Webservices and Workflows. Taverna, Biocatalgue and myExperiment.
•Transferir como PPT, PDF•
0 gostou•30 visualizações
Workshop. Proteomics Bioinformatics. WTAC. 13-17 December 2010.
Recomendados
Recomendados
Mais conteúdo relacionado
Mais procurados
Mais procurados (9)
Semelhante a Webservices and Workflows. Taverna, Biocatalgue and myExperiment.
Semelhante a Webservices and Workflows. Taverna, Biocatalgue and myExperiment. (20)
Mais de Rafael C. Jimenez
Mais de Rafael C. Jimenez (20)
Último
Último (20)
Webservices and Workflows. Taverna, Biocatalgue and myExperiment.
- 1. Proteomics Bioinformatics WTAC 13-17 December 2010 Rafael Jimenez rafael@ebi.ac.uk EnCORE presentation Webservices and Workflows Taverna, Biocatalgue and myExperiment Katy Wolstencroft, myGrid, University of Manchester
- 2. Introduction to Web Services at EBI Table of contents • Web Services • Workflows • myGrid solutions – Biocatalogue – Taverna – myExperiment
- 3. Introduction to Web Services at EBI Brief introduction to Web Services
- 4. Introduction to Web Services at EBI Web Service • What – API that is accessed via HTTP • Aim – Expose sources and services to third party applications • Why – Platform-independent and language-independent • Types – REST – SOAP API: Application programming interface HTTP: Hypertext Transfer Protocol
- 5. Web Services How it works How should I invoke you? Documentation Make a request Results Web serverClient 1 2 3 4 Web Service Application describes the methods and variables to query the service2
- 6. Web Services REST: REpresentational State Transfer Find documentation Documentation (html, pdf, …) HTTP request (GET, POST, … ) Results Web serverClient 1 2 3 4 Web Service Application
- 7. Parameters Web Services SOAP: Simple Object Access Protocol WSDL request WSDL SOAP request SOAP response Web serverClient 1 2 3 4 Web Service Application WSDL: Web Services Description Language XML • SOAP request Results XML • SOAP response SOAP envelopeSOAP envelope 3 4
- 8. Introduction to Web Services at EBI Workflows
- 9. Introduction to Web Services at EBI Workflow • Workflow – Sequence of tasks that produces a result of observable value • Workflow management system – Computer system to compose and execute workflows. • Workflow components – Input – Service – Output – Shims
- 10. MatchMismatch Shims: Connecting services Shim Service A Service B Service A Service B • Convert data formats and act as connectors
- 11. Finding Shims • BioCatalogue – some shims are regular SOAP or REST services • myExperiment – look for all workflows containing the scientific services. Has anyone linked them together before? • Shim Library – a dedicated resource only for shim services. Coming soon Katy Wolstencroft, myGrid, University of Manchester
- 12. Services • Data Resources • Analysis tools • Knowledge Resources • Web Services – SOAP – REST • Grid Services • Local scripts • Workflows
- 13. Introduction to Web Services at EBI myGrid solutions
- 14. Create and run workflows Share, discover and reuse workflows Discover and reuse services myGrid solutions
- 15. • A public centralised and curated registry of Life Science Web Services • ‘Web 2.0’-style website and API • Allow anyone to register, discover and curate Web Services • Community oriented with expert guidance • Open content, open source, open platform Paul Fisher, myGrid, University of Manchester Biocatalogue http://www.biocatalogue.org
- 17. Service Search
- 18. Workflow diagram Tree view of workflow structure Tree view of workflow structure Available services Taverna • Workflow management system • Java desktop application • Open source and extensible • Includes access to Biocatalogue and myExperiment • http://www.taverna.org.uk/
- 19. What do Scientists use Taverna for? – Data gathering, annotation and model building – Data analysis from distributed tools – Data mining and knowledge management – Parameter sweeps and simulation Users from Systems Biology, Proteomics, Sequence analysis, Protein structure prediction, Gene/protein annotation, Microarray data analysis, QTL studies, Chemioinformatics, Medical image analysis, Public Health care epidemiology, Heart model simulation, Phenotype studies, Phylogeny, Statistical analysis, Pharmacogenomics, Text mining, Astronomy, Music, Meteorology Katy Wolstencroft, myGrid, University of Manchester
- 20. Sharing Experiments • Taverna supports the in silico experimental process for individual scientists • How do you share your results/experiments/experiences with your – Research group – Collaborators – Scientific community • How do you compare your results with others produced by e.g. Kepler / Triana / Trident? Paul Fisher, myGrid, University of Manchester
- 22. Recycling, Reuse, Repurposing • Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis • Paul meets Jo. Jo is investigating mouse Whipworm infection. • Jo reuses one of Paul’s workflows. • Jo identifies the biological pathways involved in sex dependence in the mouse model, believed to be involved in the ability of mice to expel the parasite. • Previously a manual two year study by Jo had failed to do this. Workflows are protocols Paul Fisher, myGrid, University of Manchester
- 23. Examples from myExperiment OLS PICR Biomart and Microarray analysis ChEBI
- 24. Acknowledgements & thanks All the myGrid team, and specially to Katy Wolstencroft, Shoaib Sufi, Peter Li, Paul Fisher, Eric Nzuobontane ProteomicsServicesTeam