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Non technical introduction to Web Services & Workflows. Taverna, Biocatalogue and myExperiment
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
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
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
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,
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
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
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
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”.
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
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
Life Cycle
Create and run workflows
Taverna workflow enactment engine and GUI workflow workbench for composing workflows
Create and manage services as components
Service deployment, workflow and service monitoring
Discover and reuse services
BioCatalogue curated catalogue and Feta plugin
Share, discover and reuse workflows
myExperiment Web 2.0 social environment
Manage the metadata needed and generated
Semantic Web based technologies for the ontologies needed for service and workflow finding and provenance collection and processing.