This document provides an overview of a 3-day training on web services and workflows using Taverna, Biocatalogue and myExperiment. The training will cover workflows, web services, myGrid solutions like Biocatalogue and Taverna, installing Taverna, and building a simple workflow using the PSICQUIC service with Taverna. It includes an agenda, explanations of key concepts like workflows, web services, REST vs SOAP, and examples of real workflows from myExperiment including molecular interactions from IntAct and proteomics analyses.

1. Rafael Jimenez
rafael@ebi.ac.uk
Non technical introduction to
Web Services
& Workflows
Taverna, Biocatalogue and myExperiment
Dates: 16-18 January 2012
Venue: IT-Training Room, East Wing at the EBI
Scientific Organisers: James Watson, Vicky Schneider
Admin and Logistics: Tracey Andrew, Zoe Higney

2. Introduction to Web Services at EBI
Table of contents
• Workflows
• Web Services
• myGrid solutions
– Biocatalogue
– Taverna
– myExperiment
• Installing Taverna
• Simple PSICQUIC workflow with Taverna

3. Introduction to Web Services at EBI
Workflows

4. UniProt, InterPro
PSICQUIC
Reactome
PICR
PRIDE
BLAST
IEP

5. 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
Service A
Service B

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

7. Type of services
• Data Resources
• Analysis tools
• Web Services
– SOAP
– REST
• APIs (application programming interface)
• Grid Services
• Local scripts
• Local software
• Workflows

8. 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.

9. 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
• There are 2 main protocols in use:
– REST
– SOAP
9

10. How it works
Web services
Web serverClient
Documentation
Response
Request
Query
Response
Request
Application
Web Service
Internet
1
2
describes the methods and variables to query the service1

11. How t works
REST
Response
Request
Response
Request
Application
Web Service
1
2
URL
Data / Status
WADL
1
Web serverClient Internet
Sometimes a WADL file is available in the server to describe the service
Not a
standard
process

12. How it works
SOAP
Response
Request
Response
Request
Application
Web Service
1
2
SOAP Request
SOAP Response
2
Web serverClient Internet
WSDL
Methods / Parameters
WSDL
Method / Parameters Data
SOAP Request SOAP Response

13. REST vs. SOAP
13
• Geared to simplicity,
• A browser can be a client,
• Request as complex as a
URL can be,
• Based on Standards,
• Only accessed by software,
• Allow description of
complex data structure in
request and response,

14. PSICQUIC REST service
http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/web
services/current/search/query/(species:trypanosoma
AND detmethod:"two hybrid") AND NOT
pubid:12821657

15. PSICQUIC SOAP service
http://www.soapui.org/
WSDL file:
- http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/psicquic?wsdl
Method:
- getByQuery
Parameters:
- query:
- species:trypanosoma AND detmethod:"two hybrid“
- resultType:
- psi-mi/tab25

16. Introduction to Web Services at EBI
myGrid solutions

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

18. • 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

19. BioCatalogue’s Mission
12/13/18 19

20. Web service Search
http://www.biocatalogue.org

21. 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/

22. Sharing Experiments
• You can share results/experiments/experiences with
your
– Research group
– Collaborators
– Scientific community
A registry of workflows
Paul Fisher, myGrid, University of Manchester

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

24. 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

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

26. Rafael Jimenez
rafael@ebi.ac.uk
TavernaWorkflow Management System
Installing the workbench

27. Installing the Workbench
• Download the Taverna 2.3 workbench from
http://www.taverna.org.uk/
• Install Taverna
• Open Taverna
• Start / All programs / Taverna / Taverna Workbench 2.3
• You do not have to complete the registration now. Click on “Do
no ask me again”.

28. Workflow
Diagram
Services Panel
Workflow
Explorer
Run workflow

29. Input list
Input description
Input example
Input value

30. Output tab
Results display
List of results

31. 1. Workflow Explorer
• The Workflow Explorer is the primary editing
component within Taverna. Through it you can
load, save and edit any property of a workflow.
• The workflow explorer is also where you find
configuration details of services and advanced
options like iteration and looping. We will come
back to these things later
This is a modification of the original tutorial from Katy Wolstencroft

32. 1. Workflow Diagram
The visual representation of workflow
• Shows inputs / outputs, services and control
flows
• Allows editing of the workflow by dragging and
dropping and connecting services together
• Enables saving of workflow diagrams for
publishing and sharing
This is a modification of the original tutorial from Katy Wolstencroft

33. 1. Available Services Panel
Lists services available by default in Taverna
• ~ 3500 services
– Local java services
– Simple web services
– Soaplab services – legacy command-line application
– R Processor
– BioMart database services
– BioMoby services
– Beanshell processor
Allows the user to add new services or
workflows from the web or from file systems
This is a modification of the original tutorial from Katy Wolstencroft

34. Rafael Jimenez
rafael@ebi.ac.uk
TavernaSimple PSICQUIC workflows with Taverna

35. 1. Open one PSICQUIC workflow
1. Open Taverna and click the “myExperiment” button.
myExperiment is a repository of workflows
2. In the “Query” field, type “psicquic”
3. Find the “Molecular Interactions from IntAct PSICQUIC service (REST)”
workflow and click on the “Open” button.
2. Run a PSICQUIC workflow
1. In the menu click on “File” and “Run workflow”
3. Define your query
1. Find and click the “Set value” button
2. Specify your MIQL query. i.e
• species:trypanosoma AND detmethod:"two hybrid"
1. Click on the button “Run workflow”
4. Check your results
1. In the bottom left corner, in the “MITAB” tab, click on “Value1”
5. Save results
1. Click on the “Save value” button on the bottom right corner.
Simple PSICQUIC workflow with Taverna

36. Simple PSICQUIC workflow with Taverna

37. Do you need more examples ...
• http://www.ebi.ac.uk/~rafael/talks/2011-07-19_worksh

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