. and Goble, C. (2009) Lessons from myExperiment: Two insights into emerging e-Research practice. UK e-Science All Hands Meeting 2009, Oxford, UK. http://eprints.ecs.soton.ac.uk/17662/

De Roure, D. and Goble, C. (2009) myExperiment: A Web 2.0 Virtual Research Environment for Research using Computation and Services. In: Workshop On Integrating Digital Library Content with Computational Tools and Services at JCDL 2009, 19-06-2009, Austin, Texas, USA. http://eprints.ecs.soton.ac.uk/17607/

De Roure, D., Goble, C., Aleksejevs, S., Bechhofer, S., Bhagat, J., Cruickshank, D., Michaelides, D. and Newman, D. (2009) The myExperiment Open Repository for Scientific Workflows. In: Open Repositories 2009, May 2009, Atlanta, Georgia, US. http://eprints.ecs.soton.ac.uk/17131/

Goderis, A., Fisher, P., Gibson, A., Tanoh, F., Wolstencroft, K., De Roure, D. and Goble, C. (2009) Benchmarking Workflow Discovery: A Case Study From Bioinformatics. Concurrency: Practice and Experience . ISSN 1040-3108 (In Press) http://eprints.ecs.soton.ac.uk/17107/

De Roure, D. and Goble, C. (2009) Software Design for Empowering Scientists. IEEE Software, 26 (1). pp. 88-95. ISSN 0740-7459 http://eprints.ecs.soton.ac.uk/15032/

Goble, C., Missier, P. and De Roure, D. (2008) Scientific workflows. In: McGraw Hill 2009 Yearbook of Science & Technology, McGraw Hill. ISBN 00716056220071605622 http://eprints.ecs.soton.ac.uk/16628/

De Roure, D., Goble, C., Bhagat, J., Cruickshank, D., Goderis, A., Michaelides, D. and Newman, D. (2008) myExperiment: Defining the Social Virtual Research Environment. In: 4th IEEE International Conference on e-Science, 7-12 December 2008, Indianapolis, Indiana, USA. http://eprints.ecs.soton.ac.uk/16560/

Goble, C. and De Roure, D. (2008) Curating Scientific Web Services and Workflows. Educause Review, 43 (5). ISSN 1527-6619 http://eprints.ecs.soton.ac.uk/16561/

De Roure, D. and Goble, C. (2008) Re-evaluating the Grid: the social life of programs. In: CoreGRID series, pp. 201-212, Springer-Verlag New York Inc.. ISBN 978-0-387-78447-2 http://eprints.ecs.soton.ac.uk/15663/

Lin, Y., Poschen, M., Procter, R., Voss, A., Goble, C., Bhagat, J., De Roure, D., Cruickshank, D. and Rouncefield, M. (2008) Agile Management: Strategies for Developing a Social Networking Site for Scientists. In: 4th International Conference on e-Social Science, 18-20 June 2008, Manchester, uk.d http://eprints.ecs.soton.ac.uk/15854/

De Roure, D., Goble, C. and Stevens, R. (2009) The Design and Realisation of the myExperiment Virtual Research Environment for Social Sharing of Workflows. Future Generation Computer Systems 25, pp. 561-567. http://eprints.ecs.soton.ac.uk/15709/

Goderis, A., De Roure, D., Goble, C., Bhagat, J., Cruickshank, D., Fisher, P., Michaelides, D. and Tanoh, F. (2008) Discovering Scientific Workflows: The myExperiment Benchmarks. Technical Report, School of Electronics and Computer Science, University of Southampton. (Unpublished) http://eprints.ecs.soton.ac.uk/15662/

Goble, C. and De Roure, D. (2007) myExperiment: social networking for workflow-using e-scientists. In: Proceedings of the 2nd workshop on Workflows in support of large-scale science, 25 June 2007, Monterey, California, USA. http://eprints.ecs.soton.ac.uk/15095/

De Roure, D. and Goble, C. (2007) myExperiment - A Web 2.0 Virtual Research Environment. In: International Workshop on Virtual Research Environments and Collaborative Work Environments, May 2007, Edinburgh, UK. http://eprints.ecs.soton.ac.uk/13961/

De Roure, D., Goble, C. and Stevens, R. (2007) Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows. In: e-Science 2007: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing, December 2007, Bangalore, India. http://eprints.ecs.soton.ac.uk/15838/

Missier, P., Turi, D., Goble, C., Oinn, T. and De Roure, D. (2007) Taverna Workflows: Syntax and Semantics. In: IEEE International Conference on e-Science and Grid Computing, December 2007, Bangalore, India. http://eprints.ecs.soton.ac.uk/14700/