myGrid

The myGrid consortium produces and uses a suite of tools design to “help e-Scientists get on with science and get on with scientists”. The tools support the creation of e-laboratories and have been used in domains as diverse as systems biology, social science, music, astronomy,[1] multimedia and chemistry.[2][3]

myGrid consortium
Formation2001
Typee-Science organization
PurposeDeveloping software tools for scientists
Location
Carole Goble
Websitewww.mygrid.org.uk

The consortium is led by Carole Goble of the Department of Computer Science at the University of Manchester, UK.

Tools produced and used by myGrid

Tools developed by the myGrid consortium include:

  • The Taverna workbench for designing, editing and executing scientific workflows[4][5][6]
  • myExperiment for sharing workflows and related data[7]
  • BioCatalogue a public registry of Web services for Life Scientists[8]
  • Seek[9][10] produced in collaboration with the SysModb: Systems Biology of Micro-Organisms DataBase[11][12] Finding, sharing and exchanging data, models and processes in Systems Biology
  • MethodBox[13][14] Browse datasets and share knowledge.
  • RightField[15][16] Sharing the meaning of your data by embedding ontology annotation in spreadsheets
  • The Kidney and Urinary Pathway Database (KUPKB)[17][18][19]
  • Workflows for Ever (wf4ever)[20][21] Scientific workflow preservation

History

The consortium has three distinct phases:

Phase 1

The consortium was formed in 2001, bringing together collaborators at the Universities of Manchester, Southampton, Newcastle, Nottingham and Sheffield, The European Molecular Biology Laboratory-European Bioinformatics Institute[22] (EMBL-EBI) in Cambridge, and industrial partners GlaxoSmithKline, Merck KGaA, AstraZeneca, Sun Microsystems, IBM, GeneticXchange, Epistemics and Cerebra, (formerly Network Inference). The UK Engineering and Physical Sciences Research Council funded the first phase of the project with £3.5 million.[23]

To date, Grid development has focused on the basic issues of storage, computation and resource management needed to make a global scientific community's information and tools accessible in a high performance environment. However, from an e-Science viewpoint, the purpose of the Grid is to deliver a collaborative and supportive environment that allows geographically distributed scientists to achieve research goals more effectively. MyGrid will design, develop and demonstrate higher level functionalities over an existing Grid infrastructure that support scientists in making use of complex distributed resources.

The project has developed an e-Science workbench called Taverna[4][5][6] that supports:

  • the scientific process of experimental investigation, evidence accumulation and result assimilation;
  • the scientist's use of the community's information; and
  • scientific collaboration, allowing dynamic groupings to tackle emergent research problems.

The myGrid project has also developed myExperiment to allow sharing of scientific workflows from Taverna and other Scientific workflow systems.

The Taverna workbench supports individual scientists by providing personalisation facilities relating to resource selection, data management and process enactment. The design and development activity will be informed by and evaluated using problems in bioinformatics, which is characterised by a highly distributed community, with many shared tools resources. myGrid will develop two application environments, one that supports individual scientists in the analysis of functional genomic data, and another that supports the annotation of a pattern database. Both of these tasks require explicit representation and enactment of scientific processes, and have challenging performance requirements.

Phase 2

In phase 2, from 2006 to 2009, the consortium is funded for £2 million[24] as part of the Open Middleware Infrastructure Institute. The membership of the consortium was concentrated in the University of Manchester and EMBL-EBI.

Phase 3

In December 2008, the UK's Engineering and Physical Sciences Research Council approved the team's renewal grant proposal. The grant is for £1.15m[25] and started in January 2009. The members of the myGrid team for Phase 3 are the University of Manchester and the University of Southampton. The project is organised around 4 themes: Knowledge Management for e-Science, Metadata management in e-Laboratories, Scientific Workflow Design, Management and Enactment, and Social Computing for e-Scientists. The Social Computing theme is oriented around the myExperiment[7] Virtual research environment (VRE) for the social curation and sharing of scientific Research Objects.

