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Articles

These are papers we're aware of that make reference to myExperiment - please send us updates for this list! These papers have not been written as part of the myExperiment project - you can find those on Papers.

Articles which cite myExperiment papers

  • Vivien Marx. "My data are your data" by Vivien Marx, Nature Biotechnology 30, 509–511 (2012) doi:10.1038/nbt.2243, published online 7 June 2012.
  • Sroka, J., Włodarczyk, P., Krupa, Ł., and Hidders, J. 2010. DFL designer: collection-oriented scientific workflows with Petri nets and nested relational calculus. In Proceedings of the 1st international Workshop on Workflow Approaches To New Data-Centric Science (Indianapolis, Indiana, June 06 - 06, 2010). Wands '10. ACM, New York, NY, 1-6. DOI= http://doi.acm.org/10.1145/1833398.1833403
  • Zhiming Zhao, Adam Belloum, Marian Bubak, Special section on workflow systems and applications in e-Science, Future Generation Computer Systems, Volume 25, Issue 5, May 2009, Pages 525-527, ISSN 0167-739X, DOI: 10.1016/j.future.2008.10.011.
  • Elmroth, E., Hernández, F., Tordsson, J. Three fundamental dimensions of scientific workflow interoperability: Model of computation, language, and execution environment (2010) Future Generation Computer Systems, 26 (2), pp. 245-256. http://dx.doi.org/10.1016/j.future.2009.08.011
  • Andrew Gibson, Matthew Gamble, Katy Wolstencroft, Tom Oinn, Carole Goble, Khalid Belhajjame, Paolo Missier, The data playground: An intuitive workflow specification environment, Future Generation Computer Systems, Volume 25, Issue 4, April 2009, Pages 453-459, ISSN 0167-739X. http://dx.doi.org/10.1016/j.future.2008.09.009
  • Jeremy G. Frey, The value of the Semantic Web in the laboratory, Drug Discovery Today, Volume 14, Issues 11-12, June 2009, Pages 552-561, ISSN 1359-6446, DOI: 10.1016/j.drudis.2009.03.007
  • Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Mäsak, C., Torrance, G., Wagener, J., Willighagen, E.L., Steinbeck, C., Wikberg, J.E.S. Bioclipse 2: A scriptable integration platform for the life sciences (2009) BMC Bioinformatics, 10. http://www.biomedcentral.com/1471-2105/10/397
  • Abramson, D., Bethwaite, B., Dinh, M.N., Enticott, C., Firth, S., Garic, S., Harper, I., Lackmann, M., Nguyen, H., Ramdas, T., Russel, A.B.M., Schek, S., Vail, M. Virtual microscopy and analysis using scientific workflows (2009) e-Science 2009 - 5th IEEE International Conference on e-Science, pp. 239-246. http://doi.ieeecomputersociety.org/10.1109/e-Science.2009.41
  • Flannery, D., Matthews, B., Griffin, T., Bicarregui, J., Gleaves, M., Lerusse, L., Downing, R., Ashton, A., Sufi, S., Drinkwater, G., Kleese, K. ICAT: Integrating data infrastructure for facilities based science (2009) e-Science 2009 - 5th IEEE International Conference on e-Science, pp. 201-207. http://doi.ieeecomputersociety.org/10.1109/e-Science.2009.36
  • Karhu, K., Botero, A., Vihavainen, S., Tang, T., Hämäläinen, M. A digital ecosystem for boosting user-driven service business (2009) Proceedings of the International Conference on Management of Emergent Digital EcoSystems, MEDES '09, pp. 246-253. http://doi.acm.org/10.1145/1643823.1643869
  • Zinn, D., Bowers, S., McPhillips, T., Ludäscher, B. Scientific workflow design with data assembly lines (2009) Proceedings of the 4th Workshop on Workflows in Support of Large-Scale Science, WORKS '09, in Conjunction with SC 2009. http://doi.acm.org/10.1145/1645164.1645178
  • Gessler, D.D.G., Schiltz, G.S., May, G.D., Avraham, S., Town, C.D., Grant, D., Nelson, R.T. SSWAP: A simple semantic web architecture and protocol for semantic web services (2009) BMC Bioinformatics, 10, p. 309.
