myGrid

{{Infobox organization

| name = myGrid consortium

| image =

| image_border =

| size = frameless

| caption =

| map =

| msize =

| mcaption =

| abbreviation =

| motto =

| formation = 2001

| extinction =

| type = e-Science organization

| status =

| purpose = Developing software tools for scientists

| headquarters =

| location = Department of Computer Science, University of Manchester

| coords =

| region_served =

| membership =

| leader_title = Principal investigator

| leader_name = Carole Goble

| main_organ =

| parent_organization =

| affiliations =

| num_staff =

| num_volunteers =

| budget =

| key_people =

| website = {{URL|www.mygrid.org.uk}}

| remarks =

}}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,{{Cite book | last1 = Hook | first1 = R. N. | last2 = Romaniello | first2 = M. | last3 = Ullgrén | first3 = M. | last4 = Järveläinen | first4 = P. | last5 = Maisala | first5 = S. | last6 = Oittinen | first6 = T. | last7 = Savolainen | first7 = V. | last8 = Solin | first8 = O. | last9 = Tyynelä | first9 = J. | last10 = Peron | doi = 10.1007/978-3-540-76963-7_23 | first10 = M. | last11 = Izzo | first11 = C. | last12 = Licha | first12 = T. | chapter = ESO Reflex: A Graphical Workflow Engine for Running Recipes | title = The 2007 ESO Instrument Calibration Workshop | series = ESO Astrophysics Symposia European Southern Observatory | pages = 169 | year = 2008 | isbn = 978-3-540-76962-0 }} multimedia and chemistry.{{Cite journal | last1 = Stevens | first1 = R. D. | author-link1 = Robert David Stevens| last2 = Robinson | first2 = A. J. | last3 = Goble | first3 = C. A. | author-link3 = Carole Goble| title = MyGrid: Personalised bioinformatics on the information grid | doi = 10.1093/bioinformatics/btg1041 | journal = Bioinformatics | volume = 19 | pages = i302–i304 | year = 2003 | pmid = 12855473| doi-access = free }}{{Cite journal | last1 = Stevens | first1 = R. D. | author-link1 = Robert David Stevens| last2 = Tipney | first2 = H. J. | last3 = Wroe | first3 = C. J. | last4 = Oinn | first4 = T. M. | last5 = Senger | first5 = M. | last6 = Lord | first6 = P. W. | last7 = Goble | first7 = C. A. | author-link7 = Carole Goble| last8 = Brass | first8 = A. | author-link8 = Andy Brass| last9 = Tassabehji | first9 = M.

| title = Exploring Williams-Beuren syndrome using myGrid | doi = 10.1093/bioinformatics/bth944 | journal = Bioinformatics | volume = 20 | pages = i303–i310 | year = 2004 | pmid = 15262813| doi-access = }}

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
myExperiment for sharing workflows and related data
BioCatalogue a public registry of Web services for Life Scientists{{Cite journal | last1 = Bhagat | first1 = J. | last2 = Tanoh | first2 = F. | last3 = Nzuobontane | first3 = E. | last4 = Laurent | first4 = T. | last5 = Orlowski | first5 = J. | last6 = Roos | first6 = M. | last7 = Wolstencroft | first7 = K. | last8 = Aleksejevs | first8 = S. | last9 = Stevens | first9 = R. | last10 = Pettifer | doi = 10.1093/nar/gkq394 | first10 = S. | last11 = Lopez | first11 = R. | last12 = Goble | first12 = C. A. | title = BioCatalogue: A universal catalogue of web services for the life sciences | journal = Nucleic Acids Research | volume = 38 | issue = Web Server issue | pages = W689–W694 | year = 2010 | pmid = 20484378 | pmc =2896129 }}
Seek{{Cite book

| last1 = Wolstencroft | first1 = K.

| last2 = Owen | first2 = S.

| last3 = Du Preez | first3 = F.

| last4 = Krebs | first4 = O.

| last5 = Mueller | first5 = W.

| last6 = Goble | first6 = C.

| author-link6 = Carole Goble

| last7 = Snoep | first7 = J. L.

| chapter = The SEEK

| doi = 10.1016/B978-0-12-385118-5.00029-3

| title = Methods in Systems Biology

| series = Methods in Enzymology

| volume = 500

| pages = 629–655

| year = 2011

| isbn = 9780123851185

| pmid = 21943917

}}{{cite web |url=http://www.seek4science.org/ |title=Seek for Science | For finding, sharing and exchanging Data, Models and Processes in Systems Biology. |access-date=2012-06-21}} produced in collaboration with the SysModb: Systems Biology of Micro-Organisms DataBase{{Cite journal | last1 = Booth | first1 = I. R. | title = SysMO: Back to the future | doi = 10.1038/nrmicro1719 | journal = Nature Reviews Microbiology | volume = 5 | issue = 8 | pages = 566 | year = 2007 | pmid = 17632975| doi-access = free }}{{cite web |url=http://www.sysmo-db.org/ |title=About | SysMO-DB |access-date=2012-06-21}} Finding, sharing and exchanging data, models and processes in Systems Biology

