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
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 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.
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.
Referencesedit
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^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.
^ abHull, 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. PMC1538887. PMID 16845108.
^ abOinn, 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. S2CID 10219281.
^ abOinn, 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.
^ abGoble, 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. PMC2896080. PMID 20501605.
^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. PMC2896129. PMID 20484378.
^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. Vol. 500. pp. 629–655. doi:10.1016/B978-0-12-385118-5.00029-3. ISBN 9780123851185. PMID 21943917.
^"Seek for Science | For finding, sharing and exchanging Data, Models and Processes in Systems Biology". Retrieved 21 June 2012.
^Booth, I. R. (2007). "SysMO: Back to the future". Nature Reviews Microbiology. 5 (8): 566. doi:10.1038/nrmicro1719. PMID 17632975.
^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.
^"MethodBox Home". Archived from the original on 18 September 2011. Retrieved 21 June 2012.
^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.
^"RightField.org.uk | SysMO-DB". Retrieved 21 June 2012.
^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. S2CID 16645167.
^Jupp, S.; Klein, J.; Schanstra, J.; Stevens, R. (2011). "Developing a kidney and urinary pathway knowledge base". Journal of Biomedical Semantics. 2 (Suppl 2): S7. doi:10.1186/2041-1480-2-S2-S7. PMC3102896. PMID 21624162.
^"Kidney and Urinary Pathway Knowledge Base". Retrieved 21 June 2012.