1. Taverna workflow management system
Stian Soiland-Reyes
myGrid, School of Computer Science
University of Manchester, UK
Taverna workflow management system
UKOLN DevSci: Workflow Tools
Bath,

2. Software | Services | Content | Skills | Community
What is myGrid?
An e-Science Collaboration Since 2001
Not a grid!
Numerous partners involved:
University of Manchester
University of Southampton
University of Oxford
EMBL-EBI
Provides sustainable and production quality software
Supported by OMII-UK, EPSRC and BBSRC
Mixture of developers, bioinformaticians and researchers
Software | Services | Content | Skills | Community

3. Motivation Challenge: Bioinformatics Large amounts of data
Many open questions
Numerous freely available public datasets and analysis tools

4. How do I look at all the genes systematically?
Huge amounts of data
Microarray
1000+ Genes
QTL regions
100+ Genes
How do I look at all the genes systematically?
Next Gen Sequencing
Vast amounts of data
We now have technologies to help with identification of candidate genes
But, there is still a problem with the amount of data generated by these high-throughput methods
QTL based investigation can easily produce over 200 genes per chromosome region, if there are 5 regions then there are a lot of genes to look at
Microarray gene expression studies map entire genomes to the chip (mouse 23,000 genes)
Those genes that show a change in their expression under the studied state are chosen
These can be in the 1000’s
Numbers of genes quickly overwhelms researchers
How do researches look at these candidate genes then?
10,000+ Genes

5. Manual approach Search using public web sites and databases
Pubmed
Uniprot
EBI BioMart
Copy and paste to web tools for analysis
NCBI Blast
EBI InterPro
Further processing locally R
Perl
Python

6. Manual: disadvantages
Scale of analysis task overwhelms researchers – lots of data
User bias and premature filtering of datasets – cherry picking
Hypothesis-Driven approach to data analysis
Constant changes in data - problems with re-analysis of data
Implicit methodologies (hyper-linking through web pages)
Error proliferation from any of the listed issues – notably human error

7. Web services and workflows
Technology and standards for exposing code and data resources that can be programmatically consumed by a remote third party
Description on how to interact with the service, parameters, documentation
Workflows
General technique for describing and executing a process
Describe what you want to do running which services

8. Taverna workflows
A set of (local and remote) services to analyze or manage data
Nested workflows are also services
Data-links connects services
i.e. output from service A is input to service B and C
Describes the desired dataflow instead of process coordination
Automatic iterations
Can customize list handling and control links

9. What types of services? Public/private/secured WSDL/SOAP web services
RESTful web services
Spreadsheet import
Command line tools (local/ssh)
Inline scripts (Beanshell, R)
Java APIs
Customizations:
BioMart, BioMoby / SADI
Soaplab
Grid services (Globus, EGEE gLite, caGrid)
… your tool (Plugin tutorial on wiki)

10. Which services?
Taverna is general, can connect to standard web services for any domain
Bioinformatics:
From professional third-party organisations providing robust & open data/analysis services
..to under-the-desk web services for one particular purpose, ran by PhD students
 services from 130 providers – crowd sourced and quality monitored

12. Taverna workbench Graphical desktop tool
No server installation required
Drag-and-drop services into diagram
Connect services, run, reconnect, rerun
Integrates diverse set of tools

16. Sharing workflows
myExperiment.org allows users to share, find, download and rate workflows
“Facebook for the scientist”
3000 members, 1100 workflows

17. Extensible UI and engine
Plugins can provide new “perspectives”
i.e.: BioCatalogue, myExperiment
Provide service-specific customization
BioMart interface replicates web site
Adding new functionality
Looping, branching, dynamic service resolution
New service types
Design helpers, “Find matching service”

18. Taverna 3 “Next-gen” Under development for 2011
Interactive, component-centric and data-centric workflow design
Pre-packaged workflow components
Searching for workflow components from BioCatalogue and myExperiment
New myGrid workflow components library

19. Taverna command line Executes from a Windows/Linux/OSX shells
Takes a predefined workflow with files as inputs and outputs
Quick way to “productionize” a workflow

20. Taverna Server REST/SOAP interface to execute workflows
Client libraries for Ruby and Java
Two demonstration web interfaces
Ruby
Java Portlets
Future
Detailed execution support and control
Security delegation

21. Taverna portlet Example portlet implementation
Executes workflows using Taverna Server

23. Ruby web interface Example customized web interface
Uses Ruby gem t2-server

24. Taverna on the cloud Use-case:
SNP analysis and annotation of genome sequenced from breeds of cows in Africa – why are some of them resistent to X?
Amazon EC2 with Taverna Server and local services
Custom (built-in-a-week) Ruby on Rails web interface
Runs through 31 chromosomes in 6.5 hours using 10 instances - $26
Optimised: 2 hours for 10 instances
£10.000s for SNP retrieval in 1 week

26. Open source, open development
Taverna suite of tools are all open source and free to use
Large user community, active mailing lists
Lead developers: myGrid in Manchester
Contributors from across the world
PAL programme
myGrid provides training, tutorials and documentation

27. Acknowledgements 27

28. Norman missing! And olga. And wei.28 28

29. More information http://www.mygrid.org.uk/ http://www.taverna.org.uk/