MethodBox{{Cite journal

| last1 = Thew | first1 = S.

| last2 = Jarvis | first2 = P.

| last3 = Ainsworth | first3 = J.

| last4 = Buchan | first4 = I.

| title = Obesity atlas and methodbox: Towards an open framework for sharing public health intelligence workflows

| journal = Studies in Health Technology and Informatics

| volume = 160

| issue = Pt 1

| pages = 496–500

| year = 2010

| pmid = 20841736

}}{{cite web |url=https://www.methodbox.org/ |title=MethodBox Home |access-date=2012-06-21 |archive-url=https://web.archive.org/web/20110918045543/https://www.methodbox.org/ |archive-date=2011-09-18 |url-status=dead }} Browse datasets and share knowledge.

RightField{{Cite journal

| last1 = Wolstencroft | first1 = K.

| last2 = Owen | first2 = S.

| last3 = Horridge | first3 = M.

| last4 = Krebs | first4 = O.

| last5 = Mueller | first5 = W.

| last6 = Snoep | first6 = J. L.

| last7 = Du Preez | first7 = F.

| last8 = Goble | first8 = C.

| author-link8 = Carole Goble

| doi = 10.1093/bioinformatics/btr312

| title = RightField: Embedding ontology annotation in spreadsheets

| journal = Bioinformatics

| volume = 27

| issue = 14

| pages = 2021–2022

| year = 2011

| pmid = 21622664

| doi-access = free

}}{{cite web |url=http://www.rightfield.org.uk |title=RightField.org.uk | SysMO-DB |access-date=2012-06-21}} Sharing the meaning of your data by embedding ontology annotation in spreadsheets

The Kidney and Urinary Pathway Database (KUPKB){{Cite journal

| last1 = Klein | first1 = J.

| last2 = Jupp | first2 = S.

| last3 = Moulos | first3 = P.

| last4 = Fernandez | first4 = M.

| last5 = Buffin-Meyer | first5 = B.

| last6 = Casemayou | first6 = A.

| last7 = Chaaya | first7 = R.

| last8 = Charonis | first8 = A.

| last9 = Bascands | first9 = J. -L.

| last10 = Stevens

| doi = 10.1096/fj.11-194381 | first10 = R.

| last11 = Schanstra | first11 = J. P.

| title = The KUPKB: A novel Web application to access multiomics data on kidney disease

| journal = The FASEB Journal

| volume = 26

| issue = 5

| pages = 2145–2153

| year = 2012

| pmid = 22345404

| s2cid = 16645167

| url = http://www.fasebj.org/content/26/5/2145.full.pdf+html

| doi-access = free

}}{{Cite journal | last1 = Jupp | first1 = S. | last2 = Klein | first2 = J. | last3 = Schanstra | first3 = J. | last4 = Stevens | first4 = R. | author-link4 = Robert David Stevens| title = Developing a kidney and urinary pathway knowledge base | doi = 10.1186/2041-1480-2-S2-S7 | journal = Journal of Biomedical Semantics | volume = 2 | pages = S7 | year = 2011 | issue = Suppl 2 | pmid = 21624162| pmc = 3102896 | doi-access = free }}{{cite web |url=http://www.kupkb.org/ |title=Kidney and Urinary Pathway Knowledge Base |access-date=2012-06-21}}

Workflows for Ever (wf4ever){{cite web |url=http://www.wf4ever-project.org/ |title=Home - wf4ever |access-date=2012-06-21}}{{Cite journal | last1 = Bechhofer | first1 = S. | last2 = Buchan | first2 = I. | last3 = De Roure | first3 = D. | author-link3 = David De Roure| last4 = Missier | first4 = P. | last5 = Ainsworth | first5 = J. | last6 = Bhagat | first6 = J. | last7 = Couch | first7 = P. | last8 = Cruickshank | first8 = D. | last9 = Delderfield | first9 = M. | last10 = Dunlop | first10 = I. | last11 = Gamble | first11 = M. | last12 = Michaelides | first12 = D. | last13 = Owen | first13 = S. | last14 = Newman | first14 = D. | last15 = Sufi | first15 = S. | last16 = Goble | first16 = C. | title = Why linked data is not enough for scientists | doi = 10.1016/j.future.2011.08.004 | journal = Future Generation Computer Systems | volume = 29 | issue = 2 | pages = 599 | year = 2011 | s2cid = 16783450 | url = https://eprints.soton.ac.uk/271587/1/research-objects-final.pdf }} 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{{cite web|url=http://www.ebi.ac.uk/mygrid/|title=The myGrid Project at EBI|archive-date=2012-11-10|archive-url=https://web.archive.org/web/20121110101049/http://www.ebi.ac.uk/mygrid/|url-status=dead}}