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References
  1. Hook, R. N.; Romaniello, M.; Ullgrén, M.; Järveläinen, P.; Maisala, S.; Oittinen, T.; Savolainen, V.; Solin, O.; Tyynelä, J.; Peron, M.; Izzo, C.; Licha, T. (2008). "ESO Reflex: A Graphical Workflow Engine for Running Recipes". The 2007 ESO Instrument Calibration Workshop. ESO Astrophysics Symposia European Southern Observatory. p. 169. doi:10.1007/978-3-540-76963-7_23. ISBN 978-3-540-76962-0.
  2. Stevens, R. D.; Robinson, A. J.; Goble, C. A. (2003). "MyGrid: Personalised bioinformatics on the information grid". Bioinformatics. 19: i302–i304. doi:10.1093/bioinformatics/btg1041. PMID 12855473.
  3. Stevens, R. D.; Tipney, H. J.; Wroe, C. J.; Oinn, T. M.; Senger, M.; Lord, P. W.; Goble, C. A.; Brass, A.; Tassabehji, M. (2004). "Exploring Williams-Beuren syndrome using myGrid". Bioinformatics. 20: i303–i310. doi:10.1093/bioinformatics/bth944. PMID 15262813.
  4. Hull, D.; Wolstencroft, K.; Stevens, R.; Goble, C. A.; Pocock, M. R.; Li, P.; Oinn, T. (2006). "Taverna: A tool for building and running workflows of services". Nucleic Acids Research. 34 (Web Server issue): W729–W732. doi:10.1093/nar/gkl320. PMC 1538887. PMID 16845108.
  5. Oinn, T.; Greenwood, M.; Addis, M.; Alpdemir, M. N.; Ferris, J.; Glover, K.; Goble, C.; Goderis, A.; Hull, D.; Marvin, D.; Li, P.; Lord, P.; Pocock, M. R.; Senger, M.; Stevens, R.; Wipat, A.; Wroe, C. (2006). "Taverna: Lessons in creating a workflow environment for the life sciences" (PDF). Concurrency and Computation: Practice and Experience. 18 (10): 1067–1100. doi:10.1002/cpe.993.
  6. Oinn, T.; Li, P.; Kell, D. B.; Goble, C. A.; Goderis, A.; Greenwood, M.; Hull, D.; Stevens, R.; Turi, D.; Zhao, J. (2007). "Taverna/myGrid: Aligning a Workflow System with the Life Sciences Community". Workflows for e-Science. pp. 300–319. doi:10.1007/978-1-84628-757-2_19. ISBN 978-1-84628-519-6.
  7. Goble, C. A.; Bhagat, J.; Aleksejevs, S.; Cruickshank, D.; Michaelides, D.; Newman, D.; Borkum, M.; Bechhofer, S.; Roos, M.; Li, P.; De Roure, D. (2010). "MyExperiment: A repository and social network for the sharing of bioinformatics workflows". Nucleic Acids Research. 38 (Web Server issue): W677–W682. doi:10.1093/nar/gkq429. PMC 2896080. PMID 20501605.
  8. Bhagat, J.; Tanoh, F.; Nzuobontane, E.; Laurent, T.; Orlowski, J.; Roos, M.; Wolstencroft, K.; Aleksejevs, S.; Stevens, R.; Pettifer, S.; Lopez, R.; Goble, C. A. (2010). "BioCatalogue: A universal catalogue of web services for the life sciences". Nucleic Acids Research. 38 (Web Server issue): W689–W694. doi:10.1093/nar/gkq394. PMC 2896129. PMID 20484378.
  9. Wolstencroft, K.; Owen, S.; Du Preez, F.; Krebs, O.; Mueller, W.; Goble, C.; Snoep, J. L. (2011). "The SEEK". Methods in Systems Biology. Methods in Enzymology. 500. pp. 629–655. doi:10.1016/B978-0-12-385118-5.00029-3. ISBN 9780123851185. PMID 21943917.
  10. "Seek for Science | For finding, sharing and exchanging Data, Models and Processes in Systems Biology". Retrieved 2012-06-21.
  11. Booth, I. R. (2007). "SysMO: Back to the future". Nature Reviews Microbiology. 5 (8): 566. doi:10.1038/nrmicro1719. PMID 17632975.
  12. "About | SysMO-DB". Retrieved 2012-06-21.
  13. Thew, S.; Jarvis, P.; Ainsworth, J.; Buchan, I. (2010). "Obesity atlas and methodbox: Towards an open framework for sharing public health intelligence workflows". Studies in Health Technology and Informatics. 160 (Pt 1): 496–500. PMID 20841736.
  14. "MethodBox Home". Archived from the original on 2011-09-18. Retrieved 2012-06-21.
  15. Wolstencroft, K.; Owen, S.; Horridge, M.; Krebs, O.; Mueller, W.; Snoep, J. L.; Du Preez, F.; Goble, C. (2011). "RightField: Embedding ontology annotation in spreadsheets". Bioinformatics. 27 (14): 2021–2022. doi:10.1093/bioinformatics/btr312. PMID 21622664.
  16. "RightField.org.uk | SysMO-DB". Retrieved 2012-06-21.
  17. Klein, J.; Jupp, S.; Moulos, P.; Fernandez, M.; Buffin-Meyer, B.; Casemayou, A.; Chaaya, R.; Charonis, A.; Bascands, J. -L.; Stevens, R.; Schanstra, J. P. (2012). "The KUPKB: A novel Web application to access multiomics data on kidney disease". The FASEB Journal. 26 (5): 2145–2153. doi:10.1096/fj.11-194381. PMID 22345404.
  18. Jupp, S.; Klein, J.; Schanstra, J.; Stevens, R. (2011). "Developing a kidney and urinary pathway knowledge base". Journal of Biomedical Semantics. 2: S7. doi:10.1186/2041-1480-2-S2-S7. PMC 3102896. PMID 21624162.
  19. "Kidney and Urinary Pathway Knowledge Base". Retrieved 2012-06-21.
  20. "Home - wf4ever". Retrieved 2012-06-21.
  21. Bechhofer, S.; Buchan, I.; De Roure, D.; Missier, P.; Ainsworth, J.; Bhagat, J.; Couch, P.; Cruickshank, D.; Delderfield, M.; Dunlop, I.; Gamble, M.; Michaelides, D.; Owen, S.; Newman, D.; Sufi, S.; Goble, C. (2011). "Why linked data is not enough for scientists" (PDF). Future Generation Computer Systems. 29 (2): 599. doi:10.1016/j.future.2011.08.004.
  22. "The myGrid Project at EBI". Archived from the original on 2012-06-20.
  23. "myGrid: Directly Supporting the E-Scientist GR/R67743/01". Retrieved 2012-06-20.
  24. "myGrid: An OMII-UK Node (mymes: myGrid middleware for e-Scientists) EP/D044324/1". Retrieved 2012-06-20.
  25. "myGrid: A Platform for e-Biology Renewal EP/G026238/1". Retrieved 2012-06-20.
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