  • Eduardo Ogasawara, Carlos Paulino, Leonardo Murta, Cláudia Werner, Marta Mattoso. 2009. Experiment Line: Software Reuse in Scientific Workflows, Scientific and Statistical Database Management (2009), pp. 264-272. DOI 10.1007/978-3-642-02279-1_20 http://www.springerlink.com/content/l2142986j44gl160/
  • Groth, P. and Gil, Y. 2009. Analyzing the Gap between Workflows and their Natural Language Descriptions. In Proceedings of the 2009 Congress on Services - I - Volume 00 (July 06 - 10, 2009). SERVICES. IEEE Computer Society, Washington, DC, 299-305. DOI= http://dx.doi.org/10.1109/SERVICES-I.2009.55
  • Wassink, I., Vet, P. E., Wolstencroft, K., Neerincx, P. B., Roos, M., Rauwerda, H., and Breit, T. M. 2009. Analysing Scientific Workflows: Why Workflows Not Only Connect Web Services. In Proceedings of the 2009 Congress on Services - I (July 06 - 10, 2009). SERVICES. IEEE Computer Society, Washington, DC, 314-321. DOI= http://dx.doi.org/10.1109/SERVICES-I.2009.48
  • M. S. Avila-Garcia, A. E. Trefethen, N. Joshi, F. Gleeson, W. Ba-alawi. 2009. Sharing and Reusing Cancer Image Segmentation Algorithms Using Scientific Workflows: Pros and Cons. In 2009 Fifth IEEE International Conference on e-Science (December 2009), pp. 94-101. DOI 10.1109/e-Science.2009.22 http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5380879
  • Gil, Y., Kim, J., Florez, G., Ratnakar, V., and González-Calero, P. A. 2009. Workflow matching using semantic metadata. In Proceedings of the Fifth international Conference on Knowledge Capture (Redondo Beach, California, USA, September 01 - 04, 2009). K-CAP '09. ACM, New York, NY, 121-128. DOI= http://doi.acm.org/10.1145/1597735.1597757
  • Xiaoqiao Liu , Jianmin Wu , Jun Wang , Xiaochuan Liu , Shuqi Zhao , Zhe Li , Lei Kong , Xiaocheng Gu , Jingchu Luo , and Ge Gao WebLab: a data-centric, knowledge-sharing bioinformatic platform. Nucleic Acids Research Advance Access published on July 1, 2009. Nucl. Acids Res. 37: W33-W39. DOI 10.1093/nar/gkp428 http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_2/W33
  • Carole Goble, Robert Stevens, Duncan Hull, Katy Wolstencroft, Rodrigo Lopez. 2008. Data curation + process curation=data integration + science. Brief Bioinform, Vol. 9, No. 6. (1 November 2008), pp. 506-517. doi:10.1093/bib/bbn034
  • Elsayed, I., Muslimovic, A., and Brezany, P. 2008. Intelligent dataspaces for e-science. In Proceedings of the 7th WSEAS international Conference on Computational intelligence, Man-Machine Systems and Cybernetics (Cairo, Egypt, December 29 - 31, 2008). A. Zaharim, N. Mastorakis, and I. Gonos, Eds. Electrical And Computer Engineering Series. World Scientific and Engineering Academy and Society (WSEAS), Stevens Point, Wisconsin, 94-100.
  • Leake, D. and Kendall-Morwick, J. 2008. Towards Case-Based Support for e-Science Workflow Generation by Mining Provenance. In Proceedings of the 9th European Conference on Advances in Case-Based Reasoning (Trier, Germany, September 01 - 04, 2008). K. Althoff, R. Bergmann, M. Minor, and A. Hanft, Eds. Lecture Notes In Artificial Intelligence, vol. 5239. Springer-Verlag, Berlin, Heidelberg, 269-283. DOI= http://dx.doi.org/10.1007/978-3-540-85502-6_18
  • Gibson, A., Gamble, M., Wolstencroft, K., Oinn, T., and Goble, C. 2007. The Data Playground: An Intuitive Workflow Specification Environment. In Proceedings of the Third IEEE international Conference on E-Science and Grid Computing (December 10 - 13, 2007). http://dx.doi.org/10.1109/E-SCIENCE.2007.72