(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.{{cite web |url=http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=GR/R67743/01 |title=myGrid: Directly Supporting the E-Scientist GR/R67743/01|access-date=2012-06-20}}

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{{Cite journal

| last1 = Hull | first1 = D.

| last2 = Wolstencroft | first2 = K.

| last3 = Stevens | first3 = R.

| author-link3 = Robert David Stevens

| last4 = Goble | first4 = C. A.

| author-link4 = Carole Goble

| last5 = Pocock | first5 = M. R.

| last6 = Li | first6 = P.

| last7 = Oinn | first7 = T.

| title = Taverna: A tool for building and running workflows of services

| doi = 10.1093/nar/gkl320

| journal = Nucleic Acids Research

| volume = 34

| issue = Web Server issue

| pages = W729–W732

| year = 2006

| pmc = 1538887

| pmid = 16845108

}} {{open access}}{{Cite journal | last1 = Oinn | first1 = T. | last2 = Greenwood | first2 = M. | last3 = Addis | first3 = M. | last4 = Alpdemir | first4 = M. N. | last5 = Ferris | first5 = J. | last6 = Glover | first6 = K. | last7 = Goble | first7 = C. | author-link7 = Carole Goble| last8 = Goderis | first8 = A. | last9 = Hull | first9 = D. | doi = 10.1002/cpe.993 | last10 = Marvin | first10 = D. | last11 = Li | first11 = P. | last12 = Lord | first12 = P. | last13 = Pocock | first13 = M. R. | last14 = Senger | first14 = M. | last15 = Stevens | first15 = R. | last16 = Wipat | first16 = A. | last17 = Wroe | first17 = C. | title = Taverna: Lessons in creating a workflow environment for the life sciences | journal = Concurrency and Computation: Practice and Experience | volume = 18 | issue = 10 | pages = 1067–1100 | year = 2006 | s2cid = 10219281 | url = https://eprints.soton.ac.uk/260908/1/taverna-ccpe-reviewed.pdf }}{{Cite book | last1 = Oinn | first1 = T.| last2 = Li | first2 = P. | last3 = Kell | first3 = D. B. | author-link3 = Douglas Kell| last4 = Goble | first4 = C. A. | author-link4 = Carole Goble| last5 = Goderis | first5 = A. | last6 = Greenwood | first6 = M. | last7 = Hull | first7 = D. | last8 = Stevens | first8 = R. | author-link8 = Robert David Stevens| last9 = Turi | first9 = D. | last10 = Zhao | first10 = J. | chapter = Taverna/MyGrid: Aligning a Workflow System with the Life Sciences Community | title = Workflows for e-Science | doi = 10.1007/978-1-84628-757-2_19 | pages = 300–319 | year = 2007 | isbn = 978-1-84628-519-6 | chapter-url = https://www.springer.com/978-1-84628-519-6}} 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{{cite web |url=http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=EP/D044324/1 |title=myGrid: An OMII-UK Node (mymes: myGrid middleware for e-Scientists) EP/D044324/1|access-date=2012-06-20}} 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{{cite web |url=http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=EP/G026238/1 |title=myGrid: A Platform for e-Biology Renewal EP/G026238/1 |access-date=2012-06-20}} 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{{Cite journal | last1 = Goble | first1 = C. A. | author-link1 = Carole Goble| last2 = Bhagat | first2 = J. | last3 = Aleksejevs | first3 = S. | last4 = Cruickshank | first4 = D. | last5 = Michaelides | first5 = D. | last6 = Newman | first6 = D. | last7 = Borkum | first7 = M. | last8 = Bechhofer | first8 = S. | last9 = Roos | first9 = M. | last10 = Li | doi = 10.1093/nar/gkq429 | first10 = P. | last11 = De Roure | first11 = D. | title = MyExperiment: A repository and social network for the sharing of bioinformatics workflows | journal = Nucleic Acids Research | volume = 38 | issue = Web Server issue | pages = W677–W682 | year = 2010 | pmid = 20501605 | pmc =2896080 }} Virtual research environment (VRE) for the social curation and sharing of scientific Research Objects.

References

Category:Bioinformatics

Category:College and university associations and consortia in the United Kingdom

Category:Engineering and Physical Sciences Research Council

Category:Grid computing projects

Category:Information technology organisations based in the United Kingdom

Category:Department of Computer Science, University of Manchester

Category:Science and technology in Greater Manchester