Hands-on training at EBI. APO-SYS Data Management Meeting. June 1, 2011.

1. Sam Kerrien & Rafael Jimenez
Non technical introduction to
Web Services
& Workflows
Taverna, Biocatalogue and myExperiment
Hands-on training at EBI
APO-SYS Data Management Meeting
June 1, 2011

2. Plan
• Web services: presentation + WS game - 30‘
• Workflows presentation – 30’
– Taverna + Biocatalogue + myExperiment
• Taverna tutorial - 30‘
• myExperiment workflows - 30'

3. Introduction to Web Services at EBI
Table of contents
• Web Services
• Workflows
• myGrid solutions
– Biocatalogue
– Taverna
– myExperiment

4. Introduction to Web Services at EBI
Brief introduction to Web Services
This introduction is intended for a non technical audience;
We have purposely simplified technical aspect.

5. What is a Web Service
• It is a piece of software that runs remotely,
• It is accessible over a network (e.g. Internet),
• It is meant for machine to machine
communication,
• Independent from programming languages,
• It can be operated following specific rules (i.e.
protocol),
• There are 2 main protocols in use…
5

6. REST Web Services
6
URL
Data / Status
1
2
3
Reads WADL

7. SOAP Web Services
7
GET WSDL
WSDL
1
2
3
Reads
SOAP Request
SOAP Response
4
5
Method /
Parameters
Data
4 5
WSDL

8. 8

9. SOAP vs. REST
• Based on Standards,
• Only accessed by
software,
• Allow description of
complex data structure
in request and
response,
9
• Geared to simplicity,
• A browser can be a client,
• Request as complex as a
URL can be,

10. Introduction to Web Services at EBI
Workflows

11. 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

12. MatchMismatch
Shims: Connecting services
Shim
Service A
Service B
Service A
Service B
• Convert data formats and act as connectors

13. Services
• Data Resources
• Analysis tools
• Web Services
– SOAP
– REST
• Grid Services
• Local scripts
• Local software
• Workflows

14. Introduction to Web Services at EBI
myGrid solutions

15. Create and run workflows
Share, discover and reuse workflows
Discover and reuse services
myGrid solutions

16. • 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. BioCatalogue’s Mission
08/23/18 17

18. Service Search

19. 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/

20. 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

21. Sharing Experiments
• Taverna supports the silico experimental process for
individual scientists
• You can share results/experiments/experiences with
your
– Research group
– Collaborators
– Scientific community
A registry of workflows
Paul Fisher, myGrid, University of Manchester

22. myExperiment
http://www.myexperiment.org/

23. 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

24. Examples from myExperiment
OLS
PICR
Biomart and
Microarray analysis
ChEBI

25. APO-SYS workflows
• UniProt - DAS
– Sequence
• http://www.myexperiment.org/workflows/2157.html
• http://www.myexperiment.org/workflows/2158.html
– Annotations
• http://www.myexperiment.org/workflows/2159.html
• http://www.myexperiment.org/workflows/2160.html
• ArrayExpress/Atlas - DAS
– Annotations
• http://www.myexperiment.org/workflows/2159.html
• http://www.myexperiment.org/workflows/2160.html
• PRIDE - Biomart
• http://www.myexperiment.org/workflows/2154.html
• Reactome - Biomart
• http://www.myexperiment.org/workflows/2155.html
• IntAct - PSICQUIC
• http://www.myexperiment.org/workflows/2153.html
• http://www.myexperiment.org/workflows/2124.html
• Biomodels
• http://www.myexperiment.org/workflows/2156.html
• PICR
• http://www.myexperiment.org/workflows/2126.html

26. ProteomicsServicesTeam
Acknowledgements & thanks
All the myGrid team
Specially to …Katy Wolstencroft, Shoaib
Sufi, Peter Li, Eric Nzuobontane