Articles which cite workflows on myExperiment

  • Kazuharu Arakawa, Nobuhiro Kido, Kazuki Oshita, and Masaru Tomita. G-language genome analysis environment with REST and SOAP web service interfaces. Nucleic Acids Research 2010 38(Web Server issue):W700-W705; doi:10.1093/nar/gkq315 (http://www.myexperiment.org/workflows/799.html)

Articles which refer to the myExperiment site by URL

  • Jiten Bhagat, Franck Tanoh, Eric Nzuobontane, Thomas Laurent, Jerzy Orlowski, Marco Roos, Katy Wolstencroft, Sergejs Aleksejevs, Robert Stevens, Steve Pettifer, Rodrigo Lopez and Carole A. Goble. 2010/ BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Research. DOI 10.1093/nar/gkq394 http://nar.oxfordjournals.org/cgi/content/abstract/gkq394
  • Sean Ekins and Antony J. Williams. 2010. Reaching Out to Collaborators: Crowdsourcing for Pharmaceutical Research. Pharmaceutical Research Volume 27, Number 3 / March, 2010, pp. 393-395, Springer Netherlands. DOI 10.1007/s11095-010-0059-0 http://www.springerlink.com/content/u4g8255810208185/
  • Paul Fisher, Harry Noyes, Stephen Kemp, Robert Stevens, Andrew Brass. 2009. A systematic strategy for the discovery of candidate genes responsible for phenotypic variation. Methods in molecular biology (Clifton, N.J.), Vol. 573 (2009), pp. 329-345. 10.1007/978-1-60761-247-6_1 http://www.springerlink.com/content/g2w612u38303057m/
  • Sun, P., Liu, Z., Davidson, S. B., and Chen, Y. 2009. Detecting and resolving unsound workflow views for correct provenance analysis. In Proceedings of the 35th SIGMOD international Conference on Management of Data (Providence, Rhode Island, USA, June 29 - July 02, 2009). C. Binnig and B. Dageville, Eds. SIGMOD '09. ACM, New York, NY, 549-562. DOI= http://doi.acm.org/10.1145/1559845.1559903
  • Barker, A., van Hemert, J. I., Baldock, R. A., and Atkinson, M. P. 2009. An E-infrastructure to Support Collaborative Embryo Research. In Proceedings of the 2009 9th IEEE/ACM international Symposium on Cluster Computing and the Grid - Volume 00 (May 18 - 21, 2009). CCGRID. IEEE Computer Society, Washington, DC, 520-525. DOI= http://dx.doi.org/10.1109/CCGRID.2009.78
  • Deelman, E., Gannon, D., Shields, M., and Taylor, I. 2009. Workflows and e-Science: An overview of workflow system features and capabilities. Future Gener. Comput. Syst. 25, 5 (May. 2009), 528-540. DOI= http://dx.doi.org/10.1016/j.future.2008.06.012
  • Paul Fisher, Cornelia Hedeler, Katherine Wolstencroft, Helen Hulme, Harry Noyes, Stephen Kemp, Robert Stevens, and Andrew Brass. A systematic strategy for large-scale analysis of genotype–phenotype correlations: identification of candidate genes involved in African trypanosomiasis. Nucleic Acids Research 2007 35(16):5625-5633; doi:10.1093/nar/gkm623

Press Articles

Keynotes

  • Foster, I. 2009. Computing outside the box. In Proceedings of the 23rd international Conference on Supercomputing (Yorktown Heights, NY, USA, June 08 - 12, 2009). ICS '09. ACM, New York, NY, 3-3. DOI= http://doi.acm.org/10.1145/1542275.1542281

Blog mentions

  • Lablogs by Duncan Hull. 29 February 2008.

Web sites

JISC Web page for myExperiment

The Microsoft Technical Computing Initiative Microsoft Scholarly Communication

Project SmartLab - myExperiment is at 3 minutes 47 seconds of the video on the home page(mention contributed by Paul Fisher 2010-07-23